Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_000350.3(ABCA4):c.4457C>T (p.Pro1486Leu)

CA227192

99283 (ClinVar)

Gene: ABCA4 (HGNC:24)

Condition: ABCA4-related retinopathy (MONDO:0800406)

Inheritance Mode: Autosomal recessive inheritance

UUID: 99cef40a-cd37-4a13-bec4-6b893231e171

Approved on: 2025-12-05

Published on: 2025-12-23

HGVS expressions

NM_000350.3:c.4457C>T

NM_000350.3(ABCA4):c.4457C>T (p.Pro1486Leu)

NC_000001.11:g.94029527G>A

CM000663.2:g.94029527G>A

NC_000001.10:g.94495083G>A

CM000663.1:g.94495083G>A

NC_000001.9:g.94267671G>A

NG_009073.1:g.96623C>T

ENST00000370225.4:c.4457C>T

ENST00000370225.3:c.4457C>T

ENST00000536513.5:c.833C>T

NM_000350.2:c.4457C>T

Pathogenic

PS4 PP4 PM3 PP3_Moderate PM2_Supporting

Evidence Links 0

Expert Panel

ABCA4 VCEP

Criteria Specification Information

Criteria Specification: ClinGen ABCA4 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ABCA4 Version 1.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

ABCA4 VCEP

The NM_000350.3(ABCA4):c.4457C>T variant in ABCA4 is a missense variant predicted to cause substitution of proline by leucine at amino acid 1486 (p.Pro1486Leu). The total minor allele frequency in gnomAD v4.1.0 is 0.00003787 (61/1610682 alleles), which is lower than the ClinGen ABCA4 VCEP’s threshold for PM2_Supporting (<0.0001). The computational predictor REVEL gives a score of 0.88 which is above the threshold of >0.772, evidence that predicts a damaging effect on ABCA4 function (PP3_Moderate). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. The OR is 58.8 and the CI is (30.38-124.55), which is above the ABCA4 VCEP threshold of >5, where the CI does not contain 1 (PS4; PMID: 35120629). At least one proband meeting phenotypic criteria for ABCA4-related retinopathy (PP4, PMID:33841504). This variant has been detected in at least 4 individuals with ABCA4-related retinopathy who were homozygous for the variant (PM3; PMID: 32619608, 32036094). In summary, this variant meets the criteria to be classified as pathogenic for ABCA4-related retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen ABCA4 VCEP (Specification Version 1.0): PS4, PM3, PP3_Moderate, PP4, PM2_Supporting.

PS4

The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. The OR is 58.8 and the CI is (30.38-124.55), which is above the ABCA4 VCEP threshold of >5, where the CI does not contain 1 (PS4; PMID: 35120629).

PP4

At least one patient with this variant displayed presence of at least two ABCA4 variants, onset under 18 years of age, macular flecks on imaging, decreased central visual acuity, and macular atrophy, which is highly specific for ABCA4-related retinopathy (PP4, PMID:33841504).

PM3

This variant has been detected in at least 4 individuals with ABCA4-related retinopathy. Four individuals were homozygous for the variant (PM3= 1 point; PM3; PMID: 32619608, 32036094).

PP3_Moderate

The computational predictor REVEL gives a score of 0.88 which is above the threshold of >0.772, evidence that predicts a damaging effect on ABCA4 function (PP3_Moderate).

PM2_Supporting

The total minor allele frequency in gnomAD v4.1.0 is 0.00003787 (61/1610682 alleles), which is lower than the ClinGen ABCA4 VCEP’s threshold for PM2_Supporting (<0.0001), meeting this criterion (PM2_Supporting).

Curation History

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