Is TAF1 p.Phe403Val (c.1207T>G) pathogenic?

TAF1 p.Phe403Val (c.1207T>G) is classified Pathogenic/Likely pathogenic in TAF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-08). AlphaMissense: likely pathogenic (0.9513); Absent from gnomAD v4.1; Associated with intellectual disability, X-linked, syndromic 33.

What condition is associated with TAF1 p.Phe403Val (c.1207T>G)?

TAF1 p.Phe403Val (c.1207T>G) is associated with intellectual disability, X-linked, syndromic 33 (ClinVar).

How common is TAF1 p.Phe403Val (c.1207T>G) in the general population?

TAF1 p.Phe403Val (c.1207T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TAF1 p.Phe403Val (c.1207T>G)?

AlphaMissense predicts likely pathogenic (score 0.9513) — an in-silico prediction, not a clinical call.

TAF1 p.Phe403Val

c.1207T>G · rs2033670961 · VCV985730

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9513 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

intellectual disability, X-linked, syndromic 33

Computational evidence

Protein change
AlphaMissense	0.9513	likely pathogenic ✓ concordant with ClinVar
REVEL	0.552	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.2, phastCons 1
Regional constraint	o/e 0.48	unconstrained · MANE · 11 kb · p 7e-27 · regional, not allelic
Overall
CADD	24.5	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM F402V vs ClinVar F403V) — 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.Phe403Val
Coding: c.1207T>G
MANE Select: NM_004606
dbSNP: rs2033670961
Type: single nucleotide variant
Location: chrX:71378878 (GRCh38)
Structure: AlphaFold pLDDT 62.62 · 65 PDB

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

Disease context

intellectual disability, X-linked, syndromic 33 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TAF1 p.Arg1234Gln Pathogenic/Likely pathogenic ★★ same condition
TAF1 p.Arg1432His Pathogenic ★★ same condition
TAF1 p.Arg870Cys Pathogenic/Likely pathogenic ★★ same condition
TAF1 p.Asn1497His Pathogenic/Likely pathogenic ★★ same condition
TAF1 p.Ile1317Thr Pathogenic ★★ same condition
TAF1 c.4821+3A>G Uncertain significance ★★ same condition
TAF1 p.Ala298Thr Uncertain significance ★★ same condition
TAF1 p.Arg707Trp Uncertain significance ★★ same condition

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-phe403val (accessed [today's date]).

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