Is BATF p.Thr100Lys (c.299C>A) pathogenic?

BATF p.Thr100Lys (c.299C>A) is classified Uncertain significance in BATF (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-02). AlphaMissense: likely benign (0.1706); Very rare (popmax 0.000339%, nfe).

How common is BATF p.Thr100Lys (c.299C>A) in the general population?

BATF p.Thr100Lys (c.299C>A) is very rare (popmax 0.000339%, nfe) (gnomAD).

What do computational predictors say about BATF p.Thr100Lys (c.299C>A)?

AlphaMissense predicts likely benign (score 0.1706) — an in-silico prediction, not a clinical call.

BATF p.Thr100Lys

c.299C>A · rs765283183 · VCV2475099

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1706 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1706	likely benign
REVEL	0.149	moderately benign-leaning
SaProt	LLR -5.52	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP -0.49, phastCons 0.3
Regional constraint	o/e 1.19	unconstrained · MANE · 104 bp · p 0.19 · regional, not allelic
Overall
CADD	15.49	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.000339% European (non-Finnish) · 4/1,179,968 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000274% 4/1,461,670 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: BATF
Protein: p.Thr100Lys
Coding: c.299C>A
MANE Select: NM_006399
dbSNP: rs765283183
Type: single nucleotide variant
Location: chr14:75546592 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI 0.56 (gnomAD)
Structure: AlphaFold pLDDT 81.59

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.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

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-thr100lys (accessed [today's date]).

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