Is TP53 p.Lys370= (c.1110G>A) pathogenic?

TP53 p.Lys370= (c.1110G>A) is classified Likely benign in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-07). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Lys370= (c.1110G>A)?

TP53 p.Lys370= (c.1110G>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is TP53 p.Lys370= (c.1110G>A) in the general population?

TP53 p.Lys370= (c.1110G>A) is absent from gnomAD v4.1 (gnomAD).

TP53 p.Lys370=

c.1110G>A · rs1567540533 · VCV628982

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.52	GERP -3.4, phastCons 1
Overall
CADD	5.058	PHRED · no single calibrated threshold — expert panels disagree

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: TP53
Protein: p.Lys370=
Coding: c.1110G>A
MANE Select: NM_000546
dbSNP: rs1567540533
Type: single nucleotide variant
Location: chr17:7669681 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 370: a UniProt-annotated variant site (in a sporadic cancer; somatic mutation); the 'interaction with carm1' region; the 'disordered' region; the 'basic (repression of dna-binding)' region; a modified residue (n6,n6-dimethyllysine; alternate); a modified residue (n6-methyllysine; by smyd2; alternate); the 'interaction with hipk1' 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.Lys370Met Uncertain significance ★ same residue
TP53 p.Lys370Thr Conflicting classifications of pathogenicity ★ same residue
TP53 p.Lys370Arg Uncertain significance ★ ⚠ 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
TP53 p.Ala138Val 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-lys370 (accessed [today's date]).

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