Is MAP3K7 p.Val50del (c.145GTT[1]) pathogenic?

MAP3K7 p.Val50del (c.145GTT[1]) is classified Pathogenic/Likely pathogenic in MAP3K7 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2022-05-04). No gnomAD frequency available for this variant; Associated with MAP3K7-related disorder.

What condition is associated with MAP3K7 p.Val50del (c.145GTT[1])?

MAP3K7 p.Val50del (c.145GTT[1]) is associated with MAP3K7-related disorder, cardiospondylocarpofacial syndrome (ClinVar).

How common is MAP3K7 p.Val50del (c.145GTT[1]) in the general population?

MAP3K7 p.Val50del (c.145GTT[1]) is no gnomAD frequency available for this variant (gnomAD).

MAP3K7 p.Val50del

c.145GTT[1] · rs886039236 · VCV264704

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

MAP3K7-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.8, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MAP3K7
Protein: p.Val50del
Coding: c.145GTT[1]
MANE Select: NM_145331
dbSNP: rs886039236
Type: Microsatellite
Location: chr6:90571778 (GRCh38)
Gene constraint: LOEUF 0.397 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 70.27 · 25 PDB
Residue 50: the protein kinase domain; a binding site; the 'interaction with mapk8ip1' region; a UniProt-annotated variant site (in cscf); a β-strand

Full MAP3K7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MAP3K7-related disorder

Also linked: cardiospondylocarpofacial syndrome

Similar variants

MAP3K7 p.Val42del Likely pathogenic ★ same condition
MAP3K7 p.Cys266del Uncertain significance ★ same condition
MAP3K7 p.Arg155_Asp156delinsAsn Likely pathogenic ★ same condition
MAP3K7 p.Gly110Cys Likely pathogenic ★ same condition
MAP3K7 p.Gly168Arg Pathogenic ★ same condition
MAP3K7 p.His185_Thr187del Likely pathogenic ★ same condition
MAP3K7 p.Ser192Asn Likely pathogenic ★ same condition
MAP3K7 p.Ser272Tyr Likely pathogenic ★ ⚠ 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/map3k7-p-val50del (accessed [today's date]).

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