ABCA6 p.Ile540=
c.1620C>T · rs138479597 · VCV2648165
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.71%, nfe)
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 1.9 | GERP 0.18, phastCons 1 |
| Overall | ||
| CADD | 6.575 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.71%
European (non-Finnish) · 8,350/1,175,818 alleles
Filtering AF
0.697%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.692%
Overall
0.568%
9,125/1,606,976 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.71% | 141 |
| Amishnot grpmax-eligible | 0.658% | 152 |
| Middle Eastern | 0.498% | 201 |
| Remaining individualsnot grpmax-eligible | 0.468% | 214 |
| Ashkenazi Jewishnot grpmax-eligible | 0.377% | 265 |
| Admixed American | 0.31% | 323 |
| African / African-American | 0.11% | 910 |
| Finnishnot grpmax-eligible | 0.0927% | 1,078 |
| South Asian | 0.0133% | 7,521 |
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.Ile540=
- Coding
- c.1620C>T
- MANE Select
- NM_080284
- dbSNP
- rs138479597
- Type
- single nucleotide variant
- Location
- chr17:69114924 (GRCh38)
- Gene constraint
- LOEUF 1.041 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.38
- Residue 540
- the abc transporter 1 domain
Similar variants
- ABCA6 p.Ile540Asn Uncertain significance ★ ⚠ same residue
- ABCA6 p.Ile540Val Uncertain significance ★ ⚠ same residue
- 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
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-ile540 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown