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 between message contents CDKL5 and cspec object contents RS1
  • No ClinVar Id was directly found from the curated document
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_003159.3:c.2714-1488C>G

CA412371778

Gene: CDKL5 (HGNC:6792)
Condition: X-linked retinoschisis (MONDO:0010725)
Inheritance Mode: X-linked inheritance
UUID: 8412f6f3-ea2a-43fd-ad63-78f0be1ad982
Approved on: 2026-09-26
Published on: 2026-09-26

HGVS expressions

NM_003159.3:c.2714-1488C>G
NC_000023.11:g.18644519C>G
CM000685.2:g.18644519C>G
NC_000023.10:g.18662639C>G
CM000685.1:g.18662639C>G
NC_000023.9:g.18572560C>G
NG_008475.1:g.223915C>G
NG_008659.3:g.37930G>C
ENST00000379984.4:c.433G>C
ENST00000379984.3:c.433G>C
ENST00000379989.6:c.2714-1488C>G
ENST00000379996.7:c.2714-1488C>G
ENST00000476595.1:n.924G>C
NM_000330.3:c.433G>C
NM_001037343.1:c.2714-1488C>G
NM_003159.2:c.2714-1488C>G
NM_000330.4:c.433G>C
NM_001037343.2:c.2714-1488C>G
More

Likely Pathogenic

Met criteria codes 5
PS4_Supporting PP4_Moderate PP3_Moderate PS3_Supporting PM2_Supporting

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.433G>C (p.Asp145His) variant is a missense variant encoding the substitution of Aspartic acid and Histidine at amino acid 145. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.916, 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 0.04 for acceptor loss, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RS1 splicing. Hek 293, Murine RS1h-/Y retinal and kidney cells exogenously expressing the variant exhibit loss of RS1 secretion into the medium relative to the wild-type control (PMID: 30040949, PS3_Supporting). At least one proband harboring this variant exhibits a phenotype including the 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: 7615541, PP4_Moderate). 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: 18369700, 32300273, 34624300, 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, PS3_Supporting, PP4_Moderate, and PS4_Supporting.
Met criteria codes
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: 18369700, 32300273, 34624300, PS4_Supporting).
PP4_Moderate
At least one proband harboring this variant exhibits a phenotype including the 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: 7615541, PP4_Moderate).
PP3_Moderate
The computational predictor REVEL gives a score of 0.916, 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 0.04 for acceptor loss, 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
Hek 293, Murine RS1h-/Y retinal and kidney cells exogenously expressing the variant exhibit loss of RS1 secretion into the medium relative to the wild-type control (PMID: 30040949, PS3_Supporting).

PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
Curation History
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