Is MAP4K1 p.Ser377= (c.1131T>A) pathogenic?

MAP4K1 p.Ser377= (c.1131T>A) is classified Likely benign in MAP4K1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-01). Absent from gnomAD v4.1.

How common is MAP4K1 p.Ser377= (c.1131T>A) in the general population?

MAP4K1 p.Ser377= (c.1131T>A) is absent from gnomAD v4.1 (gnomAD).

MAP4K1 p.Ser377=

c.1131T>A · rs1468227943 · VCV3234627

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -14	GERP -3
Overall
CADD	0.005	PHRED · no single calibrated threshold — expert panels disagree

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: MAP4K1
Protein: p.Ser377=
Coding: c.1131T>A
MANE Select: NM_001042600
dbSNP: rs1468227943
Type: single nucleotide variant
Location: chr19:38607890 (GRCh38)
Gene constraint: LOEUF 0.395 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.83 · 50 PDB
Residue 377: the 'disordered' region

Full MAP4K1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP4K1 p.Ala246Ser Uncertain significance ★ ⚠ same type
MAP4K1 p.Ala313Pro Uncertain significance ★ ⚠ same type
MAP4K1 p.Ala452Ser Uncertain significance ★ ⚠ same type
MAP4K1 p.Ala452Thr Uncertain significance ★ ⚠ same type
MAP4K1 p.Ala452Val Uncertain significance ★ ⚠ same type
MAP4K1 p.Ala485Ser Uncertain significance ★ ⚠ same type
MAP4K1 p.Ala609Val Uncertain significance ★ ⚠ same type
MAP4K1 p.Ala661Gly 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/map4k1-p-ser377 (accessed [today's date]).

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