MATN1

matrilin 1, the group of Matrilins

Basic information

Region (hg38): 1:30711276-30723585

Previous symbols: [ "CRTM", "CMP" ]

Links

ENSG00000162510 ∙ NCBI:4146 ∙ OMIM:115437 ∙ HGNC:6907 ∙ Uniprot:P21941 ∙ 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 MATN1 gene.

• Inborn genetic diseases (24 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MATN1 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	2	3
missense			23	1	2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	4

Variants in MATN1

This is a list of pathogenic ClinVar variants found in the MATN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-30713592-G-C		not specified	Likely benign (Jun 22, 2021)
1-30713618-A-C		not specified	Uncertain significance (Aug 02, 2022)
1-30714319-G-C		not specified	Uncertain significance (Jul 20, 2021)
1-30715172-T-G			Benign (Apr 16, 2018)
1-30715956-C-T		not specified	Uncertain significance (Jan 20, 2023)
1-30715957-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-30716066-C-G		not specified	Uncertain significance (Apr 27, 2023)
1-30716089-G-A		not specified	Uncertain significance (Oct 12, 2022)
1-30716119-G-A		not specified	Uncertain significance (Jun 22, 2023)
1-30716151-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-30716197-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-30716205-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-30716213-G-A			Benign (Apr 20, 2018)
1-30716213-G-C		not specified	Uncertain significance (Sep 20, 2023)
1-30716216-C-G		not specified	Uncertain significance (Dec 16, 2023)
1-30716842-G-A			Benign (Feb 01, 2018)
1-30716854-G-A			Likely benign (Sep 01, 2022)
1-30716861-C-A		not specified	Uncertain significance (Nov 04, 2023)
1-30716865-T-A		not specified	Uncertain significance (Oct 03, 2022)
1-30716910-A-G		not specified	Uncertain significance (Feb 06, 2024)
1-30718808-G-T		not specified	Uncertain significance (Oct 13, 2023)
1-30718833-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-30718886-G-T		not specified	Uncertain significance (Nov 17, 2022)
1-30721415-T-C		not specified	Uncertain significance (Jun 21, 2022)
1-30721436-C-A		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MATN1	protein_coding	protein_coding	ENST00000373765	8	12311

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00256	0.984	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.545	271	297	0.911	0.0000180	3215
Missense in Polyphen		107	117.79	0.9084		1241
Synonymous	0.219	126	129	0.976	0.00000815	1027
Loss of Function	2.17	7	16.5	0.424	7.02e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000228	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000274	0.000272
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000274	0.000272
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cartilage matrix protein is a major component of the extracellular matrix of non-articular cartilage. It binds to collagen.
• Pathway: Extracellular matrix organization;ECM proteoglycans (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.329
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.466
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.562

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Matn1
• Phenotype: skeleton phenotype

Zebrafish Information Network

• Gene name: matn1
• Affected structure: chondrocyte
• Phenotype tag: abnormal
• Phenotype quality: distended

Gene ontology

• Biological process: growth plate cartilage chondrocyte morphogenesis;extracellular matrix organization;regulation of bone mineralization;protein-containing complex assembly
• Cellular component: extracellular region;extracellular space;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;calcium ion binding;protein binding