KRT19

keratin 19, the group of Keratins, type I

Basic information

Region (hg38): 17:41523616-41528308

Links

ENSG00000171345 ∙ NCBI:3880 ∙ OMIM:148020 ∙ HGNC:6436 ∙ Uniprot:P08727 ∙ 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 KRT19 gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	2

Variants in KRT19

This is a list of pathogenic ClinVar variants found in the KRT19 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-41523759-G-T		not specified	Uncertain significance (Jul 26, 2021)
17-41523832-G-A		not specified	Uncertain significance (Sep 14, 2021)
17-41523834-G-A		not specified	Uncertain significance (Oct 27, 2023)
17-41523874-G-A		not specified	Uncertain significance (Feb 28, 2024)
17-41523888-C-T		not specified	Uncertain significance (Jan 10, 2023)
17-41523916-C-T		not specified	Likely benign (Dec 15, 2023)
17-41523939-G-T		not specified	Uncertain significance (Dec 02, 2021)
17-41524145-T-C		not specified	Uncertain significance (Feb 15, 2023)
17-41524190-G-A		not specified	Uncertain significance (Apr 04, 2023)
17-41524219-A-G		not specified	Uncertain significance (Jun 26, 2023)
17-41524410-C-T		not specified	Uncertain significance (Feb 02, 2024)
17-41524467-A-G		not specified	Uncertain significance (Feb 11, 2022)
17-41524516-C-T			not provided (-)
17-41524943-C-T		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
17-41524951-G-A			not provided (-)
17-41524968-C-T		not specified	Uncertain significance (Dec 12, 2023)
17-41525218-C-G		not specified	Uncertain significance (Mar 06, 2023)
17-41525219-G-A		not specified	Uncertain significance (Oct 22, 2021)
17-41525223-A-G			not provided (-)
17-41525229-G-A			Benign (May 31, 2018)
17-41527862-T-G		not specified	Uncertain significance (Oct 20, 2021)
17-41527917-T-G		not specified	Uncertain significance (Nov 17, 2022)
17-41528017-C-A			Benign (May 31, 2018)
17-41528027-C-A		not specified	Uncertain significance (Feb 21, 2024)
17-41528028-C-A		not specified	Uncertain significance (Feb 21, 2024)

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
0.00434	0.989	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

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.358
• ghis: 0.457

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

Mouse Genome Informatics

• Gene name: Krt19
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype; embryo phenotype; neoplasm; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; skeleton phenotype

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