Is TFAP2B p.Ser266Pro (c.796T>C) pathogenic?

TFAP2B p.Ser266Pro (c.796T>C) is classified Uncertain significance in TFAP2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-26). AlphaMissense: likely pathogenic (0.9998); Absent from gnomAD v4.1; Associated with Char syndrome.

What condition is associated with TFAP2B p.Ser266Pro (c.796T>C)?

TFAP2B p.Ser266Pro (c.796T>C) is associated with Char syndrome (ClinVar).

How common is TFAP2B p.Ser266Pro (c.796T>C) in the general population?

TFAP2B p.Ser266Pro (c.796T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TFAP2B p.Ser266Pro (c.796T>C)?

AlphaMissense predicts likely pathogenic (score 0.9998) — an in-silico prediction, not a clinical call.

TFAP2B p.Ser266Pro

c.796T>C · VCV3376356

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9998 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Char syndrome

Computational evidence

Protein change
AlphaMissense	0.9998	likely pathogenic · top 8% in TFAP2B
REVEL	0.981	strongly pathogenic-leaning
SaProt	LLR -11.94	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 7.8	GERP 2.9, phastCons 1
Regional constraint	o/e 0.41	unconstrained · MANE · 4,023 bp · p 1.1e-09 · regional, not allelic
Overall
CADD	29.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TFAP2B
Protein: p.Ser266Pro
Coding: c.796T>C
MANE Select: NM_003221
Type: single nucleotide variant
Location: chr6:50836255 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 65.95 · 1 PDB
Residue 266: an α-helix

Full TFAP2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Char syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TFAP2B p.Arg236His Likely pathogenic ★★ same condition
TFAP2B p.Arg285Gln Pathogenic/Likely pathogenic ★★ same condition
TFAP2B p.Asp31Gly Uncertain significance ★★ ⚠ same condition
TFAP2B p.Ser277Trp Uncertain significance ★★ ⚠ same condition
TFAP2B p.Thr306Met Uncertain significance ★★ ⚠ same condition
TFAP2B p.Ala275Asp Pathogenic ★ same condition
TFAP2B p.Arg300Cys Pathogenic ★ same condition
TFAP2B p.Cys327Ter Likely pathogenic ★ 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/tfap2b-p-ser266pro (accessed [today's date]).

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