Is MAP3K7 p.Val42del (c.122TTG[1]) pathogenic?

MAP3K7 p.Val42del (c.122TTG[1]) is classified Likely pathogenic in MAP3K7 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-23). No gnomAD frequency available for this variant; Associated with cardiospondylocarpofacial syndrome.

What condition is associated with MAP3K7 p.Val42del (c.122TTG[1])?

MAP3K7 p.Val42del (c.122TTG[1]) is associated with cardiospondylocarpofacial syndrome (ClinVar).

How common is MAP3K7 p.Val42del (c.122TTG[1]) in the general population?

MAP3K7 p.Val42del (c.122TTG[1]) is no gnomAD frequency available for this variant (gnomAD).

MAP3K7 p.Val42del

c.122TTG[1] · rs1582233787 · VCV684731

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

cardiospondylocarpofacial syndrome

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 7.7	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.Val42del
Coding: c.122TTG[1]
MANE Select: NM_145331
dbSNP: rs1582233787
Type: Microsatellite
Location: chr6:90571801 (GRCh38)
Gene constraint: LOEUF 0.397 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 70.27 · 25 PDB
Residue 42: the protein kinase domain; a binding site; the 'interaction with mapk8ip1' region; a β-strand

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

Disease context

cardiospondylocarpofacial syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAP3K7 p.Val42Phe Uncertain significance ★ ⚠ same residue
MAP3K7 p.Val50del Pathogenic/Likely pathogenic ★★ same condition
MAP3K7 p.Cys266del Uncertain significance ★ same condition
MAP3K7 p.Gly110Cys Likely pathogenic ★ same condition
MAP3K7 p.Ser192Asn Likely pathogenic ★ same condition
MAP3K7 p.Ser272Tyr Likely pathogenic ★ ⚠ same condition
MAP3K7 p.Trp241Arg Pathogenic ★ same condition
MAP3K7 p.Tyr206Asp 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-val42del (accessed [today's date]).

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