Is TEAD1 p.Pro52= (c.156A>T) pathogenic?

TEAD1 p.Pro52= (c.156A>T) is classified Likely benign in TEAD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-27). Absent from gnomAD v4.1.

How common is TEAD1 p.Pro52= (c.156A>T) in the general population?

TEAD1 p.Pro52= (c.156A>T) is absent from gnomAD v4.1 (gnomAD).

TEAD1 p.Pro52=

c.156A>T · rs763222979 · VCV2011526

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -10	GERP -3.9
Overall
CADD	0.119	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TEAD1
Protein: p.Pro52=
Coding: c.156A>T
MANE Select: NM_021961
dbSNP: rs763222979
Type: single nucleotide variant
Location: chr11:12764388 (GRCh38)
Gene constraint: LOEUF 0.276 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.43 · 14 PDB
Residue 52: a DNA-binding region; a β-strand

Full TEAD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-pro52 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown