Is TAF1 p.Val477= (c.1431A>G) pathogenic?

TAF1 p.Val477= (c.1431A>G) is classified Benign/Likely benign in TAF1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-19). Rare (popmax 0.191%, nfe).

How common is TAF1 p.Val477= (c.1431A>G) in the general population?

TAF1 p.Val477= (c.1431A>G) is rare (popmax 0.191%, nfe) (gnomAD).

TAF1 p.Val477=

c.1431A>G · rs144087024 · VCV695418

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.191%, nfe)

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 -5.9	GERP -3.8
Overall
CADD	0.143	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.191% European (non-Finnish) · 1,706/893,150 alleles

Filtering AF 0.183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.18%

Overall 0.155% 1,866/1,206,165 alleles · rare exomes 1,732/1,094,012 · genomes 134/112,153 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	0.731%	137
Ashkenazi Jewishnot grpmax-eligible	0.215%	466
European (non-Finnish)grpmax	0.191%	524
Remaining individualsnot grpmax-eligible	0.135%	741
Middle Eastern	0.115%	869
Admixed American	0.0309%	3,235
African / African-American	0.021%	4,755
Finnishnot grpmax-eligible	0.0172%	5,814
South Asian	0.00888%	11,258

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Val477=
Coding: c.1431A>G
MANE Select: NM_004606
dbSNP: rs144087024
Type: single nucleotide variant
Location: chrX:71381813 (GRCh38)
Structure: AlphaFold pLDDT 62.62 · 65 PDB

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-val477 (accessed [today's date]).

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