Is TAF6 p.Arg63Gln (c.188G>A) pathogenic?

TAF6 p.Arg63Gln (c.188G>A) is classified Uncertain significance in TAF6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-19). AlphaMissense: likely pathogenic (0.8566); Very rare (popmax 0.000254%, nfe); Associated with Inborn genetic diseases.

What condition is associated with TAF6 p.Arg63Gln (c.188G>A)?

TAF6 p.Arg63Gln (c.188G>A) is associated with Inborn genetic diseases (ClinVar).

How common is TAF6 p.Arg63Gln (c.188G>A) in the general population?

TAF6 p.Arg63Gln (c.188G>A) is very rare (popmax 0.000254%, nfe) (gnomAD).

What do computational predictors say about TAF6 p.Arg63Gln (c.188G>A)?

AlphaMissense predicts likely pathogenic (score 0.8566) — an in-silico prediction, not a clinical call.

TAF6 p.Arg63Gln

c.188G>A · VCV4632609

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8566 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8566	likely pathogenic
REVEL	0.762	pathogenic-leaning
SaProt	LLR -14.16	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 1.9, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 2,000 bp · p 0.95 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,180,022 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000205% 3/1,461,882 alleles · very rare

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: TAF6
Protein: p.Arg63Gln
Coding: c.188G>A
MANE Select: NM_139315
Type: single nucleotide variant
Location: chr7:100113923 (GRCh38)
Gene constraint: LOEUF 0.827 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.81 · 33 PDB

Full TAF6 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

TAF6 p.Cys36Ser Uncertain significance ★★ ⚠ same condition
TAF6 p.Ser425Thr Uncertain significance ★★ ⚠ same condition
TAF6 p.Thr368Met Uncertain significance ★★ ⚠ same condition
TAF6 p.Arg320Ter Pathogenic ★ same condition
TAF6 c.-42C>T Uncertain significance ★ same condition
TAF6 c.-48C>T Uncertain significance ★ same condition
TAF6 p.Arg102Gln Uncertain significance ★ ⚠ same condition
TAF6 p.Arg46His 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/taf6-p-arg63gln (accessed [today's date]).

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