Criteria Specification Registry

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Criteria Specification

ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC9A6 Version 3.0.0

Version : 3.0.0 Release Notes :

Modification to the combining criteria such that one Benign Strong reaches Likely Benign (in the absence of conflicting evidence).

Rett and Angelman-like Disorders VCEP

Released

5/9/2023

17:23:41

Rules for SLC9A6

Gene: SLC9A6 (HGNC:11079) HGNC Name: solute carrier family 9 member A6 Transcripts: NM_006359.2 Disease: Christianson syndrome (MONDO:0010278)

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 Null variant in a gene where loss of function is a known mechanism of disease. Use as defined by ClinGen SVI working group (PMID:30192042). PVS1 is applicable up to p.A563, for canonical splice site variants predicted to result in an out-of-frame product, for canonical splice site variants or single exon in-frame deletion predicted to preserve the reading frame (exon 10), and multiple in-frame exon deletions that include exon 10. Modification Type: Disease-specific Strong Null variant in a gene where loss of function is a known mechanism of disease. PVS1_Strong is applicable for any truncating variant from p.C564 to p.T601 and for canonical splice site variants that flank exon 3 (in-frame exon).²^,³^,¹ Modification Type: Disease-specific Moderate Null variant in a gene where loss of function is a known mechanism of disease. PVS1_Moderate is applicable for any truncating variant between p.Y602 to p.A669 and any frameshift variant that results in a read-through of the stop codon. Modification Type: Disease-specific Supporting Null variant in a gene where loss of function is a known mechanism of disease. PVS1_Supporting is applicable for initiation codon variants in SLC9A6 Modification Type: Disease-specific Instructions: For intragenic deletions/duplications that are predicted to result in a product that preserves reading frame: For single exon in-frame deletions assign the same strength (PVS1, PVS1_strong, or PVS1_moderate) as for splice site variants that preserve reading frame indicated above. For multiple exon in-frame deletions PVS1 can be assigned to deletions that include single in-frame exons in the PVS1 category listed in the splice site section above OR if the exon contains a functionally important domain as specified in PM1. Not Applicable
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 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Modification Type: None Moderate Supporting 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. Stand Alone Very Strong De novo (maternity and paternity confirmed) in a patient with the disease and no family history. ≥2 independent occurrences of PS2. ≥2 independent occurrences of PM6 and one occurrence of PS2. Evidence from literature must be fully evaluated to support independent events. Modification Type: General recommendation Strong De novo (maternity and paternity confirmed) in a patient with the disease and no family history. 1 occurrence of PS2 Modification Type: None Moderate Supporting Instructions: Applicable to all genes in affected individuals identified as mosaic for the variant (as the presence of a variant in the mosaic state is confirmatory of the variant being de novo). Because of the very high de novo rate of pathogenic variants in SLC9A6, de novo observation can be attributed the highest value points per proband (2 points for confirmed de novo and 1 point for assumed de novo) if the patient is known to be affected with a neurodevelopmental phenotype consistent with the gene. 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 Strong Well-established in vitro or in vivo functional studies supportive of a damaging effect. RNA studies that demonstrate abnormal splicing and an out-of-frame transcript. Do not use for canonical splice site variants and when PVS1 is used. Modification Type: Disease-specific Moderate Supporting Well-established in vitro or in vivo functional studies supportive of a damaging effect. RNA studies that demonstrate abnormal splicing and an inframe product (unless it affects an in-frame exon specified in the PVS1 section). 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. Stand Alone Very Strong Strong The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. 5+ observations. Modification Type: Strength Moderate The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. 3-4 observations. Modification Type: Strength Supporting The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. Use for 2nd independent occurrence. Modification Type: Strength Instructions: Detailed phenotype not needed. Need to confirm patient is ‘affected with a neurodevelopmental phenotype consistent with the gene’ at a minimum. Patient can be published OR an internal case OR observed at an outside lab (i.e. via ClinVar) OR described in the reputable databases. However independent case has to be confirmed to be a different patient than yours (compare gender/age). Do not use this criterion for variants where BS1 is applied or where PM2 does not apply. 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 Moderate Supporting Not Applicable Comments: Not applicable for SLC9A6.
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 Supporting Absent/rare from controls in an ethnically-matched cohort population sample. Use if absent, zero observations in control databases. Modification Type: 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 Strong Moderate Supporting Not Applicable Comments: Not applicable for SLC9A6.
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 Moderate Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. Modification Type: No change Supporting Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. Smaller in-frame events (< 3 amino acid residues). Modification Type: Strength Not Applicable
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 Missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ≥2 different missense changes affecting the amino acid residue. Do not apply PM1 in these situations. Modification Type: Strength Moderate Missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. A Grantham or BLOSUM score comparison can be used to determine if the variant is predicted to be as or more damaging than the established pathogenic variant. Modification Type: None Supporting 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. Stand Alone Very Strong Confirmed de novo without confirmation of paternity and maternity. ≥4 independent occurrences of PM6. Evidence from literature must be fully evaluated to support independent events. Modification Type: Strength Strong Confirmed de novo without confirmation of paternity and maternity. ≥2 independent occurrences of PM6. Evidence from literature must be fully evaluated to support independent events. Modification Type: Strength Moderate Confirmed de novo without confirmation of paternity and maternity. 1 occurrence of PM6 Modification Type: None Supporting Instructions: Because of the very high de novo rate of pathogenic variants in SLC9A6, de novo observation can be attributed the highest value points per proband (2 points for confirmed de novo and 1 point for assumed de novo) if the patient is known to be affected with a neurodevelopmental phenotype consistent with the gene. Not Applicable
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 Co-segregation with disease in multiple affected family members. ≥5 informative meiosis Modification Type: Strength Moderate Co-segregation with disease in multiple affected family members. 3-4 informative meiosis Modification Type: Strength Supporting Co-segregation with disease in multiple affected family members. 2 informative meiosis Modification Type: Strength Instructions: Note: individuals must have disease consistent with reported phenotype (even if on the mild end of spectrum of the disease). 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 Not Applicable Comments: Not applicable for SLC9A6.
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 Moderate Supporting Multiple lines of computational evidence support a deleterious effect on the gene or gene product. For missense variants use REVEL with a score ≥ 0.75. For splice site variants use MaxEntScan, NNSPLICE and SpliceSiteFinder-like when all of the prediction programs support significant splicing alteration (significant splicing alterations defined as ≥15% decrease to the natural splice site and ≥70% gain in prediction strength of cryptic splice site). Modification Type: General recommendation 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 Moderate Supporting Phenotype specific for disease with single genetic etiology. See gene specific clinical phenotype guidelines. 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 Use large population databases (i.e. gnomAD). Use if variant is present at ≥0.0003 (0.03%) in any sub-population. Use if allele frequency is met in any general continental population dataset of at least 2,000 observed alleles. Modification Type: Disease-specific Very Strong Strong Moderate Supporting Instructions: The frequency cutoff is based on summation of prevalence of genes covered in the Rett/Angelman-like working group. The prevalence values were determined using the most conservative numbers found in the literature. 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 Use large population databases (i.e. gnomAD). Use if variant is present at ≥0.00008 (0.008%) and <0.0003 (0.03%) in any sub-population. Use if allele frequency is met in any general continental population dataset of at least 2,000 observed alleles. Modification Type: Disease-specific Moderate Supporting Instructions: The frequency cutoffs are based on MECP2 expected disease allele frequency (1 in 8500 females/1.5 alleles [assumes 50/50 male/female ratio]). MECP2 is the most prevalent of the genes covered in the Rett/Angelman-like working group and was chosen as most conservative number. 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 Observed in the heterozygous/hemizygous state in a healthy adult. 2 unaffected (related or unrelated) hemizygotes Modification Type: Strength Moderate Supporting Observed in the heterozygous/hemizygous state in a healthy adult. 1 unaffected (related or unrelated) hemizygote Modification Type: Strength Instructions: Should be applied in cases where the healthy adult is devoid of neurodevelopmental phenotypes. Best to use with internal curated data that includes clinical information or published patients that have been phenotyped. Not Applicable
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 Well-established in vitro or in vivo functional studies shows no damaging effect on protein function. RNA functional studies that demonstrate no impact on splicing and transcript composition. It can be downgraded based on quality of data. Not applicable for these genes for other functional studies (see tables for other accepted functional studies). Modification Type: Disease-specific Moderate Supporting 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 Lack of segregation in affected members of a family. Absent in a similarly affected family member, when seen in two or more families Modification Type: Strength Moderate Supporting Lack of segregation in affected members of a family. Absent in a similarly affected family member Modification Type: Strength Instructions: Need to confirm that the family member is ‘affected with a neurodevelopmental phenotype consistent with the gene’ at a minimum. 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 Moderate Supporting Not Applicable Comments: Not applicable for SLC9A6.
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 Moderate Supporting 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. BP2 is not applicable for SLC9A6 for in trans state. Modification Type: Disease-specific Instructions: Knock out of SLC9A6 results in disease but viable phenotype.⁴ Not Applicable
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 Moderate Supporting Not Applicable Comments: Not applicable for SLC9A6.
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 Moderate Supporting For missense variants use REVEL with a score ≤ 0.15. For splice site variants use MaxEntScan, NNSPLICE and SpliceSiteFinder-like when the majority of the prediction programs do not support significant splicing alteration (significant splicing alterations defined as ≥15% decrease to the natural splice site and ≥70% gain in prediction strength of a cryptic splice site). Modification Type: None 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 Variant found in a case with an alternate molecular basis for disease. ≥3 cases with alternate molecular basis for disease. Modification Type: Strength Moderate Supporting Variant found in a case with an alternate molecular basis for disease. 1-2 cases with alternate molecular basis for disease Modification Type: Disease-specific Instructions: For example if a variant in SLC9A6 is identified in a patient with lissencephaly in whom a pathogenic variant is identified in the PAFAH1B1 gene. The variant should be in the hemizygous state in the case with an alternate molecular basis for disease for this criteria to be used. Do not apply if variant is de novo. 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 Moderate Supporting A synonymous (silent) 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. Defined 'not highly conserved' regions in BP7 as those with PhastCons score <1 and/or PhyloP score <0.1 and/or the variant is the reference nucleotide in one primate and/or three mammal species. Modification Type: None Instructions: For silent variants BP4 and BP7 can be added. Not Applicable

Rules for Combining Criteria

Pathogenic

1 Very Strong (PVS1, PS2_Very Strong, PM6_Very Strong) AND ≥ 1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM5_Strong, PM6_Strong, PP1_Strong)

1 Very Strong (PVS1, PS2_Very Strong, PM6_Very Strong) AND ≥ 2 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate)

1 Very Strong (PVS1, PS2_Very Strong, PM6_Very Strong) AND 1 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate) AND 1 Supporting (PVS1_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

1 Very Strong (PVS1, PS2_Very Strong, PM6_Very Strong) AND ≥ 2 Supporting (PVS1_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

≥ 2 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM5_Strong, PM6_Strong, PP1_Strong)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM5_Strong, PM6_Strong, PP1_Strong) AND ≥ 3 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM5_Strong, PM6_Strong, PP1_Strong) AND 2 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate) AND ≥ 2 Supporting (PVS1_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM5_Strong, PM6_Strong, PP1_Strong) AND 1 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate) AND ≥ 4 Supporting (PVS1_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

Likely Pathogenic

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM5_Strong, PM6_Strong, PP1_Strong) AND ≥ 1 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM5_Strong, PM6_Strong, PP1_Strong) AND ≥ 2 Supporting (PVS1_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

≥ 3 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate)

≥ 2 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate) AND 2 Supporting (PVS1_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

≥ 1 Moderate (PVS1_Moderate, PS4_Moderate, PM4, PM5, PM6, PP1_Moderate) AND 4 Supporting (PVS1_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

1 Very Strong (PVS1, PS2_Very Strong, PM6_Very Strong) AND 1 Supporting (PVS1_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM4_Supporting, PP1, PP3, PP4)

Benign

≥ 2 Strong (BS1, BS2, BS3, BS4, BP5_Strong)

1 Stand Alone (BA1)

Likely Benign

≥ 2 Supporting (BS2_Supporting, BS4_Supporting, BP2, BP4, BP5, BP7)

1 Strong (BS1, BS2, BS3, BS4, BP5_Strong)

Files & Images

PVS1 Flowchart for SLC9A6:

Clinical Phenotype Guidelines for SLC9A6: Phenotype guidelines for SLC9A6 mentioned in PP4.

References

1. Gilfillan GD Selmer KK et al. SLC9A6 mutations cause X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome. Am J Hum Genet (2008) 82 (4) p. 1003-10. 10.1016/j.ajhg.2008.01.013 18342287

2. Masurel-Paulet A Piton A et al. A new family with an SLC9A6 mutation expanding the phenotypic spectrum of Christianson syndrome. Am J Med Genet A (2016) 170 (8) p. 2103-10. 10.1002/ajmg.a.37765 27256868

3. Tarpey PS Smith R et al. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nat Genet (2009) 41 (5) p. 535-43. 10.1038/ng.367 19377476

4. Strømme P Dobrenis K et al. X-linked Angelman-like syndrome caused by Slc9a6 knockout in mice exhibits evidence of endosomal-lysosomal dysfunction. Brain (2011) 134 (Pt 11) p. 3369-83. 10.1093/brain/awr250 21964919