MSI2

musashi RNA binding protein 2, the group of RNA binding motif containing

Basic information

Region (hg38): 17:57255850-57684689

Links

ENSG00000153944 ∙ NCBI:124540 ∙ OMIM:607897 ∙ HGNC:18585 ∙ Uniprot:Q96DH6 ∙ 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 MSI2 gene.

• Inborn genetic diseases (7 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.

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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in MSI2

This is a list of pathogenic ClinVar variants found in the MSI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-57257477-G-A		not specified	Uncertain significance (Feb 16, 2023)
17-57401451-T-C			Uncertain significance (Aug 30, 2023)
17-57529695-T-C		not specified	Uncertain significance (Jul 09, 2021)
17-57596940-A-G		not specified	Uncertain significance (Oct 26, 2022)
17-57616024-G-A		not specified	Uncertain significance (Jan 04, 2024)
17-57674992-G-A		not specified	Uncertain significance (Sep 20, 2023)
17-57675040-G-A		not specified	Uncertain significance (Sep 17, 2021)
17-57675049-A-G		not specified	Uncertain significance (May 11, 2022)
17-57675068-G-A		not specified	Uncertain significance (Feb 09, 2022)
17-57675112-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-57676999-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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