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 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.575C>A (p.Pro192His)

CA412370412

1066639 (ClinVar)

Gene: RS1 (HGNC:6247)
Condition: X-linked retinoschisis (MONDO:0010725)
Inheritance Mode: X-linked inheritance
UUID: b7d788c2-e3b4-45e1-ab0e-0f6739f0b2ef
Approved on: 2026-09-26
Published on: 2026-09-26

HGVS expressions

NM_000330.4(RS1):c.575C>A (p.Pro192His)
NM_000330.4:c.575C>A
NC_000023.11:g.18642104G>T
CM000685.2:g.18642104G>T
NC_000023.10:g.18660224G>T
CM000685.1:g.18660224G>T
NC_000023.9:g.18570145G>T
NG_008475.1:g.221500G>T
NG_008659.3:g.40345C>A
ENST00000379984.4:c.575C>A
ENST00000379984.3:c.575C>A
ENST00000379989.6:c.2714-3903G>T
ENST00000379996.7:c.2714-3903G>T
ENST00000476595.1:n.1066C>A
NM_000330.3:c.575C>A
NM_001037343.1:c.2714-3903G>T
NM_003159.2:c.2714-3903G>T
NM_001037343.2:c.2714-3903G>T
NM_003159.3:c.2714-3903G>T
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Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP4 PM5 PS4_Supporting PP3_Moderate

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.575C>A (p.Pro192His) variant is a missense variant encoding the substitution of Proline and Histidine at amino acid 192. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.914, which is within the ClinGen X-linked IRD VCEP range between 0.931 and 0.773 and predicts a damaging effect on RS1 function (PP3_moderate). 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. Another missense variant in the same codon, NM_000330.4(RS1):c.574C>T (p.Pro192Ser), (PMIDs: 9326935, 10636421, 17987333, 19093009, 28348004, 30551202, 30652005, 34828422, 39293640, 17515881, 20809529) has been classified as pathogenic for X-linked retinoschisis by the ClinGen X-linked IRD VCEP, while no benign missense variants have been identified in this codon. The present variant has a higher Grantham’s distance (77) than the comparison variant (74), and SpliceAI has been used to confirm that neither variant has a predicted impact on RS1 splicing (PM5). At least one proband harboring this variant exhibits the following phenotypes, including the appearance of schisis and reduced visual acuity before age 13 years, which together are specific for X-linked retinoschisis (PMID: 33460243, 31106028, 34645606, PP4). This variant has been reported in at least 1 proband meeting one of the PS4 requirements of a male diagnosed with XLRS, as well as a second apparently unrelated proband previously used for the PP4 code (PMIDs: 28559085, PS4_Supporting). In summary, this variant is classified as likely 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_moderate, PM5, PP4, and PS4_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
PP4
At least one proband harboring this variant exhibits the following phenotypes, including the appearance of schisis and reduced visual acuity before age 13 years, which together are specific for X-linked retinoschisis (PMID: 33460243, 31106028, 34645606, PP4).
PM5
Another missense variant in the same codon, NM_000330.4(RS1):c.574C>T (p.Pro192Ser), (PMIDs: 9326935, 10636421, 17987333, 19093009, 28348004, 30551202, 30652005, 34828422, 39293640, 17515881, 20809529) has been classified as pathogenic for X-linked retinoschisis by the ClinGen X-linked IRD VCEP, while no benign missense variants have been identified in this codon. The present variant has a higher Grantham’s distance (77) than the comparison variant (74), and SpliceAI has been used to confirm that neither variant has a predicted impact on RS1 splicing (PM5).
PS4_Supporting
This variant has been reported in at least 1 proband meeting one of the PS4 requirements of a male diagnosed with XLRS, as well as a second apparently unrelated proband previously used for the PP4 code (PMIDs: 28559085, PS4_Supporting).
PP3_Moderate
The computational predictor REVEL gives a score of 0.914, which is within the ClinGen X-linked IRD VCEP range between 0.931 and 0.773 and predicts a damaging effect on RS1 function (PP3_moderate). 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.
Curation History
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