KLK13

kallikrein related peptidase 13, the group of Kallikreins

Basic information

Region (hg38): 19:51055626-51065114

Links

ENSG00000167759 ∙ NCBI:26085 ∙ OMIM:605505 ∙ HGNC:6361 ∙ Uniprot:Q9UKR3 ∙ 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 KLK13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLK13 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in KLK13

This is a list of pathogenic ClinVar variants found in the KLK13 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51056633-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-51056645-C-T		not specified	Uncertain significance (Jan 03, 2022)
19-51056646-G-T		not specified	Uncertain significance (Aug 02, 2021)
19-51056672-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-51056733-C-T		not specified	Uncertain significance (Mar 20, 2023)
19-51058554-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-51058611-T-C		not specified	Uncertain significance (Apr 06, 2023)
19-51058615-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-51058633-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-51058648-C-T		not specified	Uncertain significance (Jun 18, 2021)
19-51059867-T-G		not specified	Uncertain significance (Oct 21, 2021)
19-51059894-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-51059917-T-G		not specified	Uncertain significance (Jul 05, 2023)
19-51059927-G-A		not specified	Uncertain significance (May 03, 2023)
19-51059938-G-T		not specified	Uncertain significance (Oct 12, 2022)
19-51059941-T-G		not specified	Uncertain significance (May 25, 2022)
19-51059984-T-G		not specified	Uncertain significance (Aug 10, 2021)
19-51059995-C-T		not specified	Likely benign (Aug 10, 2021)
19-51060004-G-A		not specified	Uncertain significance (Aug 05, 2023)
19-51060017-A-C		not specified	Uncertain significance (Sep 06, 2022)
19-51060047-C-T		not specified	Uncertain significance (Nov 22, 2023)
19-51060053-C-T		not specified	Uncertain significance (Apr 28, 2023)
19-51060059-C-A		not specified	Uncertain significance (Jan 10, 2023)
19-51060074-C-T		not specified	Uncertain significance (Aug 22, 2023)
19-51060443-A-G		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLK13	protein_coding	protein_coding	ENST00000595793	5	8909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00454	0.885	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.384	148	162	0.915	0.00000924	1752
Missense in Polyphen		55	67.262	0.8177		781
Synonymous	0.772	57	64.9	0.878	0.00000343	594
Loss of Function	1.35	5	9.50	0.526	4.03e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000549	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Keratinization;Developmental Biology;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0997

Intolerance Scores

• loftool: 0.199
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.0478
• hipred: N
• hipred_score: 0.487
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.689

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klk13

Gene ontology

• Biological process: proteolysis;protein processing;cornification
• Cellular component: extracellular region;extracellular space;cytoplasm;secretory granule
• Molecular function: serine-type endopeptidase activity;protein binding;hydrolase activity