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.574C>T (p.Pro192Ser)

CA226787

98990 (ClinVar)

Gene: RS1 (HGNC:6247)
Condition: X-linked retinoschisis (MONDO:0010725)
Inheritance Mode: X-linked inheritance
UUID: 141cdf4b-7cbd-45bc-9438-2ad083ba8cf2
Approved on: 2026-09-26
Published on: 2026-09-26

HGVS expressions

NM_000330.4:c.574C>T
NM_000330.4(RS1):c.574C>T (p.Pro192Ser)
NC_000023.11:g.18642105G>A
CM000685.2:g.18642105G>A
NC_000023.10:g.18660225G>A
CM000685.1:g.18660225G>A
NC_000023.9:g.18570146G>A
NG_008475.1:g.221501G>A
NG_008659.3:g.40344C>T
ENST00000379984.4:c.574C>T
ENST00000379984.3:c.574C>T
ENST00000379989.6:c.2714-3902G>A
ENST00000379996.7:c.2714-3902G>A
ENST00000476595.1:n.1065C>T
NM_000330.3:c.574C>T
NM_001037343.1:c.2714-3902G>A
NM_003159.2:c.2714-3902G>A
NM_001037343.2:c.2714-3902G>A
NM_003159.3:c.2714-3902G>A
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Pathogenic

Met criteria codes 4
PP3_Strong PP4 PS4 PP1_Moderate
Not Met criteria codes 3
BS1 PM2 PS3

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.574C>T (p.Pro192Ser) variant is a missense variant encoding the substitution of Proline and Serine at amino acid 192. This variant is present in gnomAD v.4.1.0 at a frequency of 0.000002506 among hemizygous individuals, with 1 variant allele / 399069 total hemizygous alleles, which is between the ClinGen X-linked IRD VCEP PM2_Supporting and BS1 threshold of 0.000002 to 0.00002 and fails to meet these criteria. The computational predictor REVEL gives a score of 0.946, 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 0.01 for donor gain, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RS1 splicing. Vijayasarathy et al. tested this variant in comparison to wild-type and showed that anti-Flag antibody selectively identified epitope-tagged RS1 mutants, and this variant was not secreted (PMID: 20809529). 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: 17515881, PP4). This variant has been reported in at least 7 apparently unrelated probands meeting the PS4 requirement of a male diagnosed with XLRS (PMIDs: 9326935, 10636421, 17987333, 19093009, 28348004, 30551202, 30652005, 34828422, 39293640, PS4). The variant has been reported to segregate through at least 2 meioses in one family (PP1_moderate; PMID: 30551202). 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: PP3_Strong, PP4, PS4, and PP1_Moderate.
Met criteria codes
PP3_Strong
The computational predictor REVEL gives a score of 0.946, 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 0.01 for donor gain, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RS1 splicing.
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: 17515881, PP4).
PS4
This variant has been reported in at least 7 apparently unrelated probands meeting the PS4 requirement of a male diagnosed with XLRS (PMIDs: 9326935, 10636421, 17987333, 19093009, 28348004, 30551202, 30652005, 34828422, 39293640, PS4).
PP1_Moderate
The variant has been reported to segregate through at least 2 meioses in one family (PP1_moderate; PMID: 30551202).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
This variant is present in gnomAD v.4.1.0 at a frequency of 0.000002506 among hemizygous individuals, with 1 variant allele / 399069 total hemizygous alleles, which is between the ClinGen X-linked IRD VCEP PM2_Supporting and BS1 threshold of 0.000002 to 0.00002 and fails to meet these criteria.
PS3
Vijayasarathy et al. tested this variant in comparison to wild-type and showed that anti-Flag antibody selectively identified epitope-tagged RS1 mutants, and except for p.Glu72Lys, none of the mutants were secreted.
Curation History
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