TEAD1 p.Pro158=
c.474G>A · rs756312388 · VCV2994522
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, 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 -0.73 | GERP -4.7, phastCons 0.001 |
| Overall | ||
| CADD | 8.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,872 alleles
Filtering AF
0.00199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00175%
Overall
0.00223%
36/1,614,164 alleles · very rare
exomes 36/1,461,884 · genomes 0/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,436 |
| European (non-Finnish) | 0.0028% | 35,758 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
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.Pro158=
- Coding
- c.474G>A
- MANE Select
- NM_021961
- dbSNP
- rs756312388
- Type
- single nucleotide variant
- Location
- chr11:12881013 (GRCh38)
- Gene constraint
- LOEUF 0.276 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.43 · 14 PDB
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-pro158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown