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
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Variant: NM_000350.3(ABCA4):c.629T>A (p.Leu210Gln)

CA341289668

866421 (ClinVar)

Gene: ABCA4 (HGNC:24)
Condition: ABCA4-related retinopathy (MONDO:0800406)
Inheritance Mode: Autosomal recessive inheritance
UUID: 552dfa63-0471-4cd5-b589-5693756a88ba
Approved on: 2025-10-28
Published on: 2025-11-14

HGVS expressions

NM_000350.3:c.629T>A
NM_000350.3(ABCA4):c.629T>A (p.Leu210Gln)
NC_000001.11:g.94098933A>T
CM000663.2:g.94098933A>T
NC_000001.10:g.94564489A>T
CM000663.1:g.94564489A>T
NC_000001.9:g.94337077A>T
NG_009073.1:g.27217T>A
ENST00000370225.4:c.629T>A
ENST00000649773.1:c.629T>A
ENST00000370225.3:c.629T>A
NM_000350.2:c.629T>A
More

Likely Pathogenic

Met criteria codes 3
PM2_Supporting PP3_Moderate PM3_Strong
Not Met criteria codes 3
PS4 PP4 PM5

Evidence Links 0

Expert Panel

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.629T>A variant in ABCA4 is a missense variant predicted to cause substitution of leucine by glutamine at amino acid 210 (p.Leu210Gln). The total minor allele frequency in gnomAD v4.1.0 is 0.0000006198 (1/1613424 alleles), which is lower than the ClinGen ABCA4 VCEP’s threshold for PM2_Supporting (<0.0001). The computational predictor REVEL gives a score of 0.879 which is above the threshold of >0.772, evidence that predicts a damaging effect on ABCA4 function (PP3_Moderate). This variant has been detected in at least four individuals with ABCA4-related retinopathy, who were compound heterozygous for the variant and a likely pathogenic or pathogenic variant, with one confirmed via parental testing and three with phase unconfirmed (PMIDs: 32751377, 32915376, Zolnikova I.V. et al Ophthalmology in Russia. 2021, ClinVar IDs: SCV001239990.1 and SCV002993733.3; PM3_Strong). In summary, this variant meets the criteria to be classified as a likely pathogenic for ABCA4-related retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen ABCA4 VCEP (Specification Version 1.0.0): PM2_Supporting, PP3_Moderate, PM3_Strong.
Met criteria codes
PM2_Supporting
The total minor allele frequency in gnomAD v4.1.0 is 0.0000006198 (1/1613424 alleles), which is lower than the ClinGen ABCA4 VCEP’s threshold for PM2_Supporting (<0.0001), meeting this criterion (PM2_Supporting).
PP3_Moderate
The computational predictor REVEL gives a score of 0.879 which is above the threshold of >0.772, evidence that predicts a damaging effect on ABCA4 function (PP3_Moderate).
PM3_Strong
This variant has been detected in at least four individuals with ABCA4-related retinopathy, who were compound heterozygous for the variant and a likely pathogenic or pathogenic variant, with one confirmed via parental testing and three with phase unconfirmed (PM3 = 2.25 pts, PMIDs: 32751377, 32915376, Zolnikova I.V. et al Ophthalmology in Russia. 2021, ClinVar IDs: SCV001239990.1 and SCV002993733.3; PM3_Strong)
Not Met criteria codes
PS4
This variant has Odds Ratio of infinity and Confidence Interval of 0.31 to infinity, containing 1, which does not meet the ABCA4 VCEP threshold of >3, where the CI does not contain 1 (PS4 not met; PMID: 35120629).
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No other missense variants affecting the same codon was found.
Curation History
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