Is TLE6 p.Val428Met (c.1282G>A) pathogenic?

TLE6 p.Val428Met (c.1282G>A) is classified Uncertain significance in TLE6 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-01). AlphaMissense: likely benign (0.1403); Ultra-rare (popmax 0.0367%, amr).

How common is TLE6 p.Val428Met (c.1282G>A) in the general population?

TLE6 p.Val428Met (c.1282G>A) is ultra-rare (popmax 0.0367%, amr) (gnomAD).

What do computational predictors say about TLE6 p.Val428Met (c.1282G>A)?

AlphaMissense predicts likely benign (score 0.1403) — an in-silico prediction, not a clinical call.

TLE6 p.Val428Met

c.1282G>A · rs745545547 · VCV2400877

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1403 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0367%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1403	likely benign
REVEL	0.163	moderately benign-leaning
SaProt	LLR -8.02	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 3.3	phastCons 0.6
Regional constraint	o/e 1.13	unconstrained · MANE · 17 kb · p 0.00048 · regional, not allelic
Overall
CADD	18.09	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 0.0367% Admixed American · 22/59,886 alleles

Filtering AF 0.0249% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0209%

Overall 0.00335% 54/1,613,636 alleles · ultra-rare exomes 38/1,461,812 · genomes 16/151,824 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0367%	2,722
Remaining individualsnot grpmax-eligible	0.0048%	20,820
European (non-Finnish)	0.0022%	45,383
South Asian	0.0022%	45,528
African / African-American	0.00134%	74,816

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: TLE6
Protein: p.Val428Met
Coding: c.1282G>A
MANE Select: NM_001143986
dbSNP: rs745545547
Type: single nucleotide variant
Location: chr19:2991880 (GRCh38)
Gene constraint: LOEUF 1.121 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.29 · 4 PDB
Residue 428: a β-strand

Full TLE6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TLE6 p.Ala207Thr Uncertain significance ★★ ⚠ same type
TLE6 c.1537+7G>A Benign ★★ same type
TLE6 p.Glu287= Likely benign ★★ same type
TLE6 p.His285= Benign ★★ same type
TLE6 p.His564= Benign/Likely benign ★★ same type
TLE6 p.Ser490= Benign ★★ same type
TLE6 p.Val429= Benign ★★ same type
TLE6 c.741-1G>C Likely pathogenic ★ 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/tle6-p-val428met (accessed [today's date]).

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