Is KRT5 p.Arg10= (c.30G>A) pathogenic?

KRT5 p.Arg10= (c.30G>A) is classified Benign/Likely benign in KRT5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-14). Low-frequency (popmax 2.6%, afr); Associated with epidermolysis bullosa simplex.

What condition is associated with KRT5 p.Arg10= (c.30G>A)?

KRT5 p.Arg10= (c.30G>A) is associated with epidermolysis bullosa simplex (ClinVar).

How common is KRT5 p.Arg10= (c.30G>A) in the general population?

KRT5 p.Arg10= (c.30G>A) is low-frequency (popmax 2.6%, afr) (gnomAD).

KRT5 p.Arg10=

c.30G>A · rs61747182 · VCV256042

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.6%, afr)

Conditions

epidermolysis bullosa simplex

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 -1.3
Overall
CADD	6.741	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.6% African / African-American · 1,948/75,032 alleles

Filtering AF 2.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.46%

Overall 0.133% 2,149/1,613,652 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.6%	39
Admixed American	0.155%	645
Remaining individualsnot grpmax-eligible	0.141%	710
Middle Eastern	0.0671%	1,490
South Asian	0.0022%	45,533
European (non-Finnish)	0.00119%	84,289

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: KRT5
Protein: p.Arg10=
Coding: c.30G>A
MANE Select: NM_000424
dbSNP: rs61747182
Type: single nucleotide variant
Location: chr12:52520267 (GRCh38)
Gene constraint: LOEUF 0.538 · pLI 0.90 (gnomAD)
Structure: AlphaFold pLDDT 68.86 · 2 PDB
Residue 10: the 'head' region; a UniProt-annotated variant site (in ddd1); the 'disordered' region

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.Arg10Trp Uncertain significance ★ ⚠ same residue
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

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-arg10 (accessed [today's date]).

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