TEAD1 p.Phe239=
c.717C>T · rs368869959 · VCV2144747
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
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 2.8 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 15.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.0031%
50/1,614,206 alleles · ultra-rare
exomes 44/1,461,884 · genomes 6/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| South Asian | 0.00988% | 10,121 |
| Finnishnot grpmax-eligible | 0.00781% | 12,807 |
| East Asian | 0.00668% | 14,963 |
| European (non-Finnish) | 0.00246% | 40,691 |
| Admixed American | 0.00167% | 60,028 |
| African / African-American | 0.00133% | 75,038 |
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
- TEAD1
- Protein
- p.Phe239=
- Coding
- c.717C>T
- MANE Select
- NM_021961
- dbSNP
- rs368869959
- Type
- single nucleotide variant
- Location
- chr11:12901957 (GRCh38)
- Gene constraint
- LOEUF 0.276 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.43 · 14 PDB
- Residue 239
- a β-strand; the 'transcriptional activation' region
Similar variants
- TEAD1 c.575-3C>T Uncertain significance ★★ same type
- TEAD1 p.Ala123Val Uncertain significance ★★ same type
- TEAD1 p.Ala188Thr Uncertain significance ★★ ⚠ same type
- TEAD1 p.Ala200Val Uncertain significance ★★ ⚠ same type
- TEAD1 p.Ala205Pro Uncertain significance ★★ ⚠ same type
- TEAD1 p.Ala23Val Uncertain significance ★★ ⚠ same type
- TEAD1 p.Arg147His Uncertain significance ★★ ⚠ same type
- TEAD1 p.Arg229Gln 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/tead1-p-phe239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown