Is BATF p.Gln41Arg (c.122A>G) pathogenic?

BATF p.Gln41Arg (c.122A>G) is classified Uncertain significance in BATF (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-15). AlphaMissense: likely pathogenic (0.8536); Very rare (popmax 0.0022%, sas).

How common is BATF p.Gln41Arg (c.122A>G) in the general population?

BATF p.Gln41Arg (c.122A>G) is very rare (popmax 0.0022%, sas) (gnomAD).

What do computational predictors say about BATF p.Gln41Arg (c.122A>G)?

AlphaMissense predicts likely pathogenic (score 0.8536) — an in-silico prediction, not a clinical call.

BATF p.Gln41Arg

c.122A>G · VCV4834490

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8536 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.8536	likely pathogenic
REVEL	0.357	indeterminate
SaProt	LLR -10.96	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.3, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 24 kb · p 5.7e-06 · regional, not allelic
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Grpmax group 0.0022% South Asian · 2/91,060 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000342% 5/1,461,796 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,530
European (non-Finnish)	0.000254%	393,331

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: BATF
Protein: p.Gln41Arg
Coding: c.122A>G
MANE Select: NM_006399
Type: single nucleotide variant
Location: chr14:75525142 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI 0.56 (gnomAD)
Structure: AlphaFold pLDDT 81.59
Residue 41: 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.Arg32Lys 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-gln41arg (accessed [today's date]).

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