KLK1

kallikrein 1, the group of Kallikreins

Basic information

Region (hg38): 19:50819145-50823787

Links

ENSG00000167748 ∙ NCBI:3816 ∙ OMIM:147910 ∙ HGNC:6357 ∙ Uniprot:P06870 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pulmonary arterial hypertension (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLK1 gene.

• Inborn genetic diseases (12 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLK1 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			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	2

Variants in KLK1

This is a list of pathogenic ClinVar variants found in the KLK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50819220-C-T		not specified	Likely benign (Oct 20, 2021)
19-50819250-C-T		not specified	Uncertain significance (Sep 29, 2023)
19-50819252-G-A		not specified	Uncertain significance (Feb 10, 2022)
19-50819253-C-A		not specified	Uncertain significance (Feb 10, 2022)
19-50819945-A-T		not specified	Uncertain significance (Dec 26, 2023)
19-50819947-G-T		not specified	Likely benign (Dec 21, 2023)
19-50819965-G-A			Benign/Likely benign (Dec 01, 2023)
19-50820208-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-50820240-A-G		not specified	Uncertain significance (Jul 15, 2021)
19-50820268-C-T		not specified	Uncertain significance (May 05, 2023)
19-50820298-T-G		not specified	Uncertain significance (Sep 25, 2023)
19-50820307-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-50820336-A-C		not specified	Uncertain significance (Sep 29, 2023)
19-50820364-A-G		not specified	Uncertain significance (Nov 08, 2021)
19-50820382-C-A		not specified	Uncertain significance (Nov 18, 2023)
19-50820391-C-T		not specified	Uncertain significance (Jul 11, 2023)
19-50820420-C-T		Kallikrein, decreased urinary activity of	Affects (Mar 01, 2005)
19-50821713-C-T		not specified	Uncertain significance (Mar 12, 2024)
19-50821755-C-A		not specified	Uncertain significance (Feb 06, 2024)
19-50821799-G-A		not specified	Likely benign (Jun 01, 2023)
19-50821814-G-A		not specified	Uncertain significance (Dec 21, 2023)
19-50821847-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-50821859-G-C		not specified	Uncertain significance (Feb 02, 2022)
19-50821863-G-T		not specified	Uncertain significance (Feb 10, 2022)
19-50823714-A-G		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLK1	protein_coding	protein_coding	ENST00000301420	5	4640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000153	0.684	125705	0	41	125746	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.443	138	153	0.899	0.00000793	1718
Missense in Polyphen		44	51.223	0.85899		617
Synonymous	-1.19	77	64.8	1.19	0.00000368	514
Loss of Function	0.865	7	9.94	0.704	4.26e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000240	0.000237
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glandular kallikreins cleave Met-Lys and Arg-Ser bonds in kininogen to release Lys-bradykinin.
• Pathway: Renin-angiotensin system - Homo sapiens (human);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Blood Clotting Cascade;Dengue-2 Interactions with Blood Clotting Cascade;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.420

Intolerance Scores

• loftool: 0.401
• rvis_EVS: 0.68
• rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

• pHI: 0.0355
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klk1

Gene ontology

• Biological process: regulation of systemic arterial blood pressure;zymogen activation
• Cellular component: nucleus;secretory granule;extracellular exosome
• Molecular function: serine-type endopeptidase activity