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.

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.

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				4	6	10
missense			21	4	5	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	0	0	21	9	12

Variants in KLK3

This is a list of pathogenic ClinVar variants found in the KLK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50854993-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-50856231-C-G		KLK3-related disorder	Likely benign (Aug 01, 2019)
19-50856241-T-C		KLK3-related disorder	Benign (Oct 18, 2019)
19-50856247-A-G		KLK3-related disorder	Benign (Oct 18, 2019)
19-50856264-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-50856287-G-A			Benign (Jun 22, 2018)
19-50856303-C-A		not specified	Uncertain significance (Aug 17, 2021)
19-50856308-C-CA		Hereditary angioedema with normal C1Inh	not provided (Feb 01, 2020)
19-50856309-A-T			Benign (Jun 22, 2018)
19-50856310-G-A		KLK3-related disorder	Benign (Nov 06, 2019)
19-50856321-C-A		not specified	Uncertain significance (Sep 27, 2021)
19-50856327-G-A		not specified	Likely benign (Jan 07, 2022)
19-50856338-G-C		not specified	Uncertain significance (Sep 22, 2022)
19-50856347-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-50856357-T-G		not specified	Uncertain significance (Feb 06, 2023)
19-50856360-A-G		not specified	Uncertain significance (Sep 12, 2023)
19-50856389-T-C		not specified	Uncertain significance (Jul 13, 2022)
19-50858056-C-G		not specified	Uncertain significance (Apr 13, 2022)
19-50858059-C-T		KLK3-related disorder	Benign (Nov 12, 2019)
19-50858082-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-50858145-A-C		not specified	Uncertain significance (Nov 07, 2023)
19-50858148-G-A		not specified	Likely benign (Dec 14, 2023)
19-50858179-C-T		KLK3-related disorder	Likely benign (May 28, 2019)
19-50858195-C-T		KLK3-related disorder	Benign (Nov 11, 2019)
19-50858216-C-A		KLK3-related disorder	Benign (Dec 02, 2019)

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

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