Is TAF6 p.Pro82Ser (c.244C>T) pathogenic?

TAF6 p.Pro82Ser (c.244C>T) is classified Uncertain significance in TAF6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-11). AlphaMissense: likely pathogenic (0.9298); Very rare (popmax 8.48e-05%, nfe).

How common is TAF6 p.Pro82Ser (c.244C>T) in the general population?

TAF6 p.Pro82Ser (c.244C>T) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about TAF6 p.Pro82Ser (c.244C>T)?

AlphaMissense predicts likely pathogenic (score 0.9298) — an in-silico prediction, not a clinical call.

TAF6 p.Pro82Ser

c.244C>T · VCV3670257

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9298 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9298	likely pathogenic
REVEL	0.672	pathogenic-leaning
SaProt	LLR -10.38	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 12	GERP 0.75, 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 8.48e-05% European (non-Finnish) · 1/1,179,916 alleles

Overall 6.2e-05% 1/1,613,894 alleles · very rare exomes 1/1,461,690 · genomes 0/152,204 · joint denominator

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.Pro82Ser
Coding: c.244C>T
MANE Select: NM_139315
Type: single nucleotide variant
Location: chr7:100113769 (GRCh38)
Gene constraint: LOEUF 0.827 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.81 · 33 PDB
Residue 82: an α-helix

Full TAF6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TAF6 p.Cys36Ser Uncertain significance ★★ ⚠ same type
TAF6 p.Ser425Thr Uncertain significance ★★ ⚠ same type
TAF6 p.Thr368Met Uncertain significance ★★ ⚠ same type
AP4M1 c.*322A>G Benign ★★ same type
TAF6 c.1083+17T>G Benign ★★ same type
TAF6 c.1084-53G>A Benign ★★ same type
TAF6 c.1158+14G>A Benign/Likely benign ★★ same type
TAF6 c.1159-16T>C Benign/Likely benign ★★ 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/taf6-p-pro82ser (accessed [today's date]).

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