Is MAP3K15 p.Val930= (c.2790C>T) pathogenic?

MAP3K15 p.Val930= (c.2790C>T) is classified Likely benign in MAP3K15 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-28). Ultra-rare (popmax 0.0281%, afr); Associated with MAP3K15-related disorder.

What condition is associated with MAP3K15 p.Val930= (c.2790C>T)?

MAP3K15 p.Val930= (c.2790C>T) is associated with MAP3K15-related disorder (ClinVar).

How common is MAP3K15 p.Val930= (c.2790C>T) in the general population?

MAP3K15 p.Val930= (c.2790C>T) is ultra-rare (popmax 0.0281%, afr) (gnomAD).

MAP3K15 p.Val930=

c.2790C>T · rs139451743 · VCV3048709

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0281%, afr)

Conditions

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 -4.7	GERP -3.4
Overall
CADD	0.175	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0281% African / African-American · 16/57,003 alleles

Filtering AF 0.0176% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0143%

Overall 0.0112% 134/1,197,834 alleles · ultra-rare exomes 114/1,086,268 · genomes 20/111,566 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0281%	3,563
Middle Eastern	0.027%	3,699
Admixed American	0.0198%	5,049
European (non-Finnish)	0.0113%	8,850
Remaining individualsnot grpmax-eligible	0.0106%	9,472
East Asian	0.00595%	16,819

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.Val930=
Coding: c.2790C>T
MANE Select: NM_001001671
dbSNP: rs139451743
Type: single nucleotide variant
Location: chrX:19373679 (GRCh38)
Structure: AlphaFold pLDDT 75.41 · 1 PDB

Full MAP3K15 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-val930 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown