Is STAT1 p.Met202Val (c.604A>G) pathogenic?

STAT1 p.Met202Val (c.604A>G) is classified Pathogenic in STAT1 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-07-24). AlphaMissense: ambiguous (0.3858); Absent from gnomAD v4.1; Associated with immunodeficiency 31B.

How common is STAT1 p.Met202Val (c.604A>G) in the general population?

STAT1 p.Met202Val (c.604A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about STAT1 p.Met202Val (c.604A>G)?

AlphaMissense predicts ambiguous (score 0.3858) — an in-silico prediction, not a clinical call.

STAT1 p.Met202Val

Q: What condition is associated with STAT1 p.Met202Val (c.604A>G)?

STAT1 p.Met202Val (c.604A>G) is associated with immunodeficiency 31B, autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome, Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency (ClinVar).

Q: How is Susceptibility to viral and mycobacterial infections due to STAT1 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.604A>G · rs387906762 · VCV30087

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.3858 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

immunodeficiency 31B

Computational evidence

Protein change
AlphaMissense	0.3858	ambiguous
REVEL	0.291	indeterminate
SaProt	LLR -7.87	tolerated
Splicing
SpliceAI	Δ0.30	donor loss, 29 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 6.1	GERP 0.38, phastCons 1
Regional constraint	o/e 0.42	unconstrained · MANE · 5,939 bp · p 3.1e-13 · regional, not allelic
Overall
CADD	23.3	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

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: STAT1
Protein: p.Met202Val
Coding: c.604A>G
MANE Select: NM_007315
dbSNP: rs387906762
Type: single nucleotide variant
Location: chr2:190998246 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 87.78 · 10 PDB
Residue 202: a UniProt-annotated variant site (in imd31c); an α-helix

Full STAT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency 31B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency

For Susceptibility to viral and mycobacterial infections due to STAT1 deficiency (Orphanet):

Inheritance: Autosomal recessive

Similar variants

STAT1 p.Met202Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
STAT1 p.Met202Ile Pathogenic ⚠ same residue
STAT1 p.Ala267Val Pathogenic ★★ ⚠ same condition
STAT1 p.Arg274Gln Pathogenic ★★ ⚠ same condition
STAT1 p.Arg274Gly Pathogenic/Likely pathogenic ★★ same condition
STAT1 p.Arg274Trp Pathogenic ★★ same condition
STAT1 p.Asp171Asn Likely pathogenic ★★ ⚠ same condition
STAT1 p.Asp292Glu 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/stat1-p-met202val (accessed [today's date]).

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