Is TAF1 p.Pro669Ser (c.2005C>T) pathogenic?

TAF1 p.Pro669Ser (c.2005C>T) is classified Uncertain significance in TAF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-17). AlphaMissense: likely benign (0.1191); Absent from gnomAD v4.1.

How common is TAF1 p.Pro669Ser (c.2005C>T) in the general population?

TAF1 p.Pro669Ser (c.2005C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TAF1 p.Pro669Ser (c.2005C>T)?

AlphaMissense predicts likely benign (score 0.1191) — an in-silico prediction, not a clinical call.

TAF1 p.Pro669Ser

c.2005C>T · VCV4538764

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1191 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Computational evidence

Protein change
AlphaMissense	0.1191	likely benign
REVEL	0.094	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 1.4, phastCons 1
Regional constraint	o/e 0.48	unconstrained · MANE · 11 kb · p 7e-27 · regional, not allelic
Overall
CADD	19.97	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P668S vs ClinVar P669S) — verify the residue.

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: TAF1
Protein: p.Pro669Ser
Coding: c.2005C>T
MANE Select: NM_004606
Type: single nucleotide variant
Location: chrX:71384019 (GRCh38)
Structure: AlphaFold pLDDT 62.62 · 65 PDB
Residue 669: an α-helix; the 'histone acetyltransferase (hat)' region

Full TAF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TAF1 p.Arg1062Cys Likely pathogenic ★★ ⚠ same type
TAF1 p.Arg1234Gln Pathogenic/Likely pathogenic ★★ same type
TAF1 p.Arg1432His Pathogenic ★★ same type
TAF1 p.Arg870Cys Pathogenic/Likely pathogenic ★★ same type
TAF1 p.Asn1497His Pathogenic/Likely pathogenic ★★ same type
TAF1 p.Ile1317Thr Pathogenic ★★ same type
TAF1 p.Phe403Val Pathogenic/Likely pathogenic ★★ same type
TAF1 c.1774-3T>C 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/taf1-p-pro669ser (accessed [today's date]).

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