MATR3
matrin 3, the group of Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 5:139293674-139331677
Previous symbols: [ "MPD2" ]
Links
Phenotypes
GenCC
Source:
- amyotrophic lateral sclerosis type 21 (Moderate), mode of inheritance: AD
- amyotrophic lateral sclerosis type 21 (Moderate), mode of inheritance: AD
- amyotrophic lateral sclerosis (Supportive), mode of inheritance: AD
- distal myopathy with vocal cord weakness (Supportive), mode of inheritance: AD
- amyotrophic lateral sclerosis type 21 (Strong), mode of inheritance: AD
- amyotrophic lateral sclerosis type 21 (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Amyotrophic lateral sclerosis 21 | 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 | Audiologic/Otolaryngologic; Musculoskeletal | 9837826; 19344878; 24686783; 25154462 |
ClinVar
This is a list of variants' phenotypes submitted to
- Amyotrophic_lateral_sclerosis_type_21 (441 variants)
- Inborn_genetic_diseases (59 variants)
- not_provided (52 variants)
- MATR3-related_disorder (50 variants)
- not_specified (3 variants)
- Amyotrophic_lateral_sclerosis (3 variants)
- Distal_myopathy_with_vocal_cord_weakness (1 variants)
- Neurodegeneration (1 variants)
- Distal_myopathy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MATR3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018834.6. 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 | 120 | 128 | ||||
| missense | 241 | 12 | 255 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 1 | 0 | 249 | 132 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MATR3 | protein_coding | protein_coding | ENST00000394805 | 14 | 57920 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000144 | 125674 | 0 | 2 | 125676 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.73 | 289 | 452 | 0.639 | 0.0000230 | 5613 |
| Missense in Polyphen | 100 | 235.26 | 0.42505 | 3004 | ||
| Synonymous | 0.0141 | 159 | 159 | 0.999 | 0.00000845 | 1568 |
| Loss of Function | 5.68 | 0 | 37.5 | 0.00 | 0.00000183 | 507 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in transcription or may interact with other nuclear matrix proteins to form the internal fibrogranular network. In association with the SFPQ-NONO heteromer may play a role in nuclear retention of defective RNAs. Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). May bind to specific miRNA hairpins (PubMed:28431233). {ECO:0000269|PubMed:11525732, ECO:0000269|PubMed:28431233, ECO:0000269|PubMed:28712728}.;
- Disease
- DISEASE: Amyotrophic lateral sclerosis 21 (ALS21) [MIM:606070]: A neurodegenerative disorder affecting upper and lower motor neurons, resulting in muscle weakness and respiratory failure. Some patients may develop myopathic features or dementia. {ECO:0000269|PubMed:19344878, ECO:0000269|PubMed:24686783, ECO:0000269|PubMed:25771394, ECO:0000269|PubMed:26199109}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;antisense pathway
(Consensus)
Intolerance Scores
- loftool
- 0.217
- rvis_EVS
- -0.65
- rvis_percentile_EVS
- 16.36
Haploinsufficiency Scores
- pHI
- 0.726
- hipred
- Y
- hipred_score
- 0.686
- ghis
- 0.718
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Matr3
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype;
Gene ontology
- Biological process
- activation of innate immune response;posttranscriptional regulation of gene expression;innate immune response
- Cellular component
- nuclear inner membrane;membrane;nuclear matrix
- Molecular function
- RNA binding;structural molecule activity;protein binding;zinc ion binding;miRNA binding;identical protein binding