ABCA6 p.Ala1476=
c.4428G>A · rs201702880 · VCV2648161
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.12%, 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 -12 | GERP -3.8 |
| Overall | ||
| CADD | 0.314 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.12%
East Asian · 54/44,868 alleles
Filtering AF
0.0947%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0855%
Overall
0.0125%
201/1,610,752 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.12% | 831 |
| Remaining individualsnot grpmax-eligible | 0.069% | 1,449 |
| Middle Eastern | 0.0165% | 6,054 |
| European (non-Finnish) | 0.00772% | 12,958 |
| Finnishnot grpmax-eligible | 0.00626% | 15,986 |
| African / African-American | 0.00536% | 18,646 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0034% | 29,440 |
| Admixed American | 0.00339% | 29,500 |
| South Asian | 0.0011% | 90,500 |
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
- ABCA6
- Protein
- p.Ala1476=
- Coding
- c.4428G>A
- MANE Select
- NM_080284
- dbSNP
- rs201702880
- Type
- single nucleotide variant
- Location
- chr17:69083259 (GRCh38)
- Gene constraint
- LOEUF 1.041 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.38
- Residue 1476
- the abc transporter 2 domain
Similar variants
- ABCA6 p.Ala1043Gly Uncertain significance ★ ⚠ same type
- ABCA6 p.Ala107Thr Uncertain significance ★ ⚠ same type
- ABCA6 p.Ala1287Thr Uncertain significance ★ ⚠ same type
- ABCA6 p.Ala1303Thr Uncertain significance ★ ⚠ same type
- ABCA6 p.Ala1389Glu Uncertain significance ★ ⚠ same type
- ABCA6 p.Ala1392Thr Uncertain significance ★ ⚠ same type
- ABCA6 p.Ala1454Thr Uncertain significance ★ ⚠ same type
- ABCA6 p.Ala1535Val Uncertain significance ★ ⚠ 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/abca6-p-ala1476 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown