KLK6

kallikrein related peptidase 6, the group of Kallikreins|Serine proteases

Basic information

Region (hg38): 19:50958631-50969673

Previous symbols: [ "PRSS9", "PRSS18" ]

Links

ENSG00000167755 ∙ NCBI:5653 ∙ OMIM:602652 ∙ HGNC:6367 ∙ Uniprot:Q92876 ∙ 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 KLK6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLK6 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	8	1	1

Variants in KLK6

This is a list of pathogenic ClinVar variants found in the KLK6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50959185-T-A		not specified	Uncertain significance (Feb 06, 2023)
19-50959250-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-50959258-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-50959309-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-50961859-T-C		not specified	Uncertain significance (Jul 09, 2024)
19-50963367-A-G		not specified	Uncertain significance (Feb 08, 2023)
19-50963370-G-A		not specified	Uncertain significance (Sep 04, 2024)
19-50963401-C-T		not specified	Uncertain significance (Feb 02, 2022)
19-50963410-C-T		not specified	Uncertain significance (Jul 30, 2024)
19-50963446-C-T		not specified	Uncertain significance (Aug 19, 2024)
19-50963476-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-50963499-G-A		not specified	Likely benign (Aug 10, 2021)
19-50963515-G-A			Benign (Jul 10, 2018)
19-50967290-C-T		not specified	Uncertain significance (Nov 20, 2024)
19-50967314-C-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLK6	protein_coding	protein_coding	ENST00000376851	5	11043

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00601	0.914	125714	0	30	125744	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.567	122	141	0.866	0.00000740	1587
Missense in Polyphen		31	57.698	0.53728		668
Synonymous	-0.747	63	55.9	1.13	0.00000291	477
Loss of Function	1.50	5	10.2	0.492	5.31e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000439	0.000439
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine protease which exhibits a preference for Arg over Lys in the substrate P1 position and for Ser or Pro in the P2 position. Shows activity against amyloid precursor protein, myelin basic protein, gelatin, casein and extracellular matrix proteins such as fibronectin, laminin, vitronectin and collagen. Degrades alpha-synuclein and prevents its polymerization, indicating that it may be involved in the pathogenesis of Parkinson disease and other synucleinopathies. May be involved in regulation of axon outgrowth following spinal cord injury. Tumor cells treated with a neutralizing KLK6 antibody migrate less than control cells, suggesting a role in invasion and metastasis. {ECO:0000269|PubMed:11983703, ECO:0000269|PubMed:12878203, ECO:0000269|PubMed:12928483, ECO:0000269|PubMed:15557757, ECO:0000269|PubMed:16321973, ECO:0000269|PubMed:16987227}.
• Pathway: Vitamin D Receptor Pathway;Alpha-synuclein signaling (Consensus)

Recessive Scores

• pRec: 0.257

Intolerance Scores

• loftool: 0.134
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.198
• hipred: Y
• hipred_score: 0.585
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klk6
• Phenotype: 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)

Gene ontology

• Biological process: central nervous system development;response to wounding;regulation of neuron projection development;protein autoprocessing;collagen catabolic process;tissue regeneration;hormone metabolic process;myelination;amyloid precursor protein metabolic process;regulation of cell differentiation;positive regulation of G protein-coupled receptor signaling pathway
• Cellular component: extracellular region;extracellular space;nucleolus;cytoplasm;mitochondrion;endoplasmic reticulum;secretory granule
• Molecular function: serine-type endopeptidase activity;protein binding