Criteria Specification Registry

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Criteria Specification

ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3CD Version 1.0.0

Type: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 Description : This submission includes the revised PIK3CD specifications following the pilot phase.

Version : 1.0.0

Antibody Deficiencies VCEP

Released

12/16/2025

16:36:15

Rules for PIK3CD

The current specifications for PIK3CD variant curation are written in relation to autosomal dominant rather than autosomal recessive forms of disease, with a gain-of-function rather than loss-of-function mechanism of pathogenicity. Unfortunately, there is no a priori way to exclude one mode of inheritance or the other, so both need to considered initially while assessing the variant. However, in general, only variants predicted to lead to a single missense amino acid substitution have thus far been shown to have a gain-of-function (GOF) effect in PIK3CD so any other types of variants should not enter this classification criteria.

Gene: PIK3CD (HGNC:8977) HGNC Name: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta Transcripts: NM_005026.3 Disease: immunodeficiency 14 (MONDO:0014222) Mode of Inheritance: Autosomal dominant inheritance

Criteria & Strength Specifications
PVS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease. Caveats: • Beware of genes where LOF is not a known disease mechanism (e.g. GFAP, MYH7). • Use caution interpreting LOF variants at the extreme 3’ end of a gene. • Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact. • Use caution in the presence of multiple transcripts. Stand Alone Very Strong Default Point Value: 8 Strong Default Point Value: 4 Moderate Default Point Value: 2 Supporting Default Point Value: 1 Not Applicable Comments: Does not apply given gain of function disease mechanism.
PS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Example: Val->Leu caused by either G>C or G>T in the same codon. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level. Stand Alone Very Strong Strong Use at the default level (PS1) for missense variants when other variant was classified as Pathogenic for autosomal dominant PIK3CD gain-of-function-related disease by Antibody Deficiencies VCEP specifications for PIK3CD without using PS1. Beware of changes that impact splicing rather than the amino acid (based on RNA data or splicing predictors). Neither change should be predicted to affect splicing (SpliceAI Δ score <0.2). Default Point Value: 4 Modification Type: Gene-specific Moderate Use at the PS1_Moderate level for missense variants when other variant was classified as Likely Pathogenic for autosomal dominant PIK3CD gain-of-function-related disease by Antibody Deficiencies VCEP specifications for PIK3CD without using PS1. Beware of changes that impact splicing rather than the amino acid (based on RNA data or splicing predictors). Neither change should be predicted to affect splicing (SpliceAI Δ score <0.2). Default Point Value: 2 Modification Type: Gene-specific Supporting Default Point Value: 1 Not Applicable
PS2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity. VCEP Specifications: This code has been adapted to also reward de novo occurrences in cases where maternity and paternity are suspected but not confirmed, as the PM6 code is not in use. For this code use Table 1. Points awarded per de novo occurrences, Table 2. Recommendation for determining the appropriate ACMG/AMP evidence strength level for de novo occurrence(s). and Table 3. Phenotype scoring criteria per affected individual. Stand Alone Very Strong Use PS2_VeryStrong when there are four or more de novo occurrences according to the attached Recommendation for determining the appropriate ACMG/AMP evidence strength level for de novo occurrences (Table 2). The “phenotypic consistency” used on the attached Table 1 (Points awarded per de novo occurrence) will be chosen for each proband by the number of phenotype points scored by the proband on the attached Phenotype scoring criteria per affected individual (Table 3): If the proband scores at least 4 and <6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific and high genetic heterogeneity”. If the proband scores at least 6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific”. If the proband scores at least 10 phenotype points in the PS4 counting rubric AND has genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype highly specific for gene”. PS2_VeryStrong can only be applied if the variant does not meet BA or BS1. Default Point Value: 8 Modification Type: Disease-specific Strong Use PS2_Moderate when there are 2 - 3 de novo occurrences according to the attached Recommendation for determining the appropriate ACMG/AMP evidence strength level for de novo occurrences (Table 2). The “phenotypic consistency” used on the attached Table 1 (Points awarded per de novo occurrence) will be chosen for each proband by the number of phenotype points scored by the proband on the attached Phenotype scoring criteria per affected individual (Table 3): If the proband scores at least 4 and <6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific and high genetic heterogeneity”. If the proband scores at least 6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific”. If the proband scores at least 10 phenotype points in the PS4 counting rubric AND has genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype highly specific for gene”. PS2 can only be applied if the variant does not meet BA or BS1. Default Point Value: 4 Modification Type: Disease-specific Moderate Use PS2_Moderate when there is one de novo occurrence according to the attached Recommendation for determining the appropriate ACMG/AMP evidence strength level for de novo occurrences (Table 2). The “phenotypic consistency” used on the attached Table 1 (Points awarded per de novo occurrence) will be chosen for each proband by the number of phenotype points scored by the proband on the attached Phenotype scoring criteria per affected individual (Table 3): If the proband scores at least 4 and <6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific and high genetic heterogeneity”. If the proband scores at least 6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific”. If the proband scores at least 10 phenotype points in the PS4 counting rubric AND has genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype highly specific for gene”. PS2_Moderate can only be applied if the variant does not meet BA or BS1. Default Point Value: 2 Modification Type: Disease-specific Supporting Use PS2_Supporting when there is one de novo occurrence according to the attached Recommendation for determining the appropriate ACMG/AMP evidence strength level for de novo occurrences (Table 2). The “phenotypic consistency” used on the attached Table 1 (Points awarded per de novo occurrence) will be chosen for each proband by the number of phenotype points scored by the proband on the attached Phenotype scoring criteria per affected individual (Table 3): If the proband scores at least 4 and <6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific and high genetic heterogeneity”. If the proband scores at least 6 phenotype points in the PS4 counting rubric but lacks genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype consistent with gene but not highly specific”. If the proband scores at least 10 phenotype points in the PS4 counting rubric AND has genotyping to rule out variants in the PIK3R1 locus, use the number of de novo points corresponding to “Phenotype highly specific for gene”. PS2_Supporting can only be applied if the variant does not meet BA or BS1. Default Point Value: 1 Modification Type: Disease-specific Not Applicable
PS3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established. Stand Alone Very Strong Default Point Value: 8 Strong PS3 will be applied at the default level of strength for evidence from an animal model expressing the variant of interest and recapitulating the APDS phenotype. This strength level is considered particularly appropriate if multiple mouse models of the same variant recapitulate APDS features. PS3 will be applied at the default level of strength for an abnormal result in an approved in vitro assay with a calculated OddsPath >18.7 (as recommended in PMID: 31892348). One example has been found in the literature: Enrichment of the variant in high phospho-S6 and phospho-AKT T cells relative to low phospho-S6 and phospho-AKT T cells, within a next generation sequencing-based screen of donor T cells subjected to of CRISPR-mediated adenine base-editing (PMID: 40543502) Default Point Value: 4 Modification Type: Disease-specific Moderate PS3 will be applied at the moderate level of strength for an abnormal result in an approved in vitro assay with a minimum of 11 total pathogenic and benign variant controls (classified using these same specifications, as recommended in PMID: 31892348). Example assays with sufficient control variants have not yet been found in published reports at the time of these specifications, but are anticipated in the future as additional studies are published. Default Point Value: 2 Modification Type: Disease-specific Supporting PS3_Supporting can be applied based on an abnormal result in an approved in vitro assay. These are described in detail in the attached Excel file entitled “PIK3CD_Functional_Assays_PS3_BS3” Approved assay classes and specific assay instances: AKT kinase activity assay PMID: 24136356, PMID: 24165795, PMID: 28414062 Lipid kinase activity PMID: 24136356; PMID: 28167755; PMID: 28414062 Lipid vesicle affinity PMID: 24136356 Conformational dynamics: PMID: 28167755; PMID: 28414062 Please note that protein binding assays testing PIK3CD binding to PIK3R1 were also considered for inclusion in PS3_Supporting, but were excluded based on lack of evidence of altered binding by disease-associated variants compared to wild-type controls (PMID: 24165795; PMID: 28414062). Patient cell-based functional assays directly showing abnormally high activity of the disease-relevant PI3K delta pathway were considered for inclusion in the PS3_Supporting code but are viewed as part of the proband phenotype and have been recommended for consideration under the PP4_Moderate code instead. Default Point Value: 1 Modification Type: Disease-specific Not Applicable
PS4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance. Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence. VCEP Specifications: For this code use Table 3. Phenotype scoring criteria per affected individual and Table 4. Recommendation for determining the appropriate PS4 evidence strength level based on the number of affected individuals meeting the phenotype criteria and genetic testing requirements. Stand Alone Very Strong Default Point Value: 8 Strong The strength of this code is defined in Table 4. Use PS4 at the default level of strength when four or more probands meet the phenotype scoring criteria in Table 3 and genetic testing requirements described below. Please note that a proband used for PP4 or PP4_Moderate cannot be included in PS4. Point strength has been determined based on a survey of clinical experts, with the goal of quantifying the degree to which a proband’s phenotypes are specific to PIK3CD-related immunodeficiency. Phenotypes have been grouped into categories such as “respiratory findings” or “gastrointestinal disease” to prioritize the diversity of systems affected. Probands receive full points for at least one reported feature in the category. Points per category have been tailored to reward those considered most characteristic of and prevalent within patients with PIK3CD-related immunodeficiency. A proband must reach greater than or equal to 6 points in the phenotype scoring criteria above (Table 3) and, at minimum, a primary immunodeficiency or antibody gene testing panel must have identified no likely pathogenic or pathogenic variants in the PIK3R1 locus in order to be counted toward PS4 Genome or exome sequencing is acceptable in lieu of a gene panel For genes associated with autosomal recessive disorders, carrier status is acceptable. If no gene testing panel was performed, additional phenotypic features (reaching greater than or equal to 10 points) are required to count the proband toward PS4. Scoring of probands with previous genetic testing should be prioritized, particularly in the event of scoring historical or rare probands/variants. In order to be evaluated for this criterion, the variant must not meet BS1 or BA1. Default Point Value: 4 Modification Type: Disease-specific Moderate The strength of this code is defined in Table 4. Use PS4_Moderate when 2-3 probands meet the phenotype scoring criteria in Table 3 and genetic testing requirements described below. Please note that a proband used for PP4 or PP4_Moderate cannot be included in PS4_Moderate. Point strength has been determined based on a survey of clinical experts, with the goal of quantifying the degree to which a proband’s phenotypes are specific to PIK3CD-related immunodeficiency. Phenotypes have been grouped into categories such as “respiratory findings” or “gastrointestinal disease” to prioritize the diversity of systems affected. Probands receive full points for at least one reported feature in the category. Points per category have been tailored to reward those considered most characteristic of and prevalent within patients with PIK3CD-related immunodeficiency. A proband must reach greater than or equal to 6 points in the phenotype scoring criteria above (Table 3) and, at minimum, a primary immunodeficiency or antibody gene testing panel must have identified no likely pathogenic or pathogenic variants in the PIK3R1 locus in order to be counted toward PS4 Genome or exome sequencing is acceptable in lieu of a gene panel For genes associated with autosomal recessive disorders, carrier status is acceptable. If no gene testing panel was performed, additional phenotypic features (reaching greater than or equal to 10 points) are required to count the proband toward PS4. Scoring of probands with previous genetic testing should be prioritized, particularly in the event of scoring historical or rare probands/variants. In order to be evaluated for this criterion, the variant must not meet BS1 or BA1. Default Point Value: 2 Modification Type: Disease-specific Supporting The strength of this code is defined in Table 4. Use PS4_Supporting when one proband meets the phenotype scoring criteria in Table 3 and genetic testing requirements. Please note that a proband used for PP4 or PP4_Moderate cannot be included in PS4_Supporting. Point strength has been determined based on a survey of clinical experts, with the goal of quantifying the degree to which a proband’s phenotypes are specific to PIK3CD-related immunodeficiency. Phenotypes have been grouped into categories such as “respiratory findings” or “gastrointestinal disease” to prioritize the diversity of systems affected. Probands receive full points for at least one reported feature in the category. Points per category have been tailored to reward those considered most characteristic of and prevalent within patients with PIK3CD-related immunodeficiency. A proband must reach greater than or equal to 6 points in the phenotype scoring criteria above (Table 3) and, at minimum, a primary immunodeficiency or antibody gene testing panel must have identified no likely pathogenic or pathogenic variants in the PIK3R1 locus in order to be counted toward PS4 Genome or exome sequencing is acceptable in lieu of a gene panel For genes associated with autosomal recessive disorders, carrier status is acceptable. If no gene testing panel was performed, additional phenotypic features (reaching greater than or equal to 10 points) are required to count the proband toward PS4. Scoring of probands with previous genetic testing should be prioritized, particularly in the event of scoring historical or rare probands/variants. In order to be evaluated for this criterion, the variant must not meet BS1 or BA1. Default Point Value: 1 Modification Type: Disease-specific,Gene-specific Not Applicable
PM1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation. Stand Alone Very Strong Strong Default Point Value: 4 Moderate Default Point Value: 2 Supporting Default Point Value: 1 Not Applicable Comments: The PM1 code has been considered but does not apply to PIK3CD variant curation for this disease entity.
PM2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. Caveat: Population data for indels may be poorly called by next generation sequencing. Stand Alone Very Strong Strong Moderate Default Point Value: 2 Supporting Downgraded to PM2_Supporting Applicable to variants with a total allele frequency <0.00000132 across all populations in gnomAD v4.1.0. Maximum credible population allele frequency threshold determined using Whiffin/Ware calculator (https://www.cardiodb.org/allelefrequencyapp/) and the following estimated parameters (with the prevalence estimated for autosomal dominant PIK3CD-related immune disease): Prevalence: 1 in 4000 (a conservative estimate for primary immunodeficiency diseases from PMID: 17577648, PMID: 23201919) Allelic heterogeneity: 1 Genetic heterogeneity: 1 Penetrance: 0.95 (a conservative estimate based on multiple reports of incomplete but nearly complete penetrance in PMID: 27555459, PMID: 36749229, PMID: 37390899) Default Point Value: 1 Modification Type: Disease-specific,Strength Not Applicable
PM3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary For recessive disorders, detected in trans with a pathogenic variant Note: This requires testing of parents (or offspring) to determine phase. Stand Alone Very Strong Default Point Value: 8 Strong Default Point Value: 4 Moderate Default Point Value: 2 Supporting Default Point Value: 1 Not Applicable Comments: This criterion does not apply since the model of inheritance is autosomal dominant.
PM4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. Stand Alone Very Strong Strong Default Point Value: 4 Moderate Default Point Value: 2 Supporting Default Point Value: 1 Not Applicable Comments: This criterion does not apply since the mechanism of disease is the Gain of function caused by missense mutations.
PM5 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. Example: Arg156His is pathogenic; now you observe Arg156Cys. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level. Stand Alone Very Strong Strong Default Point Value: 4 Moderate Use at the default strength level (PM5) for missense variants when other variant was classified as Pathogenic for autosomal dominant PIK3CD-related disease by Antibody Deficiencies VCEP specifications for PIK3CD without using PM5. Beware of changes that impact splicing rather than the amino acid (based on RNA data or splicing predictors). Neither change should be predicted to affect splicing (SpliceAI Δ score ≤0.2). Do not apply at codon where any benign variants are known. The variant being evaluated must have a Grantham distance value greater than or equal to that of the known pathogenic variant, indicating that the variant residue is equally chemically different or more chemically different than the known pathogenic residue in comparison to the wild type residue. Default Point Value: 2 Modification Type: Clarification Supporting Use at PM5_Supporting strength for missense variants when other variant was classified as Likely Pathogenic for autosomal dominant PIK3CD-related disease by Antibody Deficiencies VCEP specifications for PIK3CD without using PM5. Beware of changes that impact splicing rather than the amino acid (based on RNA data or splicing predictors). Neither change should be predicted to affect splicing (SpliceAI Δ score <0.2). Do not apply at codon where any benign variants are known. The variant being evaluated must have a Grantham distance value greater than or equal to that of the known likely pathogenic variant, indicating that the variant residue is equally chemically different or more chemically different than the known likely pathogenic residue in comparison to the wild type residue. Default Point Value: 1 Modification Type: Clarification Not Applicable
PM6 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Assumed de novo, but without confirmation of paternity and maternity. VCEP Specifications: For this code use Table 1. Points awarded per de novo occurrences, Table 2. Recommendation for determining the appropriate ACMG/AMP evidence strength level for de novo occurrence(s). and Table 3. Phenotype scoring criteria per affected individual. Stand Alone Very Strong Default Point Value: 8 Strong Default Point Value: 4 Moderate Default Point Value: 2 Supporting Default Point Value: 1 Not Applicable Comments: De novo occurrences without confirmation of paternity and maternity can still be counted under the PS2 code, using the point system shown in Tables 1 and 2.
PP1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. Note: May be used as stronger evidence with increasing segregation data. Stand Alone Very Strong Strong PP1 will require each family member to reach at least 6 points in the PS4 counting rubric in order to be considered affected for the purpose of counting co-segregations. Met at the PP1_Strong level for co-segregation of the variant with the affected phenotype across at least 4 meioses in one family or combined across multiple unrelated families (PMID: 38103548). The combined strength of the PP1 and PP4 codes is limited so that a variant that meets PP1_Strong can meet PP4 but not PP4_Moderate (PMID: 38103548). PP1 should not be applied when a variant also has population data meeting BA1 or BS1 since a common variant may appear to segregate with the disease by chance. Default Point Value: 4 Modification Type: Disease-specific,Strength Moderate PP1 will require each family member to reach at least 6 points in the PS4 counting rubric in order to be considered affected for the purpose of counting co-segregations. Met at the PP1_Moderate level for co-segregation of the variant with the affected phenotype across at least two meioses in one family or combined across multiple unrelated families (PMID: 38103548). PP1 should not be applied when a variant also has population data meeting BA1 or BS1 since a common variant may appear to segregate with the disease by chance. Default Point Value: 2 Modification Type: Disease-specific,Strength Supporting PP1 will require each family member to reach at least 6 points in the PS4 counting rubric in order to be considered affected for the purpose of counting co-segregations. Met at the supporting level for co-segregation of the variant with the affected phenotype across at least one meiosis (i.e. the variant is present in the proband + an affected relative, PMID: 38103548). PP1 should not be applied when a variant also has population data meeting BA1 or BS1 since a common variant may appear to segregate with the disease by chance. Default Point Value: 1 Modification Type: Disease-specific,Strength Not Applicable
PP2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. Stand Alone Very Strong Strong Moderate Supporting Default Point Value: 1 Not Applicable Comments: The gnomAD v2.1.1 missense Z score for PIK3CD (Z = 4.27) suggests this gene is constrained for missense variation. However, given the gain of function disease mechanism, it is not considered reasonable to expect that a missense variant at any residue will lead to a gain of function.
PP3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only once in any evaluation of a variant. Stand Alone Very Strong Strong Default Point Value: 4 Moderate Default Point Value: 2 Supporting Met at the default (PP3) level by a missense variant with REVEL score greater than or equal to 0.644 and CADD PHRED score greater than or equal to 25.3. Higher strength levels of PP3_Moderate or PP3_Strong have not been recommended due to pilot data indicating poor performance and significant discordance between REVEL and CADD predictions for established benign and gain-of-function PIK3CD variants. SpliceAI scores should be checked for missense variants, but there currently is no evidence of variants causing autosomal dominant disease through a splicing mechanism, so PP3 cannot be met by a variant located in the boundary exonic/intronic region with a predicted splicing impact. A variant with a predicted impact on splicing (SpliceAI Δ score greater than or equal to 0.2) should not be evaluated using these specifications, but rather using alternative specifications for autosomal recessive disease with a loss-of-function mechanism, unless functional evidence indicates a gain-of-function effect. Default Point Value: 1 Modification Type: Clarification,Disease-specific Not Applicable
PP4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology. Stand Alone Very Strong Strong Default Point Value: 4 Moderate PP4_Moderate is met when a proband scores greater than or equal to 10 phenotype points in the PS4 counting rubric AND has genotyping to rule out a variant in the PIK3R1 locus AND has patient cell-based functional assays directly showing abnormally high activity of the disease-relevant PI3K delta pathway. Patient cell-based functional experiments generally isolate T cells from affected and unaffected patients and often perform stimulation by anti-CD3 and anti-CD28 antibodies, followed by assessment of PI3K delta pathway function using western blotting or flow cytometry in combination with phospho-specific antibodies. These methods detect levels of AKT phosphorylation at Ser473 (PMID: 24136356, PMID: 28414062, PMID: 28428270) or Thr308 (PMID: 24165795) and/or S6 phosphorylation at Ser235/Ser236 (PMID: 28428270) or Ser240/Ser244 (PMID: 28414062). Phosphorylation may be upregulated by 1.2-fold to 7.5-fold in cells from the affected patient relative to the healthy control, and in some assays may be shown to be abrogated by PI3K-specific inhibitor (PMID: 28428270). Please note that a proband used for PP4_Moderate cannot be included in PS4. In order to be evaluated for this criterion, the variant must not meet BS1 or BA1. Default Point Value: 2 Modification Type: Disease-specific Supporting In order to be counted for this criterion, a proband must score greater than or equal to 10 phenotype points in the PS4 counting rubric (Table 3) AND have genotyping to rule out a variant in the PIK3R1 locus. Please note that a proband used for PP4 cannot be included in PS4. In order to be evaluated for this criterion, the variant must not meet BS1 or BA1. Default Point Value: 1 Modification Type: Disease-specific Not Applicable
PP5
Original ACMG Summary Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation. Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BA1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. Stand Alone Applicable to variants with a GrpMax filtering allele frequency greater than or equal to 0.00316 in gnomAD v4.1.0. If GrpMax filtering allele frequency is not listed for the variant, this code is applicable to the maximum allele frequency among the five major continental populations (African / African-American, East Asian, European non-Finnish, Latino / Admixed-American, or South Asian). Maximum credible population allele frequency threshold determined using Whiffin/Ware calculator (https://www.cardiodb.org/allelefrequencyapp/) and the following estimated parameters (with the prevalence estimated for PIK3CD-related immune disease and the inheritance tailored to the autosomal recessive rather than autosomal dominant mode of inheritance, associated with complete penetrance): Inheritance: biallelic Prevalence: 1 in 100,000 (calculated at 1 in 7,500,000 based on the USIDNET cohort, PMID: 34352450, but adjusted based on expectation that cases are actually more common, resulting in a much more frequent / more aggressive prevalence estimate of 1 in 100,000 in order to generate a more conservative estimate) Allelic heterogeneity: 1 Genetic heterogeneity: 1 Penetrance: 1 Default Point Value: Not Applicable Modification Type: Gene-specific Very Strong Strong Moderate Supporting Not Applicable
BS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Allele frequency is greater than expected for disorder. Stand Alone Very Strong Strong Applicable to variants with a GrpMax filtering allele frequency greater than or equal to 0.000316 in gnomAD v4.1.0. If GrpMax filtering allele frequency is not listed for the variant, this code is applicable to the maximum allele frequency among the five major continental populations (African / African-American, East Asian, European non-Finnish, Latino / Admixed-American, or South Asian). The BS1 threshold was derived by decreasing the BA1 cutoff (greater than or equal to 0.00316) by one order of magnitude. Default Point Value: -4 Modification Type: Gene-specific Moderate Default Point Value: -2 Supporting Default Point Value: -1 Not Applicable
BS2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. Stand Alone Very Strong Strong Default Point Value: -4 Moderate Default Point Value: -2 Supporting Default Point Value: -1 Not Applicable Comments: Does not apply due to incomplete penetrance and variable expressivity of disease.
BS3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing. Stand Alone Very Strong Strong BS3 may potentially be applied at the default strength level of strong for evidence from an animal model expressing the variant of interest and failing to recapitulate the APDS phenotype. Animal models will be reviewed on a case-by-case basis by the VCEP to determine the appropriate strength level. Default Point Value: -4 Modification Type: Disease-specific Moderate BS3 will be applied at the moderate level of strength for an normal result in an approved in vitro assay with a minimum of 11 total pathogenic and benign variant controls (classified using these same specifications, as recommended in PMID: 31892348). Please note that an example assay with sufficient control variants has been identified in the literature, but was recommended for BS3_Supporting instead based on OddsPath ratio (PMID: 40543502). Default Point Value: -2 Modification Type: Disease-specific Supporting BS3_Supporting can be applied based on a normal result in at least two different approved in vitro assays (from two separate approved assay classes). These are described in detail in the attached Excel file entitled “PIK3CD_Functional_Assays_PS3_BS3”. Approved assay classes and specific assay instances: AKT kinase activity assay (PMID: 24136356, PMID: 24165795, PMID: 28414062) Lipid kinase activity (PMID: 24136356, PMID: 28167755, PMID: 28414062) Enrichment of the variant in high phospho-S6 and phospho-AKT T cells relative to low phospho-S6 and phospho-AKT T cells, within a next generation sequencing-based screen of donor T cells subjected to of CRISPR-mediated adenine base-editing (PMID: 40543502) Lipid vesicle affinity (PMID: 24136356) Conformational dynamics (PMID: 28167755; PMID: 28414062) Please note that protein binding assays testing PIK3CD binding to PIK3R1 were also considered for inclusion in BS3_Supporting, but were excluded based on lack of evidence of altered binding by disease-associated variants compared to wild-type controls (PMID: 24165795; PMID: 28414062). Patient cell-based functional assays directly showing normal activity of the disease-relevant PI3K delta pathway were considered for inclusion in the BS3_Supporting code but are viewed as part of the proband phenotype instead. Default Point Value: -1 Modification Type: Disease-specific Not Applicable
BS4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Lack of segregation in affected members of a family. Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation. Stand Alone Very Strong Strong Caution in case the phenotype is not highly specific. The patients lacking segregation must reach 6 or more points of the phenotypic scoring system described in Table 4. Lack of segregation should be identified in more than 1 affected family member to meet BS4 at the default level of strength. Default Point Value: -4 Modification Type: Disease-specific Moderate Default Point Value: -2 Supporting Caution in case the phenotype is not highly specific. The patient lacking segregation must reach 6 or more points of the phenotypic scoring system described in Table 4. BS4_Supporting is met if only 1 affected family member lacks segregation of the genotype. Default Point Value: -1 Modification Type: Disease-specific Not Applicable
BP1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Missense variant in a gene for which primarily truncating variants are known to cause disease. Stand Alone Very Strong Strong Default Point Value: -4 Moderate Default Point Value: -2 Supporting Default Point Value: -1 Not Applicable
BP2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern. Stand Alone Very Strong Strong Default Point Value: -4 Moderate Default Point Value: -2 Supporting Default Point Value: -1 Not Applicable Comments: BP2 is considered not applicable, as the field at present does not understand all of the potential allelic mechanisms associated with PIK3CD variants, so that the possibility of diverse combinatorial variant effects cannot be excluded. This has been described for other inborn errors of immunity genes.
BP3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary In frame-deletions/insertions in a repetitive region without a known function. Stand Alone Very Strong Strong Default Point Value: -4 Moderate Default Point Value: -2 Supporting Default Point Value: -1 Not Applicable
BP4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant. Stand Alone Very Strong Strong Default Point Value: -4 Moderate Default Point Value: -2 Supporting Met at the default (BP4) level by a missense variant with REVEL score less than or equal to 0.290 and CADD PHRED score less than or equal to 22.7. SpliceAI Δ scores should be checked for missense variants as well. Variants with a predicted impact on splicing (SpliceAI Δ score greater than or equal to 0.2) should not be evaluated using these specifications, but rather using alternative specifications for autosomal recessive disease with a loss-of-function mechanism, unless functional evidence indicates a gain-of-function effect. The current specifications are written for a PIK3CD gain-of-function disease mechanism that has so far not been reported in association with variants that disrupt splicing. Met at the default (BP4) level by a synonymous or intronic variant not predicted to impact splicing by SpliceAI (SpliceAI Δ score <0.1, PMID: 37352859). Higher strength levels of BP4_Moderate or BP4_Strong have not been recommended due to pilot data indicating poor performance and significant discordance between REVEL and CADD predictions for established benign and gain-of-function PIK3CD variants. Default Point Value: -1 Modification Type: Clarification,Disease-specific Not Applicable
BP5 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Variant found in a case with an alternate molecular basis for disease. Stand Alone Very Strong Strong Default Point Value: -4 Moderate Default Point Value: -2 Supporting Variant found in a case with an alternate molecular basis for disease. At least two such cases are required to mitigate the reliance on assertions of variant pathogenicity in genes outside of the purview of the Antibody Deficiencies VCEP. Default Point Value: -1 Modification Type: Clarification Not Applicable
BP6
Original ACMG Summary Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation. Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BP7 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. Stand Alone Very Strong Strong Default Point Value: -4 Moderate Default Point Value: -2 Supporting Met for a synonymous variant if SpliceAI does not predict a splicing defect (cut-off <0.1). Synonymous variants in the first nucleotide of an exon or the final 3 nucleotides of an exon are not eligible for this code, as they are considered part of the splice region. Met for an intronic variant if SpliceAI does not predict a splicing defect (cut-off <0.1). Intronic variants between +1 and +6 or between -1 and -20 are not eligible for this code, as they are considered part of the splice region (PMID: 37352859). Default Point Value: -1 Modification Type: Clarification Not Applicable Comments: The BP7 code is based on predicted splicing impact, and is relevant to a PIK3CD loss-of-function disease mechanism, rather than the PIK3CD gain-of-function disease mechanism which is the focus of these specifications.

Point Based Variant Classification Categories

Category	Point Ranges
Pathogenic	10
Likely Pathogenic	6 - 9
Uncertain Significance	0 - 5
Likely Benign	-6 - -1
Benign	-7

Additional Notes :

Files & Images

PIK3CD_pilot_results: Updated list of PIK3CD pilot variants, codes met, classifications, and evidence summaries

Points system to reach final classification: Rules for combining pathogenic and benign codes to reach final classification according to points system (PMID: 32720330).

Summary_of_PIK3CD_updates: Updates and responses to SVI feedback

Recommendation for determining the appropriate PS4 evidence strength level based on the number of affected individuals meeting the phenotype criteria and genetic testing requirements.:

Tables 1 & 2: Standard tables to count points for de novo occurrences (PS2)

Phenotype scoring criteria per affected individual (PS4 and PP4): Table listing scores for PIK3CD-associated phenotypes for PS4 and PP4 evaluation.