Is KRT5 p.Thr321Pro (c.961A>C) pathogenic?

KRT5 p.Thr321Pro (c.961A>C) is classified Pathogenic in KRT5 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-04-25). AlphaMissense: likely pathogenic (0.9674); Absent from gnomAD v4.1; Associated with epidermolysis bullosa simplex.

What condition is associated with KRT5 p.Thr321Pro (c.961A>C)?

KRT5 p.Thr321Pro (c.961A>C) is associated with epidermolysis bullosa simplex (ClinVar).

How common is KRT5 p.Thr321Pro (c.961A>C) in the general population?

KRT5 p.Thr321Pro (c.961A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about KRT5 p.Thr321Pro (c.961A>C)?

AlphaMissense predicts likely pathogenic (score 0.9674) — an in-silico prediction, not a clinical call.

KRT5 p.Thr321Pro

c.961A>C · rs1938635857 · VCV1047990

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9674 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

epidermolysis bullosa simplex

Computational evidence

Protein change
AlphaMissense	0.9674	likely pathogenic ✓ concordant with ClinVar
REVEL	0.912	moderately pathogenic-leaning
SaProt	LLR -14.02	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	Δ0.37	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 7.9	phastCons 1
Regional constraint	o/e 0.19	constrained · MANE · 46 bp · p 0.00024 · regional, not allelic
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

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: KRT5
Protein: p.Thr321Pro
Coding: c.961A>C
MANE Select: NM_000424
dbSNP: rs1938635857
Type: single nucleotide variant
Location: chr12:52517721 (GRCh38)
Gene constraint: LOEUF 0.538 · pLI 0.90 (gnomAD)
Structure: AlphaFold pLDDT 68.86 · 2 PDB
Residue 321: the if rod domain; a UniProt-annotated variant site (in ddd1); the 'linker 12' region; a UniProt-annotated variant site (in ebs2c)

Full KRT5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

epidermolysis bullosa simplex — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KRT5 p.Ala428Thr Pathogenic/Likely pathogenic ★★ same condition
KRT5 p.Ala428Val Pathogenic/Likely pathogenic ★★ same condition
KRT5 p.Glu170Lys Pathogenic ★★ same condition
KRT5 p.Glu466Gln Pathogenic/Likely pathogenic ★★ same condition
KRT5 p.Glu477Lys Pathogenic ★★ same condition
KRT5 p.Leu196Pro Pathogenic/Likely pathogenic ★★ same condition
KRT5 p.Leu463Pro Pathogenic ★★ same condition
KRT5 p.Pro25Leu 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/krt5-p-thr321pro (accessed [today's date]).

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