KLK2

kallikrein related peptidase 2, the group of Kallikreins

Basic information

Region (hg38): 19:50861567-50880567

Links

ENSG00000167751 ∙ NCBI:3817 ∙ OMIM:147960 ∙ HGNC:6363 ∙ Uniprot:P20151 ∙ 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 KLK2 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLK2 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						0
missense			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in KLK2

This is a list of pathogenic ClinVar variants found in the KLK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50874745-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-50874773-G-T		not specified	Uncertain significance (Aug 12, 2021)
19-50874775-A-G		not specified	Uncertain significance (Dec 08, 2023)
19-50874819-C-A		not specified	Uncertain significance (Aug 08, 2023)
19-50874837-G-C		not specified	Uncertain significance (Nov 10, 2022)
19-50876491-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-50876557-C-T		not specified	Uncertain significance (Oct 27, 2022)
19-50876576-G-A		not specified	Uncertain significance (Nov 09, 2023)
19-50876589-T-A		not specified	Uncertain significance (Apr 17, 2023)
19-50876878-G-A		not specified	Uncertain significance (Jul 13, 2021)
19-50876884-G-A		not specified	Likely benign (Dec 20, 2021)
19-50876916-T-C		not specified	Likely benign (Aug 04, 2023)
19-50876920-A-G		not specified	Uncertain significance (Dec 03, 2021)
19-50878425-G-A		not specified	Likely benign (Mar 12, 2024)
19-50878491-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-50878508-G-C		not specified	Uncertain significance (Dec 15, 2023)
19-50878521-C-T		Acute myeloid leukemia	Pathogenic (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLK2	protein_coding	protein_coding	ENST00000325321	5	19000

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000128	0.645	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.117	143	147	0.973	0.00000747	1690
Missense in Polyphen		42	49.289	0.85212		612
Synonymous	0.762	50	57.3	0.872	0.00000295	527
Loss of Function	0.782	7	9.62	0.728	4.10e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000764	0.000761
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000764	0.000761
South Asian	0.0000655	0.0000653
Other	0.000326	0.000163

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);Androgen Receptor Network in Prostate Cancer;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;Signal Transduction;Metabolism of proteins;Extracellular matrix organization;Activation of Matrix Metalloproteinases;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;RHO GTPases activate PKNs;RHO GTPase Effectors;Signaling by Rho GTPases;Coregulation of Androgen receptor activity;Degradation of the extracellular matrix;Regulation of Androgen receptor activity (Consensus)

Intolerance Scores

• loftool: 0.281
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.0786
• hipred: N
• hipred_score: 0.166
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0320

Gene Damage Prediction

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

Gene ontology

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