ABCD3 p.Lys416=
c.1248G>A · rs200036674 · VCV1478841
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00975%, 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 1.7 | GERP -1.8, phastCons 0.96 |
| Overall | ||
| CADD | 9.524 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00975%
European (non-Finnish) · 115/1,179,154 alleles
Filtering AF
0.00826%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00774%
Overall
0.00738%
119/1,612,904 alleles · very rare
exomes 115/1,460,788 · genomes 4/152,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00975% | 10,254 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,223 |
| Finnishnot grpmax-eligible | 0.00156% | 64,014 |
| African / African-American | 0.00133% | 75,012 |
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.Lys416=
- Coding
- c.1248G>A
- MANE Select
- NM_002858
- dbSNP
- rs200036674
- Type
- single nucleotide variant
- Location
- chr1:94489815 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.39 · 9 PDB
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-lys416 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown