KRT19

keratin 19, the group of Keratins, type I

Basic information

Region (hg38): 17:41523617-41528308

Links

ENSG00000171345 ∙ NCBI:3880 ∙ OMIM:148020 ∙ HGNC:6436 ∙ Uniprot:P08727 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 11.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_002276.5	NP_002267.2	6	yes	-
ENST00000361566.7	ENSP00000355124.3	6	yes	-
ENST00000455635.1	ENSP00000408759.1	4	-	-
ENST00000593096.1	ENSP00000466625.1	4	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT19 gene.

• not_specified (69 variants)
• not_provided (6 variants)
• Hereditary_breast_ovarian_cancer_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_002276.5. 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			1		2	3
missense			70	2		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	73	2	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT19	protein_coding	protein_coding	ENST00000361566	6	4692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.227	247	257	0.960	0.0000154	2561
Missense in Polyphen		104	109.98	0.94562		1141
Synonymous	-0.613	127	119	1.07	0.00000740	847
Loss of Function	2.39	7	17.9	0.391	0.00000102	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000359	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the organization of myofibers. Together with KRT8, helps to link the contractile apparatus to dystrophin at the costameres of striated muscle. {ECO:0000269|PubMed:16000376}.
• Pathway: Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology;Signaling mediated by p38-alpha and p38-beta (Consensus)

Recessive Scores

• pRec: 0.629

Intolerance Scores

• loftool: 0.161
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.16

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Gene ontology

• Biological process: Notch signaling pathway;viral process;keratinization;response to estrogen;sarcomere organization;cell differentiation involved in embryonic placenta development;cornification
• Cellular component: cytosol;intermediate filament;plasma membrane;dystrophin-associated glycoprotein complex;apicolateral plasma membrane;Z disc;sarcolemma;costamere;extracellular exosome;cell periphery;terminal web
• Molecular function: structural constituent of cytoskeleton;protein binding;structural constituent of muscle;protein-containing complex binding