ABCD3 p.Ile319=
c.957T>C · rs139507691 · VCV1601379
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.481%, afr)
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 2.8 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 9.067 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.481%
African / African-American · 361/75,048 alleles
Filtering AF
0.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.424%
Overall
0.0261%
421/1,613,664 alleles · rare
exomes 195/1,461,356 · genomes 226/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.481% | 208 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,838 |
| Admixed American | 0.03% | 3,334 |
| South Asian | 0.00439% | 22,765 |
| European (non-Finnish) | 0.000339% | 294,911 |
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.Ile319=
- Coding
- c.957T>C
- MANE Select
- NM_002858
- dbSNP
- rs139507691
- Type
- single nucleotide variant
- Location
- chr1:94487601 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.39 · 9 PDB
- Residue 319
- the abc transmembrane type-1 domain; a turn
Similar variants
- ABCD3 p.Ile319Leu Uncertain significance ★ ⚠ same residue
- ABCD3 p.Ala131Thr Uncertain significance ★★ ⚠ same type
- ABCD3 p.Ala3Val 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
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-ile319 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown