AMZ2

archaelysin family metallopeptidase 2, the group of M54 metallopeptidase family

Basic information

Region (hg38): 17:68205481-68257712

Links

ENSG00000196704 ∙ NCBI:51321 ∙ OMIM:615169 ∙ HGNC:28041 ∙ Uniprot:Q86W34 ∙ 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 AMZ2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMZ2 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	4
missense			18	1	2	21
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	18	4	4

Variants in AMZ2

This is a list of pathogenic ClinVar variants found in the AMZ2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-68250205-C-G		not specified	Uncertain significance (Jul 11, 2023)
17-68250209-G-A		not specified	Uncertain significance (Sep 29, 2022)
17-68250216-C-A		not specified	Uncertain significance (Nov 19, 2022)
17-68250225-C-T		not specified	Uncertain significance (Mar 15, 2024)
17-68250242-A-G		not specified	Uncertain significance (Dec 11, 2023)
17-68250273-T-C		not specified	Uncertain significance (Jun 13, 2024)
17-68250275-A-G		AMZ2-related disorder	Benign (Oct 17, 2019)
17-68250282-G-A		not specified	Uncertain significance (Oct 06, 2021)
17-68250291-G-A		not specified	Uncertain significance (Jun 24, 2022)
17-68250303-A-G		not specified	Uncertain significance (Apr 25, 2022)
17-68250309-T-C		not specified	Uncertain significance (Dec 15, 2023)
17-68250350-T-C		not specified	Uncertain significance (Dec 08, 2023)
17-68250446-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-68250449-A-G		not specified	Uncertain significance (May 20, 2024)
17-68250820-A-G		not specified	Uncertain significance (Mar 08, 2024)
17-68250846-G-A			Likely benign (Jun 01, 2022)
17-68251051-G-A		AMZ2-related disorder	Likely benign (Feb 19, 2019)
17-68251103-G-A		not specified	Uncertain significance (Apr 19, 2023)
17-68251103-G-T		not specified	Uncertain significance (Mar 28, 2024)
17-68251113-C-A		Monoclonal B-Cell Lymphocytosis	Uncertain significance (Dec 15, 2015)
17-68251186-G-A		AMZ2-related disorder	Likely benign (Feb 20, 2019)
17-68254411-G-T		AMZ2-related disorder	Benign (Mar 22, 2019)
17-68254524-A-T		not specified	Uncertain significance (Feb 15, 2023)
17-68255717-C-T		AMZ2-related disorder	Likely benign (Sep 18, 2019)
17-68255755-C-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMZ2	protein_coding	protein_coding	ENST00000359904	6	9583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.07e-9	0.137	125547	0	201	125748	0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.218	185	194	0.956	0.00000986	2367
Missense in Polyphen		47	51.273	0.91666		687
Synonymous	1.42	55	70.1	0.784	0.00000368	663
Loss of Function	0.267	14	15.1	0.926	7.82e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000957	0.000954
Ashkenazi Jewish	0.00576	0.00577
East Asian	0.00164	0.00163
Finnish	0.000602	0.000601
European (Non-Finnish)	0.000564	0.000563
Middle Eastern	0.00164	0.00163
South Asian	0.000300	0.000294
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Zinc metalloprotease. Exhibits activity against angiotensin-3 in vitro. Does not hydrolyze either neurogranin or angiotensin-2. {ECO:0000269|PubMed:15972818}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.995
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.167
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0222

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amz2

Gene ontology

• Biological process: proteolysis
• Cellular component: cellular_component
• Molecular function: peptidase activity;metallopeptidase activity;zinc ion binding