MAP3K7 p.Ala15=
c.45C>T · rs201710994 · VCV1911525
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00204%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.37 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.51 | GERP -2.6, phastCons 0.91 |
| Overall | ||
| CADD | 13.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00204%
European (non-Finnish) · 24/1,178,610 alleles
Filtering AF
0.00138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00116%
Overall
0.00155%
25/1,610,920 alleles · very rare
exomes 24/1,458,676 · genomes 1/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00204% | 49,109 |
| South Asian | 0.0011% | 90,986 |
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
- MAP3K7
- Protein
- p.Ala15=
- Coding
- c.45C>T
- MANE Select
- NM_145331
- dbSNP
- rs201710994
- Type
- single nucleotide variant
- Location
- chr6:90586839 (GRCh38)
- Gene constraint
- LOEUF 0.397 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.27 · 25 PDB
- Residue 15
- the 'interaction with mapk8ip1' region
Similar variants
- MAP3K7 p.Ala15Ser Uncertain significance ★ ⚠ same residue
- MAP3K7 p.Ala15Val Uncertain significance ★ ⚠ same residue
- MAP3K7 p.Arg274Cys Pathogenic/Likely pathogenic ★★ same type
- MAP3K7 p.Gly110Ser Pathogenic/Likely pathogenic ★★ same type
- MAP3K7 p.Pro512Leu Pathogenic ★★ same type
- MAP3K7 p.Ala313Thr Uncertain significance ★★ ⚠ same type
- MAP3K7 p.Ala400Thr Uncertain significance ★★ ⚠ same type
- MAP3K7 p.Ala6Thr 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/map3k7-p-ala15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown