GeneBe

KRT9

keratin 9, the group of Keratins, type I

Basic information

Region (hg38): 17:41565836-41572059

Links

ENSG00000171403 ∙ NCBI:3857 ∙ OMIM:607606 ∙ HGNC:6447 ∙ Uniprot:P35527 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • epidermolytic palmoplantar keratoderma, 1 (Strong), mode of inheritance: AD
  • epidermolytic palmoplantar keratoderma, 1 (Strong), mode of inheritance: AD
  • epidermolytic palmoplantar keratoderma, 1 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Palmoplantar keratoderma, epidermolytic 1ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingDermatologic7528239; 7512862; 7511021; 9856842; 12192490; 12838553; 17074468; 19106041

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT9 gene.

  • not_provided (95 variants)
  • Inborn_genetic_diseases (72 variants)
  • Palmoplantar_keratoderma,_epidermolytic (62 variants)
  • Epidermolytic_palmoplantar_keratoderma,_1 (23 variants)
  • KRT9-related_disorder (12 variants)
  • Prostate_cancer (1 variants)
  • Palmoplantar_keratoderma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000226.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
6
clinvar
24
clinvar
3
clinvar
 33
missense
10
clinvar
7
clinvar
103
clinvar
18
clinvar
 138
nonsense
1
clinvar
3
clinvar
 4
start loss
0
frameshift
2
clinvar
 2
splice donor/acceptor (+/-2bp)
0
Total 11 7 114 42 3

Highest pathogenic variant AF is 0.0000030983272

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KRT9protein_codingprotein_codingENST00000246662 76215
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000001130.9451257090391257480.000155
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1993383480.9700.00001984002
Missense in Polyphen6881.9770.82951125
Synonymous-0.2871341301.030.000007621252
Loss of Function1.841322.40.5800.00000113284

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004200.000420
Ashkenazi Jewish0.00009920.0000992
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001520.000149
Middle Eastern0.000.00
South Asian0.0003680.000359
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May serve an important special function either in the mature palmar and plantar skin tissue or in the morphogenetic program of the formation of these tissues. Plays a role in keratin filament assembly. {ECO:0000269|PubMed:10218578, ECO:0000269|PubMed:7507869}.;
Disease
DISEASE: Keratoderma, palmoplantar, epidermolytic (EPPK) [MIM:144200]: A dermatological disorder characterized by diffuse thickening of the epidermis on the entire surface of palms and soles sharply bordered with erythematous margins. Some patients may present knuckle pads, thick pads of skin appearing over the proximal phalangeal joints. {ECO:0000269|PubMed:10632938, ECO:0000269|PubMed:10844507, ECO:0000269|PubMed:12072061, ECO:0000269|PubMed:12192490, ECO:0000269|PubMed:12838553, ECO:0000269|PubMed:12926810, ECO:0000269|PubMed:14675368, ECO:0000269|PubMed:15099359, ECO:0000269|PubMed:15115518, ECO:0000269|PubMed:15605275, ECO:0000269|PubMed:16911293, ECO:0000269|PubMed:16961539, ECO:0000269|PubMed:19874353, ECO:0000269|PubMed:20964665, ECO:0000269|PubMed:21715251, ECO:0000269|PubMed:7511021, ECO:0000269|PubMed:7512862, ECO:0000269|PubMed:7516304, ECO:0000269|PubMed:7523529, ECO:0000269|PubMed:7532199, ECO:0000269|PubMed:8647270, ECO:0000269|PubMed:9204965, ECO:0000269|PubMed:9856842}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology (Consensus)

Recessive Scores

pRec
0.199

Intolerance Scores

loftool
0.109
rvis_EVS
-1.2
rvis_percentile_EVS
5.83

Haploinsufficiency Scores

pHI
0.166
hipred
N
hipred_score
0.132
ghis
0.431

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.533

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Krt9
Phenotype
homeostasis/metabolism phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); limbs/digits/tail phenotype; pigmentation phenotype; neoplasm;

Gene ontology

Biological process
spermatogenesis;epidermis development;keratinization;skin development;intermediate filament organization;cornification
Cellular component
extracellular space;nucleus;cytosol;intermediate filament;membrane;extracellular exosome
Molecular function
structural constituent of cytoskeleton