MATN2

protein-coding

matrilin 2, the group of Matrilins

Gene summary

This gene encodes a member of the von Willebrand factor A domain containing protein family. This family of proteins is thought to be involved in the formation of filamentous networks in the extracellular matrices of various tissues. This protein contains five von Willebrand factor A domains. The specific function of this gene has not yet been determined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002380.5

Inheritance

—

ClinVar variants

U:139B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr8:97,868,840-98,036,724

External References & Databases

Ensembl (ENSG00000132561)

Transcript & Mutation Effects

hg38 • Region Span ~167.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MATN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 131

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002380.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	1 clinvar	3
missense			134 clinvar	3 clinvar	1 clinvar	138
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	139	4	2	145

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 80 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002380.5	RefSeq	NP_002371.3	18	MANE Select
ENST00000254898.7	Ensembl	ENSP00000254898.6	18	MANE Select
NM_001317748.2	RefSeq	NP_001304677.1	17	Standard
NM_030583.4	RefSeq	NP_085072.2	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

neuron migration
growth plate cartilage chondrocyte morphogenesis
axon guidance
biological_process
glial cell migration

Molecular Function

extracellular matrix structural constituent
calcium ion binding
protein binding

Cellular Component

basement membrane
extracellular space
extracellular matrix
collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000520016
Coding exons: 18
Length: 167877
Individuals with no LoFs: 124751
Homozygous LoFs: 0
Heterozygous LoFs: 122
Defined: 124873
p: 0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	437	547	0.799	0.0000313	6300
Missense (PolyPhen)		151	204.96	0.73674		2379
Synonymous	1.34	191	216	0.884	0.0000136	1756
Loss of Function	2.22	28	43.9	0.638	0.00000229	556

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00071	0.00070	rare
Latino/Admixed American	0.0010	0.00099	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00074	0.00072	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00042	0.00039	rare
South Asian	0.00050	0.00049	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in matrix assembly. {ECO:0000250}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.153
RVIS EVS: 1.21
RVIS percentile EVS: 93.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.696

Gene Damage Prediction

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