Is KRT9 p.Tyr613= (c.1839C>T) pathogenic?

KRT9 p.Tyr613= (c.1839C>T) is classified Uncertain significance in KRT9 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.12%, eas); Associated with palmoplantar keratoderma, epidermolytic.

What condition is associated with KRT9 p.Tyr613= (c.1839C>T)?

KRT9 p.Tyr613= (c.1839C>T) is associated with palmoplantar keratoderma, epidermolytic (ClinVar).

How common is KRT9 p.Tyr613= (c.1839C>T) in the general population?

KRT9 p.Tyr613= (c.1839C>T) is rare (popmax 0.12%, eas) (gnomAD).

KRT9 p.Tyr613=

c.1839C>T · rs142173628 · VCV323113

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.12%, eas)

Conditions

palmoplantar keratoderma, epidermolytic

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 -2.9	GERP -2.6
Overall
CADD	0.982	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.12% East Asian · 54/44,884 alleles

Filtering AF 0.0946% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0855%

Overall 0.00446% 72/1,613,950 alleles · rare exomes 66/1,461,860 · genomes 6/152,090 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.12%	831
Admixed American	0.005%	20,004
African / African-American	0.004%	24,977
Remaining individualsnot grpmax-eligible	0.0016%	62,504
South Asian	0.0011%	91,078
European (non-Finnish)	0.000847%	118,000

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: KRT9
Protein: p.Tyr613=
Coding: c.1839C>T
MANE Select: NM_000226
dbSNP: rs142173628
Type: single nucleotide variant
Location: chr17:41567306 (GRCh38)
Gene constraint: LOEUF 0.873 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.43
Residue 613: the 'disordered' region; the 'tail' region

Full KRT9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

palmoplantar keratoderma, epidermolytic — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KRT9 p.Arg163Gln Pathogenic/Likely pathogenic ★★ same condition
KRT9 p.Arg163Trp Pathogenic/Likely pathogenic ★★ same condition
KRT9 p.Asn161Lys Pathogenic/Likely pathogenic ★★ same condition
KRT9 p.Gly116Asp Uncertain significance ★★ ⚠ same condition
KRT9 p.Gly193Glu Uncertain significance ★★ ⚠ same condition
KRT9 p.Gly507Arg Uncertain significance ★★ same condition
KRT9 p.Gly507Val Uncertain significance ★★ ⚠ same condition
KRT9 p.Ile341Val Uncertain significance ★★ ⚠ 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/krt9-p-tyr613 (accessed [today's date]).

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