MAP3K6 p.Ser929=
c.2787T>C · rs34558621 · VCV718416
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.11%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.05 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -3.3 |
| Overall | ||
| CADD | 0.059 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.11%
African / African-American · 3,060/74,476 alleles
Filtering AF
3.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.94%
Overall
0.23%
3,693/1,608,320 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.11% | 24 |
| Middle Eastern | 0.316% | 316 |
| Remaining individualsnot grpmax-eligible | 0.291% | 344 |
| Admixed American | 0.285% | 351 |
| European (non-Finnish) | 0.022% | 4,550 |
| South Asian | 0.011% | 9,051 |
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.Ser929=
- Coding
- c.2787T>C
- MANE Select
- NM_004672
- dbSNP
- rs34558621
- Type
- single nucleotide variant
- Location
- chr1:27358309 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.36
- Residue 929
- the 'disordered' region
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-ser929 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown