Is TAF2 p.Pro1024Ala (c.3070C>G) pathogenic?

TAF2 p.Pro1024Ala (c.3070C>G) is classified Benign/Likely benign in TAF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-04-01). AlphaMissense: likely benign (0.0537); Rare (popmax 0.647%, sas).

How common is TAF2 p.Pro1024Ala (c.3070C>G) in the general population?

TAF2 p.Pro1024Ala (c.3070C>G) is rare (popmax 0.647%, sas) (gnomAD).

What do computational predictors say about TAF2 p.Pro1024Ala (c.3070C>G)?

AlphaMissense predicts likely benign (score 0.0537) — an in-silico prediction, not a clinical call.

TAF2 p.Pro1024Ala

c.3070C>G · rs142735640 · VCV2164077

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0537 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.647%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0537	likely benign
REVEL	0.075	moderately benign-leaning
SaProt	LLR -6.24	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.5	GERP 1.9, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 53 kb · p 1.9e-07 · regional, not allelic
Overall
CADD	18.05	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.647% South Asian · 589/91,086 alleles

Filtering AF 0.603% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.586%

Overall 0.0502% 811/1,614,104 alleles · rare exomes 767/1,461,846 · genomes 44/152,258 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.647%	155
Middle Eastern	0.099%	1,010
Remaining individualsnot grpmax-eligible	0.0592%	1,689
Ashkenazi Jewishnot grpmax-eligible	0.0169%	5,920
European (non-Finnish)	0.0137%	7,284
Admixed American	0.01%	10,001
African / African-American	0.00533%	18,756
Finnishnot grpmax-eligible	0.00312%	32,014

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: TAF2
Protein: p.Pro1024Ala
Coding: c.3070C>G
MANE Select: NM_003184
dbSNP: rs142735640
Type: single nucleotide variant
Location: chr8:119746743 (GRCh38)
Gene constraint: LOEUF 0.551 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.09 · 29 PDB

Full TAF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TAF2 p.Pro1024Thr Uncertain significance ★ ⚠ same residue
TAF2 p.Ala244Val Uncertain significance ★★ ⚠ same type
TAF2 p.Arg1077Trp Uncertain significance ★★ ⚠ same type
TAF2 p.Arg1082Gln Uncertain significance ★★ ⚠ same type
TAF2 p.Arg1082Leu Uncertain significance ★★ ⚠ same type
TAF2 p.Arg1193Cys Uncertain significance ★★ ⚠ same type
TAF2 p.Arg1193His Uncertain significance ★★ ⚠ same type
TAF2 p.Arg795His 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/taf2-p-pro1024ala (accessed [today's date]).

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