Is BATF3 p.Leu5Phe (c.13C>T) pathogenic?

BATF3 p.Leu5Phe (c.13C>T) is classified Uncertain significance in BATF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-25). AlphaMissense: likely benign (0.0773); Ultra-rare (popmax 0.0479%, afr).

How common is BATF3 p.Leu5Phe (c.13C>T) in the general population?

BATF3 p.Leu5Phe (c.13C>T) is ultra-rare (popmax 0.0479%, afr) (gnomAD).

What do computational predictors say about BATF3 p.Leu5Phe (c.13C>T)?

AlphaMissense predicts likely benign (score 0.0773) — an in-silico prediction, not a clinical call.

BATF3 p.Leu5Phe

c.13C>T · VCV3479788

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0773 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0479%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0773	likely benign
REVEL	0.041	moderately benign-leaning
SaProt	LLR -7.36	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 8.7	GERP 1.5, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 13 kb · p 0.03 · regional, not allelic
Overall
CADD	20.5	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 0.0479% African / African-American · 31/64,698 alleles

Filtering AF 0.0346% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0302%

Overall 0.00256% 33/1,288,726 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0479%	2,087
Remaining individualsnot grpmax-eligible	0.00419%	23,840

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.Leu5Phe
Coding: c.13C>T
MANE Select: NM_018664
Type: single nucleotide variant
Location: chr1:212699750 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 83.05
Residue 5: 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.Gly4Arg 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-leu5phe (accessed [today's date]).

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