Is TAF4 p.Pro300= (c.900C>T) pathogenic?

TAF4 p.Pro300= (c.900C>T) is classified Likely benign in TAF4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-05). Very rare (popmax 0.00402%, afr); Associated with Inborn genetic diseases.

What condition is associated with TAF4 p.Pro300= (c.900C>T)?

TAF4 p.Pro300= (c.900C>T) is associated with Inborn genetic diseases (ClinVar).

How common is TAF4 p.Pro300= (c.900C>T) in the general population?

TAF4 p.Pro300= (c.900C>T) is very rare (popmax 0.00402%, afr) (gnomAD).

TAF4 p.Pro300=

c.900C>T · VCV3965164

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00402%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.76	GERP -0.23, phastCons 1
Overall
CADD	9.879	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00402% African / African-American · 2/49,756 alleles

Filtering AF 0.000666% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000249%

Overall 0.000436% 3/687,844 alleles · very rare exomes 1/547,776 · genomes 2/140,068 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00402%	24,878
European (non-Finnish)	0.000177%	563,831

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: TAF4
Protein: p.Pro300=
Coding: c.900C>T
MANE Select: NM_003185
Type: single nucleotide variant
Location: chr20:62064911 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.71 · 32 PDB
Residue 300: the 'disordered' region

Full TAF4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TAF4 p.Pro300Leu Uncertain significance ★ ⚠ same residue
TAF4 p.Ala153Val Uncertain significance ★★ ⚠ same condition
TAF4 p.Ala251Thr Uncertain significance ★★ ⚠ same condition
TAF4 p.Arg774Gln Uncertain significance ★★ ⚠ same condition
TAF4 p.Gly171Cys Uncertain significance ★★ ⚠ same condition
TAF4 p.Gly306Glu Uncertain significance ★★ ⚠ same condition
TAF4 p.Leu58Val Uncertain significance ★★ ⚠ same condition
TAF4 p.Pro241Leu 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/taf4-p-pro300 (accessed [today's date]).

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