MATN2

matrilin 2, the group of Matrilins

Basic information

Region (hg38): 8:97868839-98036724

Links

ENSG00000132561 ∙ NCBI:4147 ∙ OMIM:602108 ∙ HGNC:6908 ∙ Uniprot:O00339 ∙ 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 MATN2 gene.

• Inborn genetic diseases (42 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MATN2 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			40	2	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	3	2

Variants in MATN2

This is a list of pathogenic ClinVar variants found in the MATN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-97888117-C-T		not specified	Likely benign (May 11, 2022)
8-97888141-G-C			Benign (Jul 06, 2018)
8-97930985-G-A		not specified	Uncertain significance (Sep 28, 2022)
8-97931001-G-T		not specified	Uncertain significance (Nov 18, 2023)
8-97931055-A-T		not specified	Uncertain significance (Jan 02, 2024)
8-97931121-C-T		not specified	Uncertain significance (May 04, 2022)
8-97931175-G-A		not specified	Uncertain significance (Aug 04, 2023)
8-97931192-C-T		not specified	Uncertain significance (Feb 22, 2023)
8-97931218-T-G			Benign (Jul 06, 2018)
8-97931271-C-T		not specified	Uncertain significance (May 06, 2022)
8-97931274-G-A		not specified	Uncertain significance (Feb 17, 2023)
8-97931300-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-97931303-A-T		not specified	Uncertain significance (Apr 06, 2023)
8-97941777-C-T		not specified	Uncertain significance (Jun 22, 2023)
8-97941780-C-T		not specified	Likely benign (Jan 05, 2022)
8-97941810-G-T		not specified	Uncertain significance (May 23, 2023)
8-97961439-C-G		not specified	Uncertain significance (Dec 02, 2022)
8-97961476-G-A		not specified	Uncertain significance (Mar 21, 2023)
8-97978930-T-C		not specified	Uncertain significance (Feb 03, 2022)
8-97978968-T-A		not specified	Uncertain significance (Dec 27, 2023)
8-97978982-T-G		not specified	Uncertain significance (Dec 18, 2023)
8-97979000-C-T		not specified	Uncertain significance (Mar 02, 2023)
8-97994561-T-C		not specified	Uncertain significance (May 09, 2023)
8-98003762-C-A		not specified	Uncertain significance (Aug 04, 2023)
8-98007159-C-T		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MATN2	protein_coding	protein_coding	ENST00000520016	18	167877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.25e-14	0.944	124751	0	122	124873	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	437	547	0.799	0.0000313	6300
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00172	0.00170
Ashkenazi Jewish	0.00	0.00
East Asian	0.000735	0.000723
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000422	0.000389
Middle Eastern	0.000735	0.000723
South Asian	0.000496	0.000490
Other	0.000344	0.000329

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.331
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.696

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Matn2
• Phenotype: normal phenotype

Gene ontology

• Biological process: neuron migration;growth plate cartilage chondrocyte morphogenesis;axon guidance;biological_process;glial cell migration;dendrite regeneration;response to axon injury
• Cellular component: basement membrane;extracellular space;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;calcium ion binding;protein binding