MAP3K6 p.Val1118=
c.3354G>T · rs1258164419 · VCV742512
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.40 | donor loss, 5 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.87 | GERP 0.34, phastCons 1 |
| Overall | ||
| CADD | 6.986 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,936 alleles
Overall
6.2e-05%
1/1,613,754 alleles · very rare
exomes 0/1,461,546 · genomes 1/152,208 · joint denominator
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
- MAP3K6
- Protein
- p.Val1118=
- Coding
- c.3354G>T
- MANE Select
- NM_004672
- dbSNP
- rs1258164419
- Type
- single nucleotide variant
- Location
- chr1:27357019 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.36
Similar variants
- MAP3K6 c.1256-2A>G Likely benign ★★ same type
- MAP3K6 c.2915+9A>T Benign ★★ same type
- MAP3K6 p.Ala405= Benign/Likely benign ★★ same type
- MAP3K6 p.Arg499Cys Benign ★★ same type
- MAP3K6 p.Asn622Lys Benign ★★ same type
- MAP3K6 p.Gln1142Arg Benign ★★ same type
- MAP3K6 p.Glu248= Likely benign ★★ same type
- MAP3K6 p.Leu1249= 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/map3k6-p-val1118 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown