MAP3K15 p.Ser402=
c.1206G>A · rs374377938 · VCV2660131
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00981%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -4.8 |
| Overall | ||
| CADD | 0.158 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00981%
South Asian · 5/50,970 alleles
Filtering AF
0.00382%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00248%
Overall
0.00086%
10/1,162,779 alleles · very rare
exomes 8/1,051,748 · genomes 2/111,031 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00981% | 10,194 |
| East Asian | 0.00309% | 32,372 |
| Admixed American | 0.00239% | 41,895 |
| European (non-Finnish) | 0.000343% | 291,640 |
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
- MAP3K15
- Protein
- p.Ser402=
- Coding
- c.1206G>A
- MANE Select
- NM_001001671
- dbSNP
- rs374377938
- Type
- single nucleotide variant
- Location
- chrX:19426304 (GRCh38)
- Structure
- AlphaFold pLDDT 75.41 · 1 PDB
Similar variants
- MAP3K15 p.Ser402Trp Uncertain significance ★ ⚠ same residue
- MAP3K15 p.Ala859Thr Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Ile295Ser Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Leu154Phe Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Thr1229Arg Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Ser199Asn Benign ★★ same type
- MAP3K15 p.Val455Ile Likely benign ★★ same type
- PDHA1 c.*1013C>A Benign ★★ 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/map3k15-p-ser402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown