Is BATF3 p.Gly4Arg (c.10G>C) pathogenic?

BATF3 p.Gly4Arg (c.10G>C) is classified Uncertain significance in BATF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-26). AlphaMissense: likely pathogenic (0.7219); Very rare (popmax 9.86e-05%, nfe).

How common is BATF3 p.Gly4Arg (c.10G>C) in the general population?

BATF3 p.Gly4Arg (c.10G>C) is very rare (popmax 9.86e-05%, nfe) (gnomAD).

What do computational predictors say about BATF3 p.Gly4Arg (c.10G>C)?

AlphaMissense predicts likely pathogenic (score 0.7219) — an in-silico prediction, not a clinical call.

BATF3 p.Gly4Arg

c.10G>C · VCV3989039

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7219 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 9.86e-05%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7219	likely pathogenic
REVEL	0.022	moderately benign-leaning
SaProt	LLR -5.98	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.9	GERP 1.5, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 13 kb · p 0.03 · regional, not allelic
Overall
CADD	22.8	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 9.86e-05% European (non-Finnish) · 1/1,013,860 alleles

Overall 8.82e-05% 1/1,134,370 alleles · very rare

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: BATF3
Protein: p.Gly4Arg
Coding: c.10G>C
MANE Select: NM_018664
Type: single nucleotide variant
Location: chr1:212699753 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 83.05
Residue 4: the 'disordered' region

Full BATF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BATF3 p.Ala17Val Uncertain significance ★ ⚠ same type
BATF3 p.Asp119Gly Uncertain significance ★ ⚠ same type
BATF3 p.Asp34Val Uncertain significance ★ ⚠ same type
BATF3 p.Gln72Arg Uncertain significance ★ ⚠ same type
BATF3 p.Gly123Ser Uncertain significance ★ ⚠ same type
BATF3 p.Leu5Phe Uncertain significance ★ ⚠ same type
BATF3 p.Lys62Glu Uncertain significance ★ ⚠ same type
BATF3 p.Ser2Trp 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/batf3-p-gly4arg (accessed [today's date]).

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