GeneBe

KRT6B

protein-coding

keratin 6B, the group of Keratins, type II

Gene summary

The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. As many as six of this type II cytokeratin (KRT6) have been identified; the multiplicity of the genes is attributed to successive gene duplication events. The genes are expressed with family members KRT16 and/or KRT17 in the filiform papillae of the tongue, the stratified epithelial lining of oral mucosa and esophagus, the outer root sheath of hair follicles, and the glandular epithelia. Mutations in these genes have been associated with pachyonychia congenita. The type II cytokeratins are clustered in a region of chromosome 12q12-q13. [provided by RefSeq, Jul 2008]

Previous symbols:
  • KRTL1

MANE transcript

NM_005555.4

Inheritance

AD

ClinVar variants

P:4U:150B:75

Top phenotype

Pachyonychia congenita 4

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr12:52,446,651-52,452,146

External References & Databases

Ensembl (ENSG00000185479)NCBI Gene (3854)OMIM (148042)HGNC:6444GenCCUniProt (P04259)AlphaFoldClinVar (KRT6B)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~5.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pachyonychia congenita 4STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014325

Submitter: PanelApp Australia

pachyonychia congenitaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016471

Submitter: Orphanet

pachyonychia congenita 4MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014325

Submitter: Ambry Genetics

pachyonychia congenita 4STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014325

Submitter: Genomics England PanelApp

pachyonychia congenita 4STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014325

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Pachyonychia congenita 4AD

Manifestation: Dental; Dermatologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 9618173; 11886499; 20301457Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KRT6B variants in ClinVar

6 Conditions Cataloged
Inborn genetic diseasesTotal: 133
not providedTotal: 118
not specifiedTotal: 27
KRT6B-related disorderTotal: 20
Pachyonychia congenita 4Total: 8
KRT6B-related disordersTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005555.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
40
clinvar
10
clinvar
 51
missense
2
clinvar
2
clinvar
147
clinvar
22
clinvar
3
clinvar
 176
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total221506213229

Highest pathogenic variant AF is 0.0000020523682

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005555.4RefSeqNP_005546.29MANE Select
ENST00000252252.4EnsemblENSP00000252252.39MANE Select
ENST00001136554.1EnsemblENSP00000802602.19Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Keratinization
  • Developmental Biology

Biological Process

  • cytoskeleton organization
  • ectoderm development
  • keratinization
  • cornification

Molecular Function

  • structural constituent of cytoskeleton
  • protein binding

Cellular Component

  • cytosol
  • keratin filament
  • extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000252252
Coding exons
9
Length
5476
Individuals with no LoFs
125699
Homozygous LoFs
0
Heterozygous LoFs
49
Defined
125748
p
0.000195
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-2.234233121.360.00001983631
Missense (PolyPhen)129101.241.27411393
Synonymous-1.701551301.190.000008431138
Loss of Function0.6571619.10.8388.51e-7247

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.000260.00026rare
Ashkenazi Jewish00.0absent
East Asian0.000220.00022rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000180.00018rare
South Asian0.000330.00033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool
0.110
RVIS EVS
-0.3
RVIS percentile EVS
32.25

Essentials

Essential (CRISPR)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.458

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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