Is BATF p.Arg32Lys (c.95G>A) pathogenic?

BATF p.Arg32Lys (c.95G>A) is classified Uncertain significance in BATF (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). AlphaMissense: likely pathogenic (0.8743); Absent from gnomAD v4.1.

How common is BATF p.Arg32Lys (c.95G>A) in the general population?

BATF p.Arg32Lys (c.95G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BATF p.Arg32Lys (c.95G>A)?

AlphaMissense predicts likely pathogenic (score 0.8743) — an in-silico prediction, not a clinical call.

BATF p.Arg32Lys

c.95G>A · VCV4196851

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8743 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8743	likely pathogenic
REVEL	0.281	benign-leaning
SaProt	LLR -11.60	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 24 kb · p 5.7e-06 · regional, not allelic
Overall
CADD	25.4	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: BATF
Protein: p.Arg32Lys
Coding: c.95G>A
MANE Select: NM_006399
Type: single nucleotide variant
Location: chr14:75525115 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI 0.56 (gnomAD)
Structure: AlphaFold pLDDT 81.59
Residue 32: the bzip domain; the 'disordered' region; the 'basic motif' region

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

Similar variants

BATF p.Gln41Arg Uncertain significance ★ ⚠ same type
BATF p.Pro104Arg Uncertain significance ★ ⚠ same type
BATF p.Pro104Leu Uncertain significance ★ ⚠ same type
BATF p.Pro121Arg Uncertain significance ★ same type
BATF p.Pro121Leu Uncertain significance ★ ⚠ same type
BATF p.Thr100Lys 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/batf-p-arg32lys (accessed [today's date]).

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