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.276G>C (p.Trp92Cys)

CA226650

98925 (ClinVar)

Gene: RS1 (HGNC:6247)
Condition: X-linked retinoschisis (MONDO:0010725)
Inheritance Mode: X-linked inheritance (recessive (HP:0001419))
UUID: dda9b025-ece1-475b-bb70-fe508075a361
Approved on: 2025-05-19
Published on: 2025-05-20

HGVS expressions

NM_000330.4(RS1):c.276G>C (p.Trp92Cys)
NM_000330.4:c.276G>C
NC_000023.11:g.18647241C>G
CM000685.2:g.18647241C>G
NC_000023.10:g.18665361C>G
CM000685.1:g.18665361C>G
NC_000023.9:g.18575282C>G
NG_008475.1:g.226637C>G
NG_008659.3:g.35208G>C
ENST00000379984.4:c.276G>C
ENST00000379984.3:c.276G>C
ENST00000379989.6:c.2797+1151C>G
ENST00000379996.7:c.2797+1151C>G
ENST00000476595.1:n.767G>C
NM_000330.3:c.276G>C
NM_001037343.1:c.2797+1151C>G
NM_003159.2:c.2797+1151C>G
NM_001037343.2:c.2797+1151C>G
NM_003159.3:c.2797+1151C>G
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Pathogenic

Met criteria codes 5
PS4 PP1 PP4 PP3_Strong PM2_Supporting

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.276G>C variant is a missense variant encoding the substitution of Tryptophan with Cysteine at amino acid 92. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.982, 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. The variant has been reported to segregate with retinal dystrophy through at least 1 meiosis in a family, which consists of 2 brothers and an unaffected mother (PP1; PMID: 9760195). At least one proband harboring this variant exhibits a phenotype including appearance of schisis and reduced visual acuity before age 13 years, which together are specific for X-linked retinoschisis (PMID: 10636421, PP4). This variant has been reported in at least 6 apparently unrelated probands meeting the PS4 requirements of a male diagnosed with X-linked retinoschisis (PMIDs: PMID: 9760195, 28348004, 31106028, 28272453, 33608557, 34624300, 39462066, and 20809529, PS4). 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, PP1, PS4, and PP4 (date of approval 01/24/2025).
Met criteria codes
PS4
This variant has been reported in at least 5 apparently unrelated probands meeting the PS4 requirements of a male diagnosed with XLRS (PMIDs: PMID: 9760195, 28348004, 31106028, 28272453, 33608557, 34624300, and 20809529, PS4).
PP1
The variant has been reported to segregate with retinal dystrophy through at least 1 meiosis in the same family, which consists of 2 brothers and an unaffected mother (PP1; PMID: 9760195).
PP4
At least one proband harboring this variant exhibits a phenotype including appearance of schisis and reduced visual acuity before age 13 years, which together are specific for X-linked retinoschisis (PMID: 10636421, PP4).
PP3_Strong
The computational predictor REVEL gives a score of 0.982, 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.
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
Curation History
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