KLK12

kallikrein related peptidase 12, the group of Kallikreins

Basic information

Region (hg38): 19:51029092-51035230

Links

ENSG00000186474 ∙ NCBI:43849 ∙ OMIM:605539 ∙ HGNC:6360 ∙ Uniprot:Q9UKR0 ∙ 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 KLK12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLK12 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					2	2
missense			20	4		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	4	2

Variants in KLK12

This is a list of pathogenic ClinVar variants found in the KLK12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51029324-C-T		not specified	Likely benign (Jan 03, 2022)
19-51029325-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-51029375-T-A		not specified	Uncertain significance (Nov 18, 2023)
19-51029457-C-A		not specified	Uncertain significance (Dec 05, 2022)
19-51030836-C-T		not specified	Likely benign (May 20, 2024)
19-51031878-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-51031879-G-A		not specified	Likely benign (Dec 02, 2022)
19-51031918-C-T		not specified	Likely benign (Oct 16, 2023)
19-51031921-T-A		not specified	Uncertain significance (Dec 19, 2022)
19-51031932-G-T		not specified	Uncertain significance (Jul 22, 2022)
19-51031941-T-C		not specified	Likely benign (Oct 27, 2022)
19-51031963-C-T		not specified	Uncertain significance (May 16, 2024)
19-51031981-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-51031990-G-A		not specified	Uncertain significance (Nov 14, 2023)
19-51032009-G-C		not specified	Uncertain significance (Oct 05, 2021)
19-51032017-C-T		not specified	Uncertain significance (Mar 16, 2022)
19-51032027-C-T			Benign (May 09, 2018)
19-51032065-C-T		not specified	Uncertain significance (May 15, 2024)
19-51032066-G-T		not specified	Uncertain significance (Feb 06, 2023)
19-51032092-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-51032107-T-C		not specified	Uncertain significance (Nov 21, 2023)
19-51033998-G-A		not specified	Uncertain significance (Nov 02, 2023)
19-51033999-C-A		not specified	Uncertain significance (Nov 02, 2023)
19-51034008-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-51034053-C-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLK12	protein_coding	protein_coding	ENST00000250351	6	6139

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000317	0.583	25738	41678	58332	125748	0.548

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.330	168	156	1.07	0.0000107	1616
Missense in Polyphen		68	57.027	1.1924		646
Synonymous	0.173	67	68.8	0.973	0.00000524	536
Loss of Function	0.731	8	10.6	0.757	4.62e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.976	0.960
Ashkenazi Jewish	0.551	0.535
East Asian	0.660	0.662
Finnish	0.531	0.519
European (Non-Finnish)	0.589	0.539
Middle Eastern	0.660	0.662
South Asian	0.620	0.613
Other	0.597	0.579

dbNSFP

Source: dbNSFP

• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.130
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.0506
• hipred: N
• hipred_score: 0.146

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: Klk12

Gene ontology

• Biological process: proteolysis;cornification
• Cellular component: extracellular region;extracellular space;secretory granule
• Molecular function: serine-type endopeptidase activity;peptidase activity;serine-type peptidase activity