ABCA4 p.Pro68=
c.204G>A · rs201725352 · VCV1671192
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.5 |
| Overall | ||
| CADD | 0.437 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,090 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000991%
16/1,614,086 alleles · very rare
exomes 15/1,461,874 · genomes 1/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,773 |
| African / African-American | 0.00133% | 74,930 |
| European (non-Finnish) | 0.000932% | 107,275 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ABCA4
- Protein
- p.Pro68=
- Coding
- c.204G>A
- MANE Select
- NM_000350
- dbSNP
- rs201725352
- Type
- single nucleotide variant
- Location
- chr1:94111536 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.96 · 8 PDB
- Residue 68
- an α-helix; a UniProt-annotated variant site (in stgd1; uncertain significance); a UniProt-annotated variant site (in cord3; uncertain significance); a UniProt-annotated variant site (in stgd1)
Similar variants
- ABCA4 p.Pro68Leu Pathogenic ★★★ ⚠ same residue
- ABCA4 p.Pro68Arg Pathogenic/Likely pathogenic ★★ same residue
- ABCA4 c.1937+1G>A Pathogenic ★★★ same type
- ABCA4 c.3328+2T>A Pathogenic ★★★ same type
- ABCA4 c.3523-1G>A Pathogenic ★★★ same type
- ABCA4 c.4253+43G>A Pathogenic ★★★ same type
- ABCA4 c.4254-1G>C Pathogenic ★★★ same type
- ABCA4 c.4352+1G>A Pathogenic ★★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/abca4-p-pro68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown