TEAD1 p.Ala153=
c.459G>A · rs755050202 · VCV1545984
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -14 | GERP -4.5 |
| Overall | ||
| CADD | 0.441 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,890 alleles
Filtering AF
0.000688%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00112%
18/1,613,238 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,890 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,414 |
| African / African-American | 0.00133% | 74,910 |
| European (non-Finnish) | 0.00119% | 84,288 |
| South Asian | 0.0011% | 91,058 |
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.Ala153=
- Coding
- c.459G>A
- MANE Select
- NM_021961
- dbSNP
- rs755050202
- Type
- single nucleotide variant
- Location
- chr11:12879836 (GRCh38)
- Gene constraint
- LOEUF 0.276 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.43 · 14 PDB
Similar variants
- TEAD1 p.Ala153Val Uncertain significance ★ ⚠ same residue
- 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
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-ala153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown