MSI2
Basic information
Region (hg38): 17:57255851-57684689
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSI2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138962.4. 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 | 0 | |||||
| missense | 23 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 23 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MSI2 | protein_coding | protein_coding | ENST00000284073 | 13 | 428835 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.995 | 0.00522 | 124973 | 0 | 2 | 124975 | 0.00000800 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.29 | 114 | 206 | 0.552 | 0.0000121 | 2159 |
| Missense in Polyphen | 25 | 74.052 | 0.3376 | 835 | ||
| Synonymous | -0.0586 | 81 | 80.3 | 1.01 | 0.00000566 | 610 |
| Loss of Function | 3.94 | 1 | 20.0 | 0.0500 | 9.10e-7 | 248 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000893 | 0.00000888 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000333 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system (By similarity). {ECO:0000250}.;
- Disease
- DISEASE: Note=Chromosomal aberrations involving MSI2 may contribute to disease progression in chronic myeloid leukemia. Translocation t(7;17)(p15;q23) with HOXA9; translocation t(7;17)(q32-34;q23). {ECO:0000269|PubMed:12649177}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase
(Consensus)
Recessive Scores
- pRec
- 0.0983
Intolerance Scores
- loftool
- 0.238
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 63
Haploinsufficiency Scores
- pHI
- 0.226
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.412
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.785
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Msi2
- Phenotype
- neoplasm; reproductive system phenotype; 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); hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- msi2b
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- degenerate
Gene ontology
- Biological process
- stem cell development
- Cellular component
- nucleus;cytoplasm;polysome;ribonucleoprotein complex
- Molecular function
- RNA binding;protein binding;poly(U) RNA binding