ABCD3 p.Gln396=
c.1188A>G · VCV4811528
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | acceptor loss, 30 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 0.23, phastCons 1 |
| Overall | ||
| CADD | 5.822 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,922 alleles
Filtering AF
0.00901%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00682%
Overall
0.000744%
12/1,613,082 alleles · ultra-rare
exomes 11/1,461,002 · genomes 1/152,080 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 5,992 |
| South Asian | 0.0011% | 91,050 |
| European (non-Finnish) | 8.48e-05% | 1,179,422 |
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.Gln396=
- Coding
- c.1188A>G
- MANE Select
- NM_002858
- Type
- single nucleotide variant
- Location
- chr1:94489755 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.39 · 9 PDB
- Residue 396
- an α-helix
Similar variants
- 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
- 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-gln396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown