MSI1

musashi RNA binding protein 1, the group of RNA binding motif containing

Basic information

Region (hg38): 12:120341330-120369164

Links

ENSG00000135097 ∙ NCBI:4440 ∙ OMIM:603328 ∙ HGNC:7330 ∙ Uniprot:O43347 ∙ 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 MSI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSI1 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	1
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	11	0	1

Variants in MSI1

This is a list of pathogenic ClinVar variants found in the MSI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-120345616-G-A		not specified	Uncertain significance (May 24, 2023)
12-120346244-G-A		not specified	Uncertain significance (Jul 06, 2022)
12-120346286-G-A		not specified	Uncertain significance (Jun 17, 2024)
12-120347473-C-T		not specified	Uncertain significance (Aug 17, 2022)
12-120347484-G-A		not specified	Uncertain significance (Jun 26, 2023)
12-120356976-G-A		not specified	Uncertain significance (Apr 03, 2023)
12-120357820-T-G		not specified	Uncertain significance (Oct 06, 2022)
12-120357858-C-A		not specified	Uncertain significance (Dec 20, 2023)
12-120357901-A-G			Likely benign (Dec 31, 2019)
12-120364731-G-A		not specified	Uncertain significance (Dec 01, 2022)
12-120368055-C-T		not specified	Uncertain significance (May 30, 2023)
12-120368059-C-G			Benign (Dec 31, 2019)
12-120369078-G-A		not specified	Uncertain significance (Feb 28, 2024)
12-120369078-G-T		not specified	Uncertain significance (Jul 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSI1	protein_coding	protein_coding	ENST00000257552	14	27851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00643	125732	0	3	125735	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.80	100	216	0.464	0.0000128	2323
Missense in Polyphen		18	52.108	0.34544		567
Synonymous	0.449	85	90.4	0.940	0.00000664	702
Loss of Function	4.15	2	23.8	0.0839	0.00000135	254

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)	0.00000890	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'- GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'- [GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system (By similarity). {ECO:0000250}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);Developmental Biology;Regulation of expression of SLITs and ROBOs;Signaling by ROBO receptors;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.0605
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.664
• hipred: Y
• hipred_score: 0.777
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Msi1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); normal 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: msi1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: nervous system development
• Cellular component: nucleus;cytoplasm;polysome;ribonucleoprotein complex
• Molecular function: RNA binding;poly(U) RNA binding;identical protein binding