Is TAF1 p.Pro113= (c.339C>T) pathogenic?

TAF1 p.Pro113= (c.339C>T) is classified Likely benign in TAF1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-06). Very rare (popmax 0.00302%, nfe); Associated with TAF1-related disorder.

What condition is associated with TAF1 p.Pro113= (c.339C>T)?

TAF1 p.Pro113= (c.339C>T) is associated with TAF1-related disorder (ClinVar).

How common is TAF1 p.Pro113= (c.339C>T) in the general population?

TAF1 p.Pro113= (c.339C>T) is very rare (popmax 0.00302%, nfe) (gnomAD).

TAF1 p.Pro113=

c.339C>T · VCV3352844

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00302%, nfe)

Conditions

TAF1-related disorder

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 -0.61	GERP -3.7, phastCons 0.009
Overall
CADD	7.903	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00302% European (non-Finnish) · 27/894,698 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00181%

Overall 0.00231% 28/1,209,540 alleles · very rare exomes 26/1,097,423 · genomes 2/112,117 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00302%	33,137
Admixed American	0.00219%	45,731

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: TAF1
Protein: p.Pro113=
Coding: c.339C>T
MANE Select: NM_004606
Type: single nucleotide variant
Location: chrX:71368157 (GRCh38)
Structure: AlphaFold pLDDT 62.62 · 65 PDB
Residue 113: the protein kinase 1 domain

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

Disease context

TAF1-related disorder

Similar variants

TAF1 p.Arg870Cys Pathogenic/Likely pathogenic ★★ same condition
TAF1 p.Thr873Met Uncertain significance ★★ same condition
TAF1 p.Thr62Arg Likely pathogenic ★ ⚠ same condition
TAF1 p.Asp120Val Uncertain significance ★ ⚠ same condition
TAF1 p.Asp132His Uncertain significance ★ ⚠ same condition
TAF1 p.Glu179Lys Uncertain significance ★ same condition
TAF1 p.Gly366Asp Uncertain significance ★ ⚠ same condition
TAF1 p.Ile329Thr Conflicting classifications of pathogenicity ★ ⚠ 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-pro113 (accessed [today's date]).

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