MAP3K15 p.Gln692=
c.2076G>A · rs141688905 · VCV3034999
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.1%, afr)
Conditions
1
MAP3K15-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.98 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 1.241 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.1%
African / African-American · 625/56,688 alleles
Filtering AF
1.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1%
Overall
0.0586%
706/1,203,805 alleles · low-frequency
exomes 362/1,093,142 · genomes 344/110,663 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.1% | 91 |
| Admixed American | 0.0992% | 1,008 |
| Remaining individualsnot grpmax-eligible | 0.0529% | 1,891 |
| Middle Eastern | 0.0233% | 4,283 |
| South Asian | 0.00354% | 28,260 |
| European (non-Finnish) | 0.000897% | 111,457 |
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
- MAP3K15
- Protein
- p.Gln692=
- Coding
- c.2076G>A
- MANE Select
- NM_001001671
- dbSNP
- rs141688905
- Type
- single nucleotide variant
- Location
- chrX:19395199 (GRCh38)
- Structure
- AlphaFold pLDDT 75.41 · 1 PDB
- Residue 692
- the protein kinase domain
Disease context
MAP3K15-related disorder
Similar variants
- MAP3K15 p.Ile295Ser Uncertain significance ★★ ⚠ same condition
- MAP3K15 p.Leu154Phe Uncertain significance ★★ ⚠ same condition
- MAP3K15 p.Thr1229Arg Uncertain significance ★★ ⚠ same condition
- MAP3K15 p.Gln541Ter Uncertain significance same condition
- MAP3K15 c.1440-1G>T Likely benign same condition
- MAP3K15 c.719+9C>T Benign same condition
- MAP3K15 p.Ala192Thr Benign same condition
- MAP3K15 p.Ala264Val Likely 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/map3k15-p-gln692 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown