TLE2 p.Asn696=
c.2088C>T · rs376590696 · VCV2648981
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0114%, sas)
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 -9 | |
| Overall | ||
| CADD | 0.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0114%
South Asian · 10/87,534 alleles
Filtering AF
0.00616%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00494%
Overall
0.00577%
92/1,594,020 alleles · ultra-rare
exomes 86/1,441,904 · genomes 6/152,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0114% | 8,753 |
| European (non-Finnish) | 0.00658% | 15,204 |
| African / African-American | 0.00537% | 18,615 |
| Finnishnot grpmax-eligible | 0.0016% | 62,562 |
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
- TLE2
- Protein
- p.Asn696=
- Coding
- c.2088C>T
- MANE Select
- NM_003260
- dbSNP
- rs376590696
- Type
- single nucleotide variant
- Location
- chr19:3000683 (GRCh38)
- Gene constraint
- LOEUF 1.02 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.40
Similar variants
- TLE2 p.Ala110Thr Uncertain significance ★ ⚠ same type
- TLE2 p.Ala133Val Uncertain significance ★ ⚠ same type
- TLE2 p.Ala164Val Uncertain significance ★ ⚠ same type
- TLE2 p.Ala167Val Uncertain significance ★ ⚠ same type
- TLE2 p.Ala168Val Uncertain significance ★ ⚠ same type
- TLE2 p.Ala187Ser Uncertain significance ★ ⚠ same type
- TLE2 p.Ala187Val Uncertain significance ★ ⚠ same type
- TLE2 p.Ala192Val 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/tle2-p-asn696 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown