Is TP63 p.Lys375Glu (c.1123A>G) pathogenic?

TP63 p.Lys375Glu (c.1123A>G) is classified Uncertain significance in TP63 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-25). AlphaMissense: likely pathogenic (0.987); Absent from gnomAD v4.1.

How common is TP63 p.Lys375Glu (c.1123A>G) in the general population?

TP63 p.Lys375Glu (c.1123A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TP63 p.Lys375Glu (c.1123A>G)?

AlphaMissense predicts likely pathogenic (score 0.987) — an in-silico prediction, not a clinical call.

TP63 p.Lys375Glu

c.1123A>G · VCV4527445

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.987 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.987	likely pathogenic
REVEL	0.694	pathogenic-leaning
SaProt	LLR -12.64	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 9.3	GERP 1.9, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 26 kb · p 4.9e-05 · regional, not allelic
Overall
CADD	27.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: TP63
Protein: p.Lys375Glu
Coding: c.1123A>G
MANE Select: NM_003722
Type: single nucleotide variant
Location: chr3:189868710 (GRCh38)
Gene constraint: LOEUF 0.296 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 63.70 · 26 PDB
Residue 375: the 'disordered' region; the 'interaction with hipk2' region

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

Similar variants

TP63 p.Ala354Glu Likely pathogenic ★★ same type
TP63 p.Arg243Gln Pathogenic/Likely pathogenic ★★ same type
TP63 p.Arg243Trp Pathogenic ★★ same type
TP63 p.Arg266Gln Pathogenic/Likely pathogenic ★★ same type
TP63 p.Arg318Cys Pathogenic ★★ same type
TP63 p.Arg318His Pathogenic/Likely pathogenic ★★ same type
TP63 p.Arg319Cys Pathogenic/Likely pathogenic ★★ same type
TP63 p.Arg319His Pathogenic ★★ same type

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-lys375glu (accessed [today's date]).

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