Is TEAD1 p.Ser169= (c.507A>C) pathogenic?

TEAD1 p.Ser169= (c.507A>C) is classified Likely benign in TEAD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-17). Very rare (popmax 0.00223%, eas).

How common is TEAD1 p.Ser169= (c.507A>C) in the general population?

TEAD1 p.Ser169= (c.507A>C) is very rare (popmax 0.00223%, eas) (gnomAD).

TEAD1 p.Ser169=

c.507A>C · rs565795088 · VCV1578279

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 -3.4	GERP -4.7
Overall
CADD	1.547	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,874 alleles

Overall 0.000657% 1/152,300 alleles · very rare

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.Ser169=
Coding: c.507A>C
MANE Select: NM_021961
dbSNP: rs565795088
Type: single nucleotide variant
Location: chr11:12881046 (GRCh38)
Gene constraint: LOEUF 0.276 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.43 · 14 PDB
Residue 169: the 'transcriptional activation' region

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

Similar variants

TEAD1 p.Ser169Pro 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-ser169 (accessed [today's date]).

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