ABCD3 p.Ala3=
c.9C>T · rs371364095 · VCV1589644
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0681%, mid)
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 2.6 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 15.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0681%
Middle Eastern · 4/5,870 alleles
Filtering AF
0.0476%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0421%
Overall
0.015%
240/1,601,714 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0681% | 1,468 |
| Admixed American | 0.0636% | 1,572 |
| European (non-Finnish) | 0.016% | 6,234 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,531 |
| South Asian | 0.00332% | 30,157 |
| Finnishnot grpmax-eligible | 0.0018% | 55,510 |
| African / African-American | 0.00134% | 74,892 |
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
- ABCD3
- Protein
- p.Ala3=
- Coding
- c.9C>T
- MANE Select
- NM_002858
- dbSNP
- rs371364095
- Type
- single nucleotide variant
- Location
- chr1:94418487 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.39 · 9 PDB
- Residue 3
- the 'interaction with pex19' region
Similar variants
- ABCD3 p.Ala3Val Uncertain significance ★★ ⚠ same residue
- ABCD3 p.Ala131Thr Uncertain significance ★★ ⚠ same type
- ABCD3 p.Arg496Cys Uncertain significance ★★ ⚠ same type
- ABCD3 p.Asn12Tyr Uncertain significance ★★ ⚠ same type
- ABCD3 p.Ile225Val Uncertain significance ★★ ⚠ same type
- ABCD3 p.Leu23Val Uncertain significance ★★ ⚠ same type
- ABCD3 p.Leu45Val Uncertain significance ★★ ⚠ same type
- ABCD3 p.Pro425Leu 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/abcd3-p-ala3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown