MMP15

matrix metallopeptidase 15, the group of M10 matrix metallopeptidases

Basic information

Region (hg38): 16:58025753-58046901

Links

ENSG00000102996 ∙ NCBI:4324 ∙ OMIM:602261 ∙ HGNC:7161 ∙ Uniprot:P51511 ∙ 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 MMP15 gene.

• Inborn genetic diseases (45 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP15 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	2
missense			44	1		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					1	1
Total	0	0	45	2	2

Variants in MMP15

This is a list of pathogenic ClinVar variants found in the MMP15 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-58026375-G-A		not specified	Uncertain significance (Apr 28, 2022)
16-58026382-C-G		not specified	Uncertain significance (May 08, 2023)
16-58026391-C-G		not specified	Uncertain significance (Aug 13, 2021)
16-58026397-G-C		not specified	Uncertain significance (Jun 11, 2021)
16-58026490-A-C		not specified	Uncertain significance (Mar 21, 2022)
16-58037481-C-T		not specified	Uncertain significance (Nov 30, 2022)
16-58037482-G-A		not specified	Uncertain significance (Sep 19, 2022)
16-58037512-G-A		not specified	Uncertain significance (Sep 22, 2022)
16-58037526-A-C		not specified	Uncertain significance (May 24, 2023)
16-58037607-G-A		not specified	Uncertain significance (Dec 28, 2023)
16-58038282-C-A		not specified	Uncertain significance (Jan 04, 2024)
16-58038306-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-58038313-G-A		not specified	Uncertain significance (Feb 21, 2024)
16-58038331-G-A		not specified	Uncertain significance (Nov 09, 2021)
16-58039889-C-T		not specified	Uncertain significance (May 08, 2023)
16-58039928-G-A		not specified	Uncertain significance (Jan 30, 2024)
16-58039939-C-T		not specified	Uncertain significance (May 09, 2023)
16-58039968-C-T			Likely benign (May 31, 2018)
16-58039996-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-58039997-G-A		not specified	Uncertain significance (May 05, 2023)
16-58040011-A-G		not specified	Uncertain significance (Dec 19, 2022)
16-58040101-T-G		not specified	Uncertain significance (Nov 20, 2023)
16-58040181-T-A		not specified	Uncertain significance (Dec 16, 2023)
16-58040645-T-C		not specified	Uncertain significance (May 31, 2023)
16-58040665-G-A		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP15	protein_coding	protein_coding	ENST00000219271	10	21336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0734	0.927	125724	0	22	125746	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	374	453	0.825	0.0000328	4289
Missense in Polyphen		104	150.54	0.69084		1281
Synonymous	-1.00	209	191	1.09	0.0000143	1384
Loss of Function	3.73	8	30.0	0.266	0.00000172	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.00	0.00
Finnish	0.000145	0.000139
European (Non-Finnish)	0.0000834	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endopeptidase that degrades various components of the extracellular matrix. May activate progelatinase A. {ECO:0000269|PubMed:9461298}.
• Pathway: Matrix Metalloproteinases;EMT transition in Colorectal Cancer;Collagen degradation;Extracellular matrix organization;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.521
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.02

Haploinsufficiency Scores

• pHI: 0.0810
• hipred: Y
• hipred_score: 0.728
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmp15
• Phenotype: embryo phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cellular protein modification process;proteolysis;extracellular matrix disassembly;extracellular matrix organization;collagen catabolic process;response to estradiol;endodermal cell differentiation;positive regulation of catalytic activity
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane;extracellular matrix
• Molecular function: metalloendopeptidase activity;protein binding;enzyme activator activity;zinc ion binding;metalloaminopeptidase activity