Is MAP3K8 p.Gln55Pro (c.164A>C) pathogenic?

MAP3K8 p.Gln55Pro (c.164A>C) is classified Uncertain significance in MAP3K8 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-26). AlphaMissense: likely benign (0.0769); Absent from gnomAD v4.1.

How common is MAP3K8 p.Gln55Pro (c.164A>C) in the general population?

MAP3K8 p.Gln55Pro (c.164A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MAP3K8 p.Gln55Pro (c.164A>C)?

AlphaMissense predicts likely benign (score 0.0769) — an in-silico prediction, not a clinical call.

MAP3K8 p.Gln55Pro

c.164A>C · VCV4549521

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0769 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0769	likely benign
REVEL	0.183	benign-leaning
SaProt	LLR -5.96	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.2	GERP 0.51, phastCons 0.94
Regional constraint	o/e 1.09	unconstrained · MANE · 234 bp · p 0.38 · regional, not allelic
Overall
CADD	18.34	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MAP3K8
Protein: p.Gln55Pro
Coding: c.164A>C
MANE Select: NM_005204
Type: single nucleotide variant
Location: chr10:30439102 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI 0.73 (gnomAD)
Structure: AlphaFold pLDDT 74.13 · 3 PDB

Full MAP3K8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP3K8 p.Gln55Lys Uncertain significance ★ ⚠ same residue
MAP3K8 p.Ala35Ser Uncertain significance ★★ ⚠ same type
MAP3K8 p.Ala450Thr Uncertain significance ★★ same type
MAP3K8 p.Arg392Gly Uncertain significance ★★ ⚠ same type
MAP3K8 p.Arg408Ser Uncertain significance ★★ ⚠ same type
MAP3K8 p.Asn54Asp Uncertain significance ★★ ⚠ same type
MAP3K8 p.Gly67Asp Uncertain significance ★★ ⚠ same type
MAP3K8 p.Ile190Val Uncertain significance ★★ ⚠ same type

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/map3k8-p-gln55pro (accessed [today's date]).

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