MMP20

matrix metallopeptidase 20, the group of M10 matrix metallopeptidases

Basic information

Region (hg38): 11:102576832-102625332

Links

ENSG00000137674 ∙ NCBI:9313 ∙ OMIM:604629 ∙ HGNC:7167 ∙ Uniprot:O60882 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amelogenesis imperfecta hypomaturation type 2A2 (Moderate), mode of inheritance: AR
• amelogenesis imperfecta hypomaturation type 2A2 (Strong), mode of inheritance: AR
• amelogenesis imperfecta type 2 (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, hypomaturation type, IIA2	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dental	3150442; 15744043; 21597265; 23355523

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MMP20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP20 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			10	4		14
missense		1	53	2	4	60
nonsense		2	1			3
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	1	1	4
non coding			14	1	45	60
Total	0	4	78	7	49

Variants in MMP20

This is a list of pathogenic ClinVar variants found in the MMP20 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-102576842-A-G		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 12, 2018)
11-102576845-T-C		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102576861-T-C		Amelogenesis Imperfecta, Recessive	Uncertain significance (Jun 14, 2016)
11-102576899-T-A		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102576914-C-T		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102577027-C-T		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102577058-A-G		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102577099-T-G		Amelogenesis imperfecta hypomaturation type 2A2	Benign (Jun 20, 2021)
11-102577216-T-A		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 12, 2018)
11-102577348-G-C		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 12, 2018)
11-102577354-A-G		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102577356-C-T		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102577360-C-T		Amelogenesis imperfecta hypomaturation type 2A2	Uncertain significance (Jan 13, 2018)
11-102577387-T-C		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
11-102577412-A-G		Amelogenesis imperfecta hypomaturation type 2A2 • Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
11-102577416-G-C		Amelogenesis imperfecta hypomaturation type 2A2	Likely pathogenic (Mar 01, 2023)
11-102577525-A-G			Benign (Nov 12, 2018)
11-102577753-C-T			Benign (Jun 19, 2021)
11-102578736-AAAAAAAC-A			Benign (Jun 19, 2021)
11-102578736-AAAAAAACAAAAAAC-A			Benign (Jun 19, 2021)
11-102578780-A-AAC			Benign (Jun 21, 2021)
11-102578792-C-CAA			Benign (Jun 19, 2021)
11-102578800-A-AAAAC			Benign (Jun 19, 2021)
11-102578919-T-A			Benign (Jun 19, 2021)
11-102579060-C-T		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP20	protein_coding	protein_coding	ENST00000260228	10	48498

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.08e-14	0.0303	125422	0	326	125748	0.00130

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.567	301	275	1.10	0.0000152	3172
Missense in Polyphen		96	94.936	1.0112		1064
Synonymous	-1.75	126	103	1.22	0.00000619	930
Loss of Function	0.222	21	22.1	0.949	9.41e-7	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00181	0.00179
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.000235	0.000231
European (Non-Finnish)	0.00211	0.00201
Middle Eastern	0.000761	0.000761
South Asian	0.000425	0.000425
Other	0.00205	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Degrades amelogenin, the major protein component of the enamel matrix and two of the macromolecules characterizing the cartilage extracellular matrix: aggrecan and the cartilage oligomeric matrix protein (COMP). May play a central role in tooth enamel formation. Cleaves aggrecan at the '360-Asn-|-Phe-361' site. {ECO:0000269|PubMed:10922468, ECO:0000269|PubMed:9398237}.
• Disease: DISEASE: Amelogenesis imperfecta, hypomaturation type, 2A2 (AI2A2) [MIM:612529]: A defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel. {ECO:0000269|PubMed:15744043}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Matrix Metalloproteinases;Assembly of collagen fibrils and other multimeric structures;Collagen degradation;Collagen formation;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.97

Haploinsufficiency Scores

• pHI: 0.0608
• hipred: N
• hipred_score: 0.197

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0774

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmp20
• Phenotype: growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: proteolysis;extracellular matrix disassembly;protein catabolic process;extracellular matrix organization;collagen catabolic process;regulation of enamel mineralization;amelogenesis
• Cellular component: extracellular region;extracellular space;extracellular matrix
• Molecular function: metalloendopeptidase activity;serine-type endopeptidase activity;protein binding;zinc ion binding