KRT78

keratin 78, the group of Keratins, type II

Basic information

Region (hg38): 12:52837804-52849092

Links

ENSG00000170423 ∙ NCBI:196374 ∙ OMIM:611159 ∙ HGNC:28926 ∙ Uniprot:Q8N1N4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT78 gene.

• not_specified (89 variants)
• not_provided (9 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT78 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173352.4. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	3	6
missense			79	9	4	92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	12	7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT78	protein_coding	protein_coding	ENST00000304620	9	11289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.49e-15	0.0128	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.478	322	299	1.08	0.0000171	3360
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000617	0.000604
Ashkenazi Jewish	0.00	0.00
East Asian	0.00104	0.000979
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000364	0.000360
Middle Eastern	0.00104	0.000979
South Asian	0.000201	0.000196
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Keratinization;Developmental Biology (Consensus)

Recessive Scores

• pRec: 0.0813

Intolerance Scores

• loftool: 0.173
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.29

Haploinsufficiency Scores

• pHI: 0.0381
• hipred: N
• hipred_score: 0.146
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt78

Gene ontology

• Biological process: keratinization;cornification
• Cellular component: extracellular space;cytosol;keratin filament;extracellular exosome
• Molecular function: structural molecule activity