Is TAF2 p.Pro624Ser (c.1870C>T) pathogenic?

TAF2 p.Pro624Ser (c.1870C>T) is classified Uncertain significance in TAF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-20). AlphaMissense: likely pathogenic (0.9993); Very rare (popmax 8.48e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with TAF2 p.Pro624Ser (c.1870C>T)?

TAF2 p.Pro624Ser (c.1870C>T) is associated with Inborn genetic diseases (ClinVar).

How common is TAF2 p.Pro624Ser (c.1870C>T) in the general population?

TAF2 p.Pro624Ser (c.1870C>T) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about TAF2 p.Pro624Ser (c.1870C>T)?

AlphaMissense predicts likely pathogenic (score 0.9993) — an in-silico prediction, not a clinical call.

TAF2 p.Pro624Ser

c.1870C>T · VCV4632575

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9993 · ACMG-weighted

gnomAD v4.1

Rare

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

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9993	likely pathogenic · top 3% in TAF2
REVEL	0.441	indeterminate
SaProt	LLR -8.35	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 53 kb · p 1.9e-07 · regional, not allelic
Overall
CADD	26.6	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 8.48e-05% European (non-Finnish) · 1/1,179,860 alleles

Overall 6.2e-05% 1/1,613,766 alleles · very rare exomes 1/1,461,636 · genomes 0/152,130 · 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: TAF2
Protein: p.Pro624Ser
Coding: c.1870C>T
MANE Select: NM_003184
Type: single nucleotide variant
Location: chr8:119783623 (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

Disease context

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

Similar variants

TAF2 p.Arg1077Trp Uncertain significance ★★ ⚠ same condition
TAF2 p.Arg1082Gln Uncertain significance ★★ ⚠ same condition
TAF2 p.Arg1082Leu Uncertain significance ★★ ⚠ same condition
TAF2 p.Arg1193Cys Uncertain significance ★★ ⚠ same condition
TAF2 p.Arg1193His Uncertain significance ★★ ⚠ same condition
TAF2 p.Arg795His Uncertain significance ★★ ⚠ same condition
TAF2 p.Asn787Thr Uncertain significance ★★ ⚠ same condition
TAF2 p.Asp1042Asn 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/taf2-p-pro624ser (accessed [today's date]).

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