MMP19

matrix metallopeptidase 19, the group of M10 matrix metallopeptidases

Basic information

Region (hg38): 12:55835433-55842966

Previous symbols: [ "MMP18" ]

Links

ENSG00000123342

∙ NCBI:4327 ∙ OMIM:601807 ∙ HGNC:7165 ∙ Uniprot:Q99542 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

familial cavitary optic disk anomaly (Limited), mode of inheritance: Unknown
familial cavitary optic disk anomaly (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cavitary optic disc anomalies	AD	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	Ophthalmologic	17368552; 17362864; 25581579

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MMP19 gene.

not_specified (71 variants)
not_provided (10 variants)
Familial_cavitary_optic_disk_anomaly (6 variants)
MMP19-related_disorder (2 variants)
Interstitial_lung_disease_2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002429.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar	1 clinvar	5
missense			61 clinvar	12 clinvar	2 clinvar	75
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	64	16	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP19	protein_coding	protein_coding	ENST00000322569	9	7534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.00e-20	0.000880	125411	0	337	125748	0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.363	284	302	0.941	0.0000173	3268
Missense in Polyphen		122	124.28	0.98164		1366
Synonymous	0.235	115	118	0.973	0.00000670	1024
Loss of Function	-0.366	29	27.0	1.08	0.00000156	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00183	0.00183
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.00250	0.00245
Finnish	0.000418	0.000416
European (Non-Finnish)	0.00183	0.00182
Middle Eastern	0.00250	0.00245
South Asian	0.000333	0.000327
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

Function: FUNCTION: Endopeptidase that degrades various components of the extracellular matrix, such as aggrecan and cartilage oligomeric matrix protein (comp), during development, haemostasis and pathological conditions (arthritic disease). May also play a role in neovascularization or angiogenesis. Hydrolyzes collagen type IV, laminin, nidogen, nascin-C isoform, fibronectin, and type I gelatin. {ECO:0000269|PubMed:10809722, ECO:0000269|PubMed:10922468}.;
Disease: DISEASE: Cavitary optic disc anomalies (CODA) [MIM:611543]: An ocular disease characterized by a profound excavation of the optic nerve. Clinical phenotype is variable and includes congenitally excavated optic nerves as well as other features of optic pit, optic nerve coloboma, and morning glory disk anomaly. Patients with CODA have a strong predilection for retinal detachment and/or separation of the retinal layers (retinoschisis) that lead to profound central vision loss. {ECO:0000269|PubMed:25581579}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Matrix Metalloproteinases;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

pRec: 0.146

Intolerance Scores

loftool
rvis_EVS: -0.13
rvis_percentile_EVS: 44.03

Haploinsufficiency Scores

pHI: 0.442
hipred: N
hipred_score: 0.153
ghis: 0.481

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.206

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mmp19
Phenotype: immune system phenotype; hematopoietic system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); neoplasm; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: angiogenesis;ovarian follicle development;ovulation from ovarian follicle;luteolysis;proteolysis;response to hormone;extracellular matrix disassembly;cell differentiation;extracellular matrix organization;collagen catabolic process;response to cAMP
Cellular component: extracellular region;extracellular space;extracellular matrix
Molecular function: metalloendopeptidase activity;serine-type endopeptidase activity;zinc ion binding