The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: RS1 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000330.4(RS1):c.227T>A (p.Val76Asp)

CA412372934

1066419 (ClinVar)

Gene: RS1 (HGNC:6247)
Condition: X-linked retinoschisis (MONDO:0010725)
Inheritance Mode: X-linked inheritance (recessive (HP:0001419))
UUID: 7f84a812-415f-4fa6-97d8-7c5d1e9c0664
Approved on: 2025-05-19
Published on: 2025-05-20

HGVS expressions

NM_000330.4(RS1):c.227T>A (p.Val76Asp)
NM_000330.4:c.227T>A
NC_000023.11:g.18647290A>T
CM000685.2:g.18647290A>T
NC_000023.10:g.18665410A>T
CM000685.1:g.18665410A>T
NC_000023.9:g.18575331A>T
NG_008475.1:g.226686A>T
NG_008659.3:g.35159T>A
ENST00000379984.4:c.227T>A
ENST00000379984.3:c.227T>A
ENST00000379989.6:c.2797+1200A>T
ENST00000379996.7:c.2797+1200A>T
ENST00000476595.1:n.718T>A
NM_000330.3:c.227T>A
NM_001037343.1:c.2797+1200A>T
NM_003159.2:c.2797+1200A>T
NM_001037343.2:c.2797+1200A>T
NM_003159.3:c.2797+1200A>T
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Pathogenic

Met criteria codes 4
PM2_Supporting PP4_Moderate PP3_Strong PP1_Strong

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
X-linked Inherited Retinal Disease VCEP
The NM_000330.4(RS1):c.227T>A variant is a missense variant encoding the substitution of Valine with Aspartic acid at position 76. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.942, which is above the ClinGen X-linked IRD VCEP threshold of >0.932 and predicts a damaging effect on RS1 function (PP3_strong). The computational splicing predictor SpliceAI gives a delta score of 0 for all predictive splice changes, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RS1 splicing. The variant has been reported to segregate with retinal dystrophy through at least 3 meioses in the same family (PP1_Strong; PMID: 28060400). At least one proband harboring this variant exhibits a phenotype including appearance of schisis and reduced visual acuity before age 13 years and showing retinal detachment, which together are highly specific for X-linked retinoschisis (PMID: 28060400, PP4_moderate). In summary, this variant is classified as pathogenic for X-linked retinoschisis based on the ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 Version 1.0.0: PM2_supporting, PP3_strong, PP4_moderate, and PP1_strong (date of approval 01/24/2025).
Met criteria codes
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
PP4_Moderate
At least one proband harboring this variant exhibits a phenotype including appearance of schisis and reduced visual acuity before age 13 years and showing detachment, which together are highly specific for X-linked retinoschisis (PMID: 28060400, PP4_moderate).
PP3_Strong
The computational predictor REVEL gives a score of 0.942, which is above the ClinGen X-linked IRD VCEP threshold of >0.932 and predicts a damaging effect on RS1 function (PP3_strong). The computational splicing predictor SpliceAI gives a delta score of 0.00 for all predictive splice changes, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RS1 splicing.
PP1_Strong
The variant has been reported to segregate with retinal dystrophy through at least 3 meioses in the same family [proband, mother, grandfather, aunt, male cousin carry this variant- all males are affected]. (PP1_strong; PMID: 28060400).
Curation History
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