Is TP63 p.Ser533= (c.1599C>T) pathogenic?

TP63 p.Ser533= (c.1599C>T) is classified Likely benign in TP63 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2024-12-29). Ultra-rare (popmax 0.055%, nfe); Associated with ADULT syndrome.

What condition is associated with TP63 p.Ser533= (c.1599C>T)?

TP63 p.Ser533= (c.1599C>T) is associated with ADULT syndrome, ankyloblepharon-ectodermal defects-cleft lip/palate syndrome, Rapp-Hodgkin syndrome (ClinVar).

How common is TP63 p.Ser533= (c.1599C>T) in the general population?

TP63 p.Ser533= (c.1599C>T) is ultra-rare (popmax 0.055%, nfe) (gnomAD).

TP63 p.Ser533=

c.1599C>T · rs758093495 · VCV767371

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.055%, nfe)

Conditions

ADULT syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6	GERP 2.7, phastCons 1
Overall
CADD	13.05	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.055% European (non-Finnish) · 649/1,180,026 alleles

Filtering AF 0.0514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0501%

Overall 0.0426% 687/1,614,048 alleles · ultra-rare exomes 662/1,461,822 · genomes 25/152,226 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.055%	1,818
Middle Eastern	0.0329%	3,042
Remaining individualsnot grpmax-eligible	0.0224%	4,463
Admixed American	0.02%	5,001
African / African-American	0.012%	8,327
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,598

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: TP63
Protein: p.Ser533=
Coding: c.1599C>T
MANE Select: NM_003722
dbSNP: rs758093495
Type: single nucleotide variant
Location: chr3:189889431 (GRCh38)
Gene constraint: LOEUF 0.296 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 63.70 · 26 PDB

Full TP63 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: ankyloblepharon-ectodermal defects-cleft lip/palate syndrome Rapp-Hodgkin syndrome limb-mammary syndrome ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 split hand-foot malformation 4 orofacial cleft 8

Similar variants

TP63 p.Ala354Glu Likely pathogenic ★★ same condition
TP63 p.Arg243Gln Pathogenic/Likely pathogenic ★★ same condition
TP63 p.Arg243Trp Pathogenic ★★ same condition
TP63 p.Arg266Gln Pathogenic/Likely pathogenic ★★ same condition
TP63 p.Arg318Cys Pathogenic ★★ same condition
TP63 p.Arg318His Pathogenic/Likely pathogenic ★★ same condition
TP63 p.Arg319Cys Pathogenic/Likely pathogenic ★★ same condition
TP63 p.Arg319His 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/tp63-p-ser533 (accessed [today's date]).

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