ABCA4 p.Ser1071=
c.3213G>A · rs141233353 · VCV255920
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0824%, eas)
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 -10 | GERP -5.3 |
| Overall | ||
| CADD | 0.122 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0824%
East Asian · 37/44,876 alleles
Filtering AF
0.0615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0542%
Overall
0.0105%
170/1,614,188 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0824% | 1,213 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| African / African-American | 0.0266% | 3,753 |
| South Asian | 0.0176% | 5,693 |
| European (non-Finnish) | 0.00568% | 17,612 |
| Admixed American | 0.005% | 20,008 |
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.Ser1071=
- Coding
- c.3213G>A
- MANE Select
- NM_000350
- dbSNP
- rs141233353
- Type
- single nucleotide variant
- Location
- chr1:94042876 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.96 · 8 PDB
- Residue 1071
- a UniProt-annotated variant site (in cord3; uncertain significance); a UniProt-annotated variant site (in stgd1; uncertain significance); a UniProt-annotated variant site (found in a patient with chorioretinal atrophy; uncertain significance); a UniProt-annotated variant site (found in a patient with macular dystrophy; uncertain significance); a UniProt-annotated variant site (in stgd1; likely pathogenic); the abc transporter 1 domain; an α-helix; a disulfide bond
Similar variants
- ABCA4 p.Ser1071Leu Pathogenic ★★ same residue
- ABCA4 p.Ser1071Pro Pathogenic/Likely pathogenic ★★ same residue
- ABCA4 p.Ser1071fs Pathogenic ★★★ same residue
- ABCA4 p.Ser1071Valfs 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
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-ser1071 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown