GZMM

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

Basic information

Region (hg38): 19:544034-549924

Links

ENSG00000197540 ∙ NCBI:3004 ∙ OMIM:600311 ∙ HGNC:4712 ∙ Uniprot:P51124 ∙ 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 GZMM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GZMM 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					1	1
missense			25	1	2	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	3

Variants in GZMM

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

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

Position	Type	Phenotype	Significance	ClinVar
19-544079-C-T		not specified	Uncertain significance (Jan 02, 2024)
19-547327-C-G		not specified	Uncertain significance (Apr 20, 2023)
19-547337-C-T		not specified	Uncertain significance (Oct 30, 2023)
19-547385-T-G		not specified	Uncertain significance (Jan 31, 2024)
19-547414-G-A		not specified	Uncertain significance (Apr 23, 2024)
19-547435-C-T		not specified	Uncertain significance (Jun 10, 2022)
19-548577-C-A		not specified	Uncertain significance (Feb 12, 2025)
19-548582-G-A		not specified	Uncertain significance (May 26, 2023)
19-548586-G-A		not specified	Uncertain significance (May 26, 2024)
19-548591-G-A		not specified	Uncertain significance (Oct 12, 2021)
19-548623-G-T		not specified	Uncertain significance (Oct 27, 2023)
19-548630-C-A			Benign (Dec 31, 2019)
19-548630-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-548662-C-A		not specified	Uncertain significance (Apr 28, 2023)
19-548928-G-C		not specified	Uncertain significance (Jan 09, 2025)
19-548947-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-548955-C-T			Benign (May 31, 2018)
19-549004-G-A		not specified	Uncertain significance (Oct 12, 2024)
19-549012-A-G		not specified	Likely benign (Oct 26, 2021)
19-549022-G-C		not specified	Uncertain significance (Mar 07, 2023)
19-549077-C-T			Benign (Sep 09, 2018)
19-549091-C-A		not specified	Uncertain significance (Oct 03, 2023)
19-549094-G-A		not specified	Uncertain significance (Dec 13, 2022)
19-549180-T-G		not specified	Uncertain significance (May 26, 2023)
19-549181-G-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GZMM	protein_coding	protein_coding	ENST00000264553	5	5886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0113	0.853	125594	2	21	125617	0.0000916

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0733	166	163	1.02	0.0000108	1596
Missense in Polyphen		61	55.157	1.1059		577
Synonymous	-1.00	86	74.9	1.15	0.00000511	568
Loss of Function	1.22	4	7.62	0.525	3.25e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000109
Finnish	0.000323	0.000277
European (Non-Finnish)	0.0000322	0.0000264
Middle Eastern	0.000116	0.000109
South Asian	0.000440	0.000327
Other	0.000199	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves peptide substrates after methionine, leucine, and norleucine. Physiological substrates include EZR, alpha- tubulins and the apoptosis inhibitor BIRC5/Survivin. Promotes caspase activation and subsequent apoptosis of target cells. {ECO:0000269|PubMed:18523284, ECO:0000269|PubMed:20406824}.
• Pathway: Innate Immune System;Immune System;Initial triggering of complement;Complement cascade;Alternative complement activation (Consensus)

Intolerance Scores

• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.38

Haploinsufficiency Scores

• pHI: 0.0569
• 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: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gzmm
• Phenotype: immune system phenotype

Gene ontology

• Biological process: T cell mediated cytotoxicity;proteolysis;apoptotic process;cell death;cytolysis;innate immune response
• Cellular component: extracellular region;membrane
• Molecular function: serine-type endopeptidase activity;protein binding;serine-type peptidase activity