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.

• Inborn_genetic_diseases (76 variants)
• Amelogenesis_imperfecta_hypomaturation_type_2A2 (57 variants)
• not_provided (21 variants)
• MMP20-related_disorder (8 variants)
• Amelogenesis_Imperfecta,_Recessive (3 variants)
• not_specified (1 variants)
• Schizophrenia (1 variants)
• Intellectual_disability,_autosomal_dominant_56 (1 variants)

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. These statistics are base on transcript: NM_000004771.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous	1		13	5	1	20
missense	4	2	90	8	1	105
nonsense	2	2				4
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)	2					2
Total	9	5	103	13	2

Highest pathogenic variant AF is 0.0023370972

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