MAP3K13 p.Ala465=
c.1395G>A · rs56098590 · VCV784471
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.42%, eas) — too common for a highly-penetrant pathogenic allele
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 -1.8 | GERP -5.6 |
| Overall | ||
| CADD | 4.134 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.42%
East Asian · 2,429/44,856 alleles
Filtering AF
5.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.16%
Overall
0.218%
3,508/1,612,794 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 5.42% | 18 |
| Admixed American | 1.02% | 98 |
| Remaining individualsnot grpmax-eligible | 0.216% | 463 |
| Ashkenazi Jewishnot grpmax-eligible | 0.199% | 502 |
| Middle Eastern | 0.132% | 758 |
| South Asian | 0.107% | 939 |
| African / African-American | 0.0453% | 2,207 |
| European (non-Finnish) | 0.0112% | 8,931 |
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
- MAP3K13
- Protein
- p.Ala465=
- Coding
- c.1395G>A
- MANE Select
- NM_004721
- dbSNP
- rs56098590
- Type
- single nucleotide variant
- Location
- chr3:185465753 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.92
Similar variants
- MAP3K13 p.Ala465Thr Uncertain significance ★ ⚠ same residue
- MAP3K13 p.Ala416Thr Uncertain significance ★ ⚠ same type
- MAP3K13 p.Ala96Val Uncertain significance ★ ⚠ same type
- MAP3K13 p.Arg278His Uncertain significance ★ ⚠ same type
- MAP3K13 p.Arg326Trp Uncertain significance ★ ⚠ same type
- MAP3K13 p.Arg401Gln Uncertain significance ★ ⚠ same type
- MAP3K13 p.Arg449Gln Uncertain significance ★ same type
- MAP3K13 p.Arg474Gln 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/map3k13-p-ala465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown