GZMK

granzyme K, the group of Granule associated serine proteases of immune defence

Basic information

Region (hg38): 5:55024256-55034570

Links

ENSG00000113088 ∙ NCBI:3003 ∙ OMIM:600784 ∙ HGNC:4711 ∙ Uniprot:P49863 ∙ 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 GZMK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GZMK 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in GZMK

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

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

Position	Type	Phenotype	Significance	ClinVar
5-55024360-T-C		not specified	Uncertain significance (Apr 29, 2024)
5-55024681-G-A		not specified	Uncertain significance (Feb 27, 2023)
5-55024693-T-A		not specified	Uncertain significance (Mar 28, 2024)
5-55024747-T-C		not specified	Uncertain significance (Dec 03, 2021)
5-55024756-G-T		not specified	Uncertain significance (Apr 13, 2023)
5-55030540-A-G		not specified	Uncertain significance (Dec 09, 2023)
5-55031443-A-G		not specified	Uncertain significance (Jan 26, 2023)
5-55031472-G-A		not specified	Likely benign (Mar 29, 2024)
5-55031589-A-C		not specified	Uncertain significance (Dec 19, 2022)
5-55033807-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-55033847-A-C		not specified	Uncertain significance (Feb 15, 2023)
5-55033858-T-C		not specified	Uncertain significance (Nov 12, 2021)
5-55033880-A-G		not specified	Uncertain significance (Mar 17, 2023)
5-55033900-A-G		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GZMK	protein_coding	protein_coding	ENST00000231009	5	10318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00815	0.937	125673	0	72	125745	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.318	132	143	0.925	0.00000706	1701
Missense in Polyphen		58	58.34	0.99416		682
Synonymous	-0.321	57	54.0	1.06	0.00000293	528
Loss of Function	1.66	5	10.9	0.458	6.09e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00294	0.00294
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000662	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.303
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.144
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0788

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gzmk

Gene ontology

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