MMP16

matrix metallopeptidase 16, the group of M10 matrix metallopeptidases

Basic information

Region (hg38): 8:88032010-88328025

Previous symbols: [ "C8orf57" ]

Links

ENSG00000156103 ∙ NCBI:4325 ∙ OMIM:602262 ∙ HGNC:7162 ∙ Uniprot:P51512 ∙ 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 MMP16 gene.

• Inborn genetic diseases (11 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP16 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	11	0	3

Variants in MMP16

This is a list of pathogenic ClinVar variants found in the MMP16 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-88039069-C-T			Benign (Oct 29, 2020)
8-88056203-C-G		not specified	Uncertain significance (Jan 19, 2022)
8-88056249-T-C		not specified	Uncertain significance (Feb 17, 2023)
8-88074617-C-A		not specified	Uncertain significance (Feb 28, 2024)
8-88074626-C-T		not specified	Uncertain significance (Oct 06, 2023)
8-88074655-C-T		not specified	Uncertain significance (Jan 23, 2024)
8-88074671-G-A		not specified	Uncertain significance (Feb 22, 2023)
8-88074696-G-A			Benign (Aug 16, 2018)
8-88074721-C-T		not specified	Uncertain significance (Sep 20, 2023)
8-88074728-G-A			Uncertain significance (Feb 01, 2024)
8-88116529-C-T		not specified	Uncertain significance (Mar 23, 2022)
8-88116581-C-T		not specified	Uncertain significance (Jul 19, 2023)
8-88116661-C-T		not specified	Uncertain significance (Mar 06, 2023)
8-88118746-G-T		not specified	Uncertain significance (Nov 17, 2022)
8-88167930-T-G		not specified	Uncertain significance (Sep 12, 2023)
8-88186546-T-G		not specified	Uncertain significance (Dec 20, 2021)
8-88186584-G-A		not specified	Uncertain significance (Nov 30, 2022)
8-88186601-GCAA-G			Likely benign (Dec 31, 2019)
8-88197209-T-G		not specified	Uncertain significance (Sep 16, 2021)
8-88327105-G-C			Benign (May 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP16	protein_coding	protein_coding	ENST00000286614	10	296018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.918	0.0820	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.52	163	348	0.469	0.0000185	4003
Missense in Polyphen		43	157.01	0.27387		1788
Synonymous	0.535	110	117	0.937	0.00000624	1140
Loss of Function	4.24	5	30.1	0.166	0.00000159	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000580	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.0000580	0.0000544
South Asian	0.0000654	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endopeptidase that degrades various components of the extracellular matrix, such as collagen type III and fibronectin. Activates progelatinase A. Involved in the matrix remodeling of blood vessels. Isoform short cleaves fibronectin and also collagen type III, but at lower rate. It has no effect on type I, II, IV and V collagen. However, upon interaction with CSPG4, it may be involved in degradation and invasion of type I collagen by melanoma cells. {ECO:0000269|PubMed:11278606}.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);Matrix Metalloproteinases;Extracellular matrix organization;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.338
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.216
• hipred: Y
• hipred_score: 0.768
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.556

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmp16
• Phenotype: growth/size/body region phenotype; vision/eye phenotype; craniofacial phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: skeletal system development;endochondral ossification;proteolysis;protein processing;protein metabolic process;extracellular matrix disassembly;extracellular matrix organization;collagen catabolic process;chondrocyte proliferation;positive regulation of catalytic activity;embryonic cranial skeleton morphogenesis;craniofacial suture morphogenesis
• Cellular component: extracellular space;Golgi lumen;plasma membrane;integral component of plasma membrane;cell surface;extracellular matrix
• Molecular function: metalloendopeptidase activity;enzyme activator activity;zinc ion binding;metalloaminopeptidase activity