MSRB2
Basic information
Region (hg38): 10:23095579-23122013
Previous symbols: [ "MSRB" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSRB2 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 | 0 | |||||
missense | 19 | 19 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 19 | 0 | 0 |
Variants in MSRB2
This is a list of pathogenic ClinVar variants found in the MSRB2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
10-23095615-C-T | not specified | Uncertain significance (Nov 22, 2023) | ||
10-23095622-T-G | not specified | Uncertain significance (May 06, 2022) | ||
10-23095652-C-T | not specified | Uncertain significance (Apr 08, 2022) | ||
10-23095663-C-T | not specified | Uncertain significance (Mar 16, 2022) | ||
10-23095669-G-A | not specified | Uncertain significance (Mar 23, 2023) | ||
10-23095682-C-A | not specified | Uncertain significance (May 15, 2023) | ||
10-23095700-G-C | not specified | Uncertain significance (Jun 18, 2021) | ||
10-23095702-A-C | not specified | Uncertain significance (Oct 20, 2021) | ||
10-23095721-A-G | not specified | Uncertain significance (Oct 21, 2021) | ||
10-23104176-A-G | not specified | Uncertain significance (Dec 06, 2022) | ||
10-23104218-G-A | not specified | Uncertain significance (Mar 09, 2022) | ||
10-23104221-A-G | not specified | Uncertain significance (Jun 18, 2021) | ||
10-23104237-C-T | not specified | Uncertain significance (Jun 13, 2024) | ||
10-23110265-T-A | not specified | Uncertain significance (Jun 10, 2024) | ||
10-23110293-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
10-23110314-T-C | not specified | Uncertain significance (Nov 06, 2023) | ||
10-23119428-C-T | not specified | Uncertain significance (Dec 17, 2023) | ||
10-23119429-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
10-23120785-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
10-23120839-A-G | not specified | Uncertain significance (Mar 17, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MSRB2 | protein_coding | protein_coding | ENST00000376510 | 5 | 26508 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000554 | 0.466 | 124753 | 1 | 37 | 124791 | 0.000152 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.635 | 75 | 92.2 | 0.814 | 0.00000526 | 1149 |
Missense in Polyphen | 34 | 40.627 | 0.83688 | 469 | ||
Synonymous | 0.967 | 31 | 38.6 | 0.802 | 0.00000253 | 378 |
Loss of Function | 0.403 | 7 | 8.25 | 0.848 | 3.50e-7 | 107 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000559 | 0.000559 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000557 | 0.0000556 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000535 | 0.0000530 |
Middle Eastern | 0.0000557 | 0.0000556 |
South Asian | 0.000459 | 0.000458 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Methionine-sulfoxide reductase that specifically reduces methionine (R)-sulfoxide back to methionine. While in many cases, methionine oxidation is the result of random oxidation following oxidative stress, methionine oxidation is also a post- translational modification that takes place on specific residue. Upon oxidative stress, may play a role in the preservation of mitochondrial integrity by decreasing the intracellular reactive oxygen species build-up through its scavenging role, hence contributing to cell survival and protein maintenance. {ECO:0000269|PubMed:18424444}.;
- Pathway
- S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;Cystathionine Beta-Synthase Deficiency;Sulindac Metabolic Pathway;Methionine De Novo and Salvage Pathway;Metabolism of proteins;Protein repair
(Consensus)
Recessive Scores
- pRec
- 0.167
Intolerance Scores
- loftool
- 0.541
- rvis_EVS
- 0.66
- rvis_percentile_EVS
- 84.35
Haploinsufficiency Scores
- pHI
- 0.188
- hipred
- N
- hipred_score
- 0.284
- ghis
- 0.400
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0242
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Msrb2
- Phenotype
Gene ontology
- Biological process
- actin filament polymerization;protein repair;cellular response to oxidative stress;oxidation-reduction process
- Cellular component
- mitochondrion;cytosol
- Molecular function
- actin binding;zinc ion binding;peptide-methionine (R)-S-oxide reductase activity;L-methionine-(R)-S-oxide reductase activity