MAP3K6 p.Ala106=
c.318T>C · rs537500636 · VCV3038960
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.293%, afr)
Conditions
1
MAP3K6-related disorder
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 -1.3 | GERP -3.2 |
| Overall | ||
| CADD | 8.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.293%
African / African-American · 192/65,486 alleles
Filtering AF
0.259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.246%
Overall
0.0159%
213/1,337,820 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.293% | 341 |
| Admixed American | 0.0367% | 2,721 |
| Remaining individualsnot grpmax-eligible | 0.0221% | 4,519 |
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.Ala106=
- Coding
- c.318T>C
- MANE Select
- NM_004672
- dbSNP
- rs537500636
- Type
- single nucleotide variant
- Location
- chr1:27366280 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.36
Disease context
MAP3K6-related disorder
Similar variants
- MAP3K6 c.1415+9C>T Likely benign same condition
- MAP3K6 c.2584-6C>T Benign same condition
- MAP3K6 c.3259-10C>T Benign same condition
- MAP3K6 c.3711+7C>T Likely benign same condition
- MAP3K6 p.Ala1061Thr Likely benign same condition
- MAP3K6 p.Arg668Gly Benign ⚠ same condition
- MAP3K6 p.Arg913His Benign same condition
- MAP3K6 p.Gly1233Ala Benign same condition
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-ala106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown