TLE6 p.Asn392=
c.1176C>T · rs142873734 · VCV784384
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.26%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.65 | |
| Overall | ||
| CADD | 2.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.26%
African / African-American · 195/75,058 alleles
Filtering AF
0.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.218%
Overall
0.0142%
229/1,614,236 alleles · rare
exomes 101/1,461,882 · genomes 128/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.26% | 385 |
| Admixed American | 0.025% | 4,002 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| European (non-Finnish) | 0.000424% | 236,009 |
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.Asn392=
- Coding
- c.1176C>T
- MANE Select
- NM_001143986
- dbSNP
- rs142873734
- Type
- single nucleotide variant
- Location
- chr19:2989717 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.29 · 4 PDB
- Residue 392
- a turn
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-asn392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown