AMZ1

archaelysin family metallopeptidase 1, the group of M54 metallopeptidase family

Basic information

Region (hg38): 7:2679521-2775500

Links

ENSG00000174945 ∙ NCBI:155185 ∙ OMIM:615168 ∙ HGNC:22231 ∙ Uniprot:Q400G9 ∙ 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 AMZ1 gene.

• Inborn genetic diseases (41 variants)
• not provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMZ1 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	4	5
missense			39	6	3	48
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	39	8	7

Variants in AMZ1

This is a list of pathogenic ClinVar variants found in the AMZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-2700470-G-T		not specified	Uncertain significance (Jul 12, 2022)
7-2700488-G-A		not specified	Uncertain significance (Apr 08, 2022)
7-2700507-A-T		not specified	Uncertain significance (Feb 22, 2023)
7-2700508-C-A		not specified	Uncertain significance (Feb 22, 2023)
7-2700666-A-C		not specified	Uncertain significance (Apr 07, 2022)
7-2700695-G-A		not specified	Uncertain significance (Oct 05, 2022)
7-2700750-C-T		not specified	Uncertain significance (May 18, 2022)
7-2702737-C-T		not specified	Uncertain significance (Jan 07, 2022)
7-2702742-G-A		not specified	Uncertain significance (Mar 06, 2023)
7-2702754-C-A		not specified	Uncertain significance (Jun 22, 2023)
7-2702815-C-T		not specified	Uncertain significance (Jun 29, 2022)
7-2702859-C-T		not specified	Uncertain significance (Dec 09, 2023)
7-2702860-G-A		not specified	Likely benign (Apr 08, 2022)
7-2702871-A-G		not specified	Uncertain significance (Apr 25, 2023)
7-2702880-C-T		not specified	Uncertain significance (Feb 09, 2023)
7-2708599-T-A		not specified	Uncertain significance (May 24, 2023)
7-2708622-A-G			Likely benign (Jun 29, 2018)
7-2708678-C-A		not specified	Uncertain significance (Nov 03, 2023)
7-2709063-ATC-A			Benign (Jun 04, 2018)
7-2709098-C-T		not specified	Uncertain significance (Aug 16, 2022)
7-2709134-G-A			Likely benign (Aug 11, 2018)
7-2709153-T-C			Likely benign (Aug 15, 2018)
7-2709162-C-T		not specified	Uncertain significance (Oct 13, 2023)
7-2709196-G-T		not specified	Uncertain significance (May 24, 2023)
7-2709202-G-C		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMZ1	protein_coding	protein_coding	ENST00000312371	6	95979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.71e-23	0.0000112	125608	1	127	125736	0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.59	485	308	1.58	0.0000208	3143
Missense in Polyphen		122	82.009	1.4876		885
Synonymous	-4.68	212	141	1.50	0.0000103	1032
Loss of Function	-2.36	28	17.4	1.61	8.33e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00223	0.00219
Ashkenazi Jewish	0.00	0.00
East Asian	0.000390	0.000381
Finnish	0.000197	0.000185
European (Non-Finnish)	0.000553	0.000519
Middle Eastern	0.000390	0.000381
South Asian	0.000393	0.000359
Other	0.000499	0.000489

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.84

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.146
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.263

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amz1

Gene ontology

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