MATN4

matrilin 4, the group of Matrilins

Basic information

Region (hg38): 20:45293444-45308529

Links

ENSG00000124159 ∙ NCBI:8785 ∙ OMIM:603897 ∙ HGNC:6910 ∙ Uniprot:O95460 ∙ 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 MATN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MATN4 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	4	5
missense			38	3	4	45
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding			3		2	5
Total	0	0	41	5	10

Variants in MATN4

This is a list of pathogenic ClinVar variants found in the MATN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45293763-G-A		MATN4-related disorder	Benign (Oct 28, 2019)
20-45293788-G-T		MATN4-related disorder	Benign (Oct 28, 2019)
20-45293832-G-T		Holoprosencephaly sequence	Uncertain significance (Apr 30, 2021)
20-45293914-G-T		MATN4-related disorder	Likely benign (Aug 01, 2022)
20-45293944-G-A		MATN4-related disorder	Benign/Likely benign (Jan 02, 2020)
20-45293992-C-T		not specified	Uncertain significance (Feb 17, 2024)
20-45293994-G-C		not specified	Uncertain significance (Jun 16, 2024)
20-45293997-C-T		MATN4-related disorder	Benign (May 08, 2019)
20-45297911-C-T		MATN4-related disorder	Likely benign (Nov 26, 2019)
20-45297920-G-A		not specified	Uncertain significance (Dec 19, 2023)
20-45297926-A-T		not specified	Uncertain significance (Jul 19, 2023)
20-45297933-C-T		MATN4-related disorder	Benign (Oct 17, 2019)
20-45297977-G-A		not specified	Uncertain significance (May 11, 2022)
20-45297981-A-G		not specified	Uncertain significance (Mar 25, 2024)
20-45298022-A-C		not specified	Uncertain significance (Jun 07, 2024)
20-45298166-C-G		MATN4-related disorder	Likely benign (Feb 22, 2019)
20-45298247-G-A		not specified	Uncertain significance (Apr 05, 2023)
20-45298260-C-G		not specified	Uncertain significance (Dec 28, 2022)
20-45298284-C-T		not specified	Uncertain significance (Oct 27, 2022)
20-45298285-G-A		MATN4-related disorder	Likely benign (Jun 04, 2019)
20-45298307-T-C		not specified	Uncertain significance (Mar 31, 2023)
20-45298344-T-G		not specified	Uncertain significance (May 31, 2023)
20-45298353-C-T		not specified	Uncertain significance (Sep 06, 2022)
20-45298364-G-A		not specified	Uncertain significance (Apr 12, 2022)
20-45298400-A-G		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MATN4	protein_coding	protein_coding	ENST00000537548	9	15085

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-8	0.785	125404	2	342	125748	0.00137

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	340	404	0.843	0.0000289	3709
Missense in Polyphen		136	171.31	0.79387		1553
Synonymous	2.05	148	183	0.807	0.0000145	1203
Loss of Function	1.49	16	23.8	0.672	0.00000127	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00215
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000234	0.000217
Finnish	0.000232	0.000231
European (Non-Finnish)	0.00215	0.00208
Middle Eastern	0.000234	0.000217
South Asian	0.000726	0.000719
Other	0.00198	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major component of the extracellular matrix of cartilage.
• Pathway: Extracellular matrix organization;ECM proteoglycans (Consensus)

Intolerance Scores

• loftool: 0.122
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.85

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.399
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.783

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Matn4

Gene ontology

• Biological process: growth plate cartilage chondrocyte morphogenesis;extracellular matrix organization
• Cellular component: extracellular region;extracellular space;extracellular matrix
• Molecular function: calcium ion binding;protein binding