Is TP53 p.Leu145= (c.433C>T) pathogenic?

TP53 p.Leu145= (c.433C>T) is classified Likely benign in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-12-31). Very rare (popmax 0.0011%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Leu145= (c.433C>T)?

TP53 p.Leu145= (c.433C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is TP53 p.Leu145= (c.433C>T) in the general population?

TP53 p.Leu145= (c.433C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

TP53 p.Leu145=

c.433C>T · rs786203928 · VCV187696

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

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 3.2	GERP -3.7, phastCons 1
Overall
CADD	8.226	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,090 alleles

Overall 6.19e-05% 1/1,614,210 alleles · very rare exomes 1/1,461,888 · genomes 0/152,322 · 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: TP53
Protein: p.Leu145=
Coding: c.433C>T
MANE Select: NM_000546
dbSNP: rs786203928
Type: single nucleotide variant
Location: chr17:7675179 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 145: a DNA-binding region; the 'interaction with axin1' region; a β-strand; the 'interaction with ccar2' region; a UniProt-annotated variant site (in sporadic cancers; somatic mutation); the 'interaction with hipk1' region; the 'required for interaction with znf385a' region; the 'required for interaction with fbxo42' region

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

Similar variants

TP53 p.Leu145Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Leu145Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Leu145Val Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Leu145Arg 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
TP53 p.Ala138Pro 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/tp53-p-leu145 (accessed [today's date]).

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