Is MAP3K7 p.Arg437His (c.1310G>A) pathogenic?

MAP3K7 p.Arg437His (c.1310G>A) is classified Conflicting classifications of pathogenicity in MAP3K7 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-02-16). AlphaMissense: likely benign (0.2394); Ultra-rare (popmax 0.0268%, eas); Associated with Inborn genetic diseases.

What condition is associated with MAP3K7 p.Arg437His (c.1310G>A)?

MAP3K7 p.Arg437His (c.1310G>A) is associated with Inborn genetic diseases (ClinVar).

How common is MAP3K7 p.Arg437His (c.1310G>A) in the general population?

MAP3K7 p.Arg437His (c.1310G>A) is ultra-rare (popmax 0.0268%, eas) (gnomAD).

What do computational predictors say about MAP3K7 p.Arg437His (c.1310G>A)?

AlphaMissense predicts likely benign (score 0.2394) — an in-silico prediction, not a clinical call.

MAP3K7 p.Arg437His

c.1310G>A · rs537649538 · VCV1168258

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2394 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0268%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2394	likely benign
REVEL	0.355	indeterminate
SaProt	LLR -7.45	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 33 kb · p 0.12 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0268% East Asian · 12/44,836 alleles

Filtering AF 0.0154% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0121%

Overall 0.00211% 34/1,611,996 alleles · ultra-rare exomes 30/1,459,972 · genomes 4/152,024 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0268%	3,736
Admixed American	0.00501%	19,972
Remaining individualsnot grpmax-eligible	0.00481%	20,796
African / African-American	0.00401%	24,961
Finnishnot grpmax-eligible	0.00313%	31,931
South Asian	0.0011%	91,006
European (non-Finnish)	0.000848%	117,861

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: MAP3K7
Protein: p.Arg437His
Coding: c.1310G>A
MANE Select: NM_145331
dbSNP: rs537649538
Type: single nucleotide variant
Location: chr6:90536383 (GRCh38)
Gene constraint: LOEUF 0.397 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 70.27 · 25 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAP3K7 p.Arg437Gly Uncertain significance ★ ⚠ same residue
MAP3K7 p.Arg437Cys Uncertain significance ★ same residue
MAP3K7 p.Ala313Thr Uncertain significance ★★ ⚠ same condition
MAP3K7 p.Ala400Thr Uncertain significance ★★ ⚠ same condition
MAP3K7 p.Ala6Thr Uncertain significance ★★ ⚠ same condition
MAP3K7 p.Arg289Gln Uncertain significance ★★ ⚠ same condition
MAP3K7 p.Arg347His Uncertain significance ★★ ⚠ same condition
MAP3K7 p.Asn342Asp Uncertain significance ★★ ⚠ 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-arg437his (accessed [today's date]).

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