ABCD3 p.Arg390Gln
c.1169G>A · VCV4636240
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8394 | likely pathogenic |
|---|---|---|
| REVEL | 0.953 | strongly pathogenic-leaning |
| SaProt | LLR -13.59 | damaging |
| ⇒ AlphaMissense, REVEL and SaProt all call this damaging. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
| Pangolin | Δ0.47 | gain · loss 0.22 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.5, phastCons 1 |
| Regional constraint | o/e 0.81 | unconstrained · MANE · 29 kb · p 0.00033 · regional, not allelic |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,428 |
| African / African-Americangrpmax | 0.00133% | 74,908 |
| European (non-Finnish) | 0.000509% | 196,498 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Arg390Gln
- Coding
- c.1169G>A
- MANE Select
- NM_002858
- Type
- single nucleotide variant
- Location
- chr1:94489736 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.39 · 9 PDB
- Residue 390
- 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-arg390gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown