ABCA5 p.Leu691=
c.2073G>A · rs201730590 · VCV797479
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0307%, 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 1.8 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 11.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0307%
European (non-Finnish) · 361/1,174,780 alleles
Filtering AF
0.0281%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.027%
Overall
0.0239%
380/1,591,740 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0307% | 3,254 |
| Remaining individualsnot grpmax-eligible | 0.0162% | 6,163 |
| African / African-American | 0.00819% | 12,217 |
| Admixed American | 0.00579% | 17,277 |
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
- ABCA5
- Protein
- p.Leu691=
- Coding
- c.2073G>A
- MANE Select
- NM_172232
- dbSNP
- rs201730590
- Type
- single nucleotide variant
- Location
- chr17:69286280 (GRCh38)
- Gene constraint
- LOEUF 0.97 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.12
- Residue 691
- the abc transporter 1 domain
Similar variants
- ABCA5 p.Ser288Phe Uncertain significance ★★ ⚠ same type
- ABCA5 c.4765+3A>G Likely benign ★★ same type
- ABCA5 p.Asn190Ser Likely benign ★★ ⚠ same type
- ABCA5 p.Asn768Asp Benign ★★ same type
- ABCA5 p.Asp817Tyr Likely benign ★★ ⚠ same type
- ABCA5 p.Gly1159Arg Likely benign ★★ ⚠ same type
- ABCA5 p.Gly128= Benign/Likely benign ★★ same type
- ABCA5 p.Ile1173Val Likely benign ★★ 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/abca5-p-leu691 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown