KLK3

kallikrein related peptidase 3, the group of Kallikreins

Basic information

Region (hg38): 19:50854915-50860764

Previous symbols: [ "APS" ]

Links

ENSG00000142515

∙ NCBI:354 ∙ OMIM:176820 ∙ HGNC:6364 ∙ Uniprot:P07288 ∙ 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 KLK3 gene.

not_specified (39 variants)
KLK3-related_disorder (9 variants)
not_provided (4 variants)
Hereditary_angioedema_with_normal_C1Inh (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLK3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001648.2. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	2 clinvar	7
missense			35 clinvar	5 clinvar	3 clinvar	43
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	10	5

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLK3	protein_coding	protein_coding	ENST00000326003	5	5850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000443	0.407	125715	0	31	125746	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.253	170	161	1.06	0.00000926	1682
Missense in Polyphen		60	56.816	1.056		640
Synonymous	-1.63	84	67.0	1.25	0.00000429	539
Loss of Function	0.475	9	10.7	0.843	5.24e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000218	0.000217
South Asian	0.000131	0.000131
Other	0.000489	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Hydrolyzes semenogelin-1 thus leading to the liquefaction of the seminal coagulum.;
Pathway: Prostate cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Androgen receptor signaling pathway;Androgen Receptor Network in Prostate Cancer;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;miRNA regulation of prostate cancer signaling pathways;Signal Transduction;antigen processing and presentation;Metabolism of proteins;DroToll-like;IGF signaling;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;FOXA1 transcription factor network;Regulation of Androgen receptor activity (Consensus)

Recessive Scores

pRec: 0.410

Intolerance Scores

loftool: 0.0825
rvis_EVS: 0.2
rvis_percentile_EVS: 67.36

Haploinsufficiency Scores

pHI: 0.604
hipred: N
hipred_score: 0.330
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.528

Gene Damage Prediction

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

Gene ontology

Biological process: antibacterial peptide production;regulation of systemic arterial blood pressure;proteolysis;negative regulation of angiogenesis;zymogen activation;cellular protein metabolic process
Cellular component: extracellular region;extracellular space;nucleus;secretory granule;protein-containing complex;extracellular exosome
Molecular function: endopeptidase activity;serine-type endopeptidase activity;protein binding;serine-type peptidase activity;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides