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.214G>A (p.Glu72Lys)

CA226621

9888 (ClinVar)

Gene: RS1
Condition: X-linked retinoschisis
Inheritance Mode: X-linked inheritance (recessive (HP:0001419))
UUID: 95356f66-b18e-41aa-8a7a-37d6d3af7f5c
Approved on: 2025-05-19
Published on: 2025-05-20

HGVS expressions

NM_000330.4:c.214G>A
NM_000330.4(RS1):c.214G>A (p.Glu72Lys)
NC_000023.11:g.18647303C>T
CM000685.2:g.18647303C>T
NC_000023.10:g.18665423C>T
CM000685.1:g.18665423C>T
NC_000023.9:g.18575344C>T
NG_008475.1:g.226699C>T
NG_008659.3:g.35146G>A
ENST00000379984.4:c.214G>A
ENST00000379984.3:c.214G>A
ENST00000379989.6:c.2797+1213C>T
ENST00000379996.7:c.2797+1213C>T
ENST00000476595.1:n.705G>A
NM_000330.3:c.214G>A
NM_001037343.1:c.2797+1213C>T
NM_003159.2:c.2797+1213C>T
NM_001037343.2:c.2797+1213C>T
NM_003159.3:c.2797+1213C>T
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Pathogenic

Met criteria codes 6
PP4 PM1 PP1_Strong PP3_Moderate PS3_Supporting PS4
Not Met criteria codes 2
PM2 BS1

Evidence Links 1

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.214G>A variant is a missense variant encoding the substitution of Glutamic acid with Lysine at amino acid 72. This variant is present in gnomAD v.4.1.0 at a frequency of 0.000002508 among hemizygous individuals, with 1 variant alleles / 398646 total hemizygous alleles, which is between the ClinGen X-linked IRD VCEP PM2_Supporting and BS1 thresholds of <0.000002 and >0.00002 and fails to meet these criteria. The computational predictor REVEL gives a score of 0.921, which is within the ClinGen X-linked IRD VCEP range between 0.931 to 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. HEK293 cells exogenously expressing the variant exhibit loss of RS1 secretion into the medium relative to the wild-type control (PMID: 12746437, PS3_Supporting). This variant p.Glu72Lys, of the RS1 gene, is an established residue involved in cross-linking the adjacent RS1 subunit by the ClinGen X-linked IRD VCEP (PMID: 27114531, PM1). The variant has been reported to segregate with retinal dystrophy through at least 3 meioses in the same family (PP1_Strong; PMID: 11246454, 38317323, 19324861). 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: 23288992, PP4). This variant has been reported in at least 6 apparently unrelated probands meeting one of the PS4 requirements of a male diagnosed with X-linked retinoschisis (PMIDs: 30025115, 28348004, 19324861, 22245991, 32531858, 29851975, 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: PP3_moderate, PP1_strong, PP4, PS4, PS3_supporting, and PM1 (date of approval 01/24/2025).
Met criteria codes
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: 23288992, PP4).
PM1
This variant p.Glu72Lys, of the RS1 gene, is an established residue involved in cross-linking the adjacent RS1 subunit by the ClinGen X-linked IRD VCEP (PMID: 27114531, PM1_moderate).
PP1_Strong
The variant has been reported to segregate with retinal dystrophy through at least 3 meioses in the same family (PP1_Strong; PMID: 11246454, 38317323, 19324861).
PP3_Moderate
The computational predictor REVEL gives a score of 0.921, which is within the ClinGen X-linked IRD VCEP range between 0.931 to 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.
PS3_Supporting
293 cells exogenously expressing the variant exhibit loss of RS1 secretion into the medium relative to the wild-type control (PMID: 12746437, PS3_Supporting).

PS4
This variant has been reported in at least 6 apparently unrelated probands meeting one of the PS4 requirements of a male diagnosed with XLRS (PMIDs: 30025115, 28348004, 19324861, 22245991, 32531858, 29851975, PS4).
Not Met criteria codes
PM2
This variant is present in gnomAD v.4.1.0 at a frequency of 0.000002508 among hemizygous individuals, with 1 variant alleles / 398646 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.
BS1
This variant is present in gnomAD v.4.1.0 at a frequency of 0.000002508 among hemizygous individuals, with 1 variant alleles / 398646 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.
Curation History
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