KLK5

kallikrein related peptidase 5, the group of Kallikreins

Basic information

Region (hg38): 19:50943303-50953093

Links

ENSG00000167754 ∙ NCBI:25818 ∙ OMIM:605643 ∙ HGNC:6366 ∙ Uniprot:Q9Y337 ∙ 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 KLK5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLK5 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			22	4		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	4	0

Variants in KLK5

This is a list of pathogenic ClinVar variants found in the KLK5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50943699-G-A		not specified	Uncertain significance (Dec 21, 2022)
19-50943710-C-T		not specified	Likely benign (Jul 25, 2023)
19-50943711-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-50943714-C-A		not specified	Uncertain significance (Dec 28, 2022)
19-50943777-C-T		not specified	Uncertain significance (Oct 27, 2023)
19-50948689-T-C		not specified	Uncertain significance (Sep 29, 2023)
19-50948698-C-T		not specified	Uncertain significance (Dec 02, 2022)
19-50948701-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-50948702-G-A		not specified	Uncertain significance (Dec 20, 2021)
19-50948714-C-T		not specified	Likely benign (Feb 17, 2024)
19-50948743-T-C		not specified	Uncertain significance (Nov 02, 2023)
19-50948871-T-C		not specified	Uncertain significance (Sep 26, 2023)
19-50948960-C-T		not specified	Likely benign (Jul 20, 2022)
19-50948970-T-C		not specified	Uncertain significance (Jul 15, 2021)
19-50949006-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-50949008-G-C		not specified	Uncertain significance (Mar 15, 2024)
19-50949030-G-C		not specified	Uncertain significance (Dec 14, 2023)
19-50949042-C-A		not specified	Uncertain significance (Jan 03, 2022)
19-50949897-A-G		not specified	Uncertain significance (Jul 08, 2022)
19-50949952-A-G		not specified	Uncertain significance (May 29, 2024)
19-50949976-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-50950029-G-A		not specified	Uncertain significance (Apr 28, 2022)
19-50950113-T-C		not specified	Likely benign (Dec 22, 2023)
19-50952593-C-A		not specified	Uncertain significance (Dec 16, 2023)
19-50952600-G-C		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLK5	protein_coding	protein_coding	ENST00000336334	5	9791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00701	0.926	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.287	166	177	0.939	0.0000105	1911
Missense in Polyphen		53	66.064	0.80225		676
Synonymous	0.578	71	77.5	0.916	0.00000534	592
Loss of Function	1.58	5	10.5	0.474	4.51e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000435	0.000435
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in desquamation.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.267

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.203
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.350

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klk5

Gene ontology

• Biological process: positive regulation of antibacterial peptide production;proteolysis;epidermis development;extracellular matrix disassembly;positive regulation of G protein-coupled receptor signaling pathway;cornification;amelogenesis
• Cellular component: extracellular region;extracellular space;cytosol;secretory granule;epidermal lamellar body
• Molecular function: endopeptidase activity;serine-type endopeptidase activity;protein binding;peptidase activity;serine-type peptidase activity