KRT78

protein-coding

keratin 78, the group of Keratins, type II

Gene summary

This gene is a member of the type II keratin gene family and encodes a protein with an intermediate filament domain. Keratins are the major structural proteins in epithelial cells, forming a cytoplasmic network of 10 to 12 nm wide intermediate filaments and creating a scaffold that gives cells the ability to withstand mechanical and non-mechanical stresses. The genes of the type II keratin family are located as a gene cluster at 12p13.13. Four pseudogenes of this gene family have been identified. [provided by RefSeq, Jul 2008]

MANE transcript

NM_173352.4

Inheritance

—

ClinVar variants

U:92B:20

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr12:52,837,804-52,849,092

External References & Databases

Ensembl (ENSG00000170423)

Transcript & Mutation Effects

hg38 • Region Span ~11.3 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 KRT78 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 102

not providedTotal: 9

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173352.4. 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				3 clinvar	3 clinvar	6
missense			92 clinvar	10 clinvar	4 clinvar	106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	92	13	7	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173352.4	RefSeq	NP_775487.2	9	MANE Select
ENST00000304620.5	Ensembl	ENSP00000306261.4	9	MANE Select
NM_001300814.1	RefSeq	NP_001287743.1	9	Standard
ENST00000359499.8	Ensembl	ENSP00000352479.4	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

Cellular Component

extracellular space
cytosol
keratin filament
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304620
Coding exons: 9
Length: 11289
Individuals with no LoFs: 125665
Homozygous LoFs: 0
Heterozygous LoFs: 83
Defined: 125748
p: 0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.478	322	299	1.08	0.0000171	3360
Missense (PolyPhen)		104	95.28	1.0915		1188
Synonymous	-0.0635	125	124	1.01	0.00000698	1050
Loss of Function	0.0671	23	23.4	0.985	0.00000107	265

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0010	0.00098	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00036	0.00036	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0813

Intolerance Scores

LoFtool: 0.173
RVIS EVS: 1.34
RVIS percentile EVS: 94.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.766

Gene Damage Prediction

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