MAP3K10 p.Phe249=
c.747C>T · rs142393148 · VCV737698
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0439%, sas)
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 -3.4 | GERP -4.5 |
| Overall | ||
| CADD | 12.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0439%
South Asian · 40/91,090 alleles
Filtering AF
0.039%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0378%
Overall
0.0372%
600/1,614,038 alleles · ultra-rare
exomes 556/1,461,836 · genomes 44/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0439% | 2,277 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,314 |
| European (non-Finnish) | 0.0421% | 2,374 |
| African / African-American | 0.0294% | 3,406 |
| Middle Eastern | 0.0164% | 6,084 |
| Finnishnot grpmax-eligible | 0.0109% | 9,141 |
| Admixed American | 0.00833% | 11,999 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- MAP3K10
- Protein
- p.Phe249=
- Coding
- c.747C>T
- MANE Select
- NM_002446
- dbSNP
- rs142393148
- Type
- single nucleotide variant
- Location
- chr19:40198439 (GRCh38)
- Gene constraint
- LOEUF 0.506 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 61.33 · 1 PDB
- Residue 249
- the protein kinase domain
Similar variants
- MAP3K10 p.Ala240Thr Uncertain significance ★ ⚠ same type
- MAP3K10 p.Ala263Thr Uncertain significance ★ ⚠ same type
- MAP3K10 p.Ala364Thr Uncertain significance ★ ⚠ same type
- MAP3K10 p.Ala488Thr Uncertain significance ★ ⚠ same type
- MAP3K10 p.Ala603Thr Uncertain significance ★ ⚠ same type
- MAP3K10 p.Ala648Val Uncertain significance ★ ⚠ same type
- MAP3K10 p.Ala658Thr Uncertain significance ★ ⚠ same type
- MAP3K10 p.Ala661Thr 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/map3k10-p-phe249 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown