KRT79

protein-coding

keratin 79, the group of Keratins, type II

Gene summary

Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This gene encodes an epithelial keratin that is expressed in skeletal muscle, skin and scalp. The type II keratins are clustered in a region of chromosome 12q13.[provided by RefSeq, Jun 2009]

MANE transcript

NM_175834.3

Inheritance

—

ClinVar variants

U:76B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.04

Max pathogenic AF

—

Genomic locus

chr12:52,821,408-52,834,311

External References & Databases

Ensembl (ENSG00000185640)

Transcript & Mutation Effects

hg38 • Region Span ~12.9 kb

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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 KRT79 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 78

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_175834.3. 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			74 clinvar	2 clinvar		76
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	4	0	80

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_175834.3	RefSeq	NP_787028.1	9	MANE Select
ENST00000330553.6	Ensembl	ENSP00000328358.5	9	MANE Select
ENST00000549255.1	Ensembl	ENSP00000449159.1	2	Standard
ENST00001141424.1	Ensembl	ENSP00000807149.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Keratinization
Developmental Biology

Biological Process

keratinization
cornification

Molecular Function

structural molecule activity
protein binding
enzyme binding

Cellular Component

cytosol
keratin filament
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330553
Coding exons: 9
Length: 12886
Individuals with no LoFs: 125597
Homozygous LoFs: 1
Heterozygous LoFs: 150
Defined: 125748
p: 0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.110	330	324	1.02	0.0000197	3479
Missense (PolyPhen)		82	88.395	0.92765		1059
Synonymous	-1.01	154	139	1.11	0.00000866	1111
Loss of Function	-0.190	24	23.0	1.04	0.00000115	248

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00043	0.00038	rare
Ashkenazi Jewish	0.0031	0.0031	notable
East Asian	0.0011	0.0011	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.0010	0.0010	notable
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0992

Intolerance Scores

LoFtool: 0.313
RVIS EVS: 1.34
RVIS percentile EVS: 94.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.555

Gene Damage Prediction

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