Is TP53 p.Val10= (c.30C>T) pathogenic?

TP53 p.Val10= (c.30C>T) is classified Benign/Likely benign in TP53 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-02-03). Ultra-rare (popmax 0.0134%, eas); Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Val10= (c.30C>T)?

TP53 p.Val10= (c.30C>T) is associated with hereditary neoplastic syndrome, hereditary breast carcinoma, Li-Fraumeni syndrome (ClinVar).

How common is TP53 p.Val10= (c.30C>T) in the general population?

TP53 p.Val10= (c.30C>T) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

TP53 p.Val10=

c.30C>T · rs568171603 · VCV183952

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.9	GERP -4.6
Overall
CADD	5.041	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,874 alleles

Filtering AF 0.00579% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00394%

Overall 0.000867% 14/1,613,982 alleles · ultra-rare exomes 14/1,461,828 · genomes 0/152,154 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,479
South Asian	0.0011%	91,082
European (non-Finnish)	0.000593%	168,575

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: TP53
Protein: p.Val10=
Coding: c.30C>T
MANE Select: NM_000546
dbSNP: rs568171603
Type: single nucleotide variant
Location: chr17:7676565 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 10: a turn; the 'interaction with ccar2' region; the 'interaction with hrmt1l2' region; the 'transcription activation (acidic)' region; a UniProt-annotated variant site (in a sporadic cancer; somatic mutation)

Full TP53 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: hereditary breast carcinoma Li-Fraumeni syndrome

Similar variants

TP53 p.Val10Ile Benign ★★★ same residue
TP53 p.Val10Leu Likely benign ★★★ same residue
TP53 p.Val10Asp Uncertain significance ★ ⚠ same residue
TP53 p.Val10Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Val10Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 c.375+5G>A Likely pathogenic ★★★ same condition
TP53 c.919+1G>A Pathogenic ★★★ same condition
TP53 c.97-1G>A 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/tp53-p-val10 (accessed [today's date]).

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