Is TP53I3 p.Ser268= (c.804T>C) pathogenic?

TP53I3 p.Ser268= (c.804T>C) is classified Likely benign in TP53I3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-03-17). Ultra-rare (popmax 0.0183%, amr); Associated with TP53I3-related disorder.

What condition is associated with TP53I3 p.Ser268= (c.804T>C)?

TP53I3 p.Ser268= (c.804T>C) is associated with TP53I3-related disorder (ClinVar).

How common is TP53I3 p.Ser268= (c.804T>C) in the general population?

TP53I3 p.Ser268= (c.804T>C) is ultra-rare (popmax 0.0183%, amr) (gnomAD).

TP53I3 p.Ser268=

c.804T>C · rs752742554 · VCV3054842

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0183%, amr)

Conditions

TP53I3-related disorder

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.31	GERP -4.7, phastCons 0.71
Overall
CADD	6.736	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0183% Admixed American · 11/60,000 alleles

Filtering AF 0.0102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00785%

Overall 0.000682% 11/1,614,070 alleles · ultra-rare exomes 8/1,461,886 · genomes 3/152,184 · 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: TP53I3
Protein: p.Ser268=
Coding: c.804T>C
MANE Select: NM_004881
dbSNP: rs752742554
Type: single nucleotide variant
Location: chr2:24079456 (GRCh38)

Full TP53I3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TP53I3-related disorder

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/tp53i3-p-ser268 (accessed [today's date]).

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