KRT15

protein-coding

keratin 15, the group of Keratins, type I|MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene is a member of the keratin gene family. The keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into cytokeratins and hair keratins. Most of the type I cytokeratins consist of acidic proteins which are arranged in pairs of heterotypic keratin chains and are clustered in a region on chromosome 17q21.2. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002275.4

Inheritance

—

ClinVar variants

U:72B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.08

Max pathogenic AF

—

Genomic locus

chr17:41,513,745-41,522,529

External References & Databases

Ensembl (ENSG00000171346)

Transcript & Mutation Effects

hg38 • Region Span ~8.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KRT15 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002275.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			71 clinvar	3 clinvar	1 clinvar	75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	5	1	78

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002275.4	RefSeq	NP_002266.3	8	MANE Select
ENST00000254043.8	Ensembl	ENSP00000254043.3	8	MANE Select
ENST00000393974.7	Ensembl	ENSP00000377544.3	7	Standard
ENST00000393976.6	Ensembl	ENSP00000377546.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Estrogen signaling pathway - Homo sapiens (human)
Keratinization
Developmental Biology

Biological Process

cytoskeleton organization
epidermis development
keratinization
cornification

Molecular Function

structural constituent of cytoskeleton
protein binding
scaffold protein binding

Cellular Component

nucleus
cytosol
intermediate filament
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254043
Coding exons: 8
Length: 8787
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 101
Defined: 125748
p: 0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.000895	268	268	1.00	0.0000165	2962
Missense (PolyPhen)		105	103.02	1.0192		1238
Synonymous	-0.768	121	111	1.09	0.00000714	934
Loss of Function	-0.335	23	21.3	1.08	0.00000128	219

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00040	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0015	0.0015	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00027	0.00027	rare
South Asian	0.00065	0.00062	rare
Other	0.00086	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.213

Intolerance Scores

LoFtool: 0.181
RVIS EVS: 0.8
RVIS percentile EVS: 87.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.572

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium