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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 34.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_002442.4	NP_002433.1	14	yes	-
ENST00000257552.7	ENSP00000257552.2	14	yes	-
NM_001414485.1	NP_001401414.1	14	-	-
NM_001414486.1	NP_001401415.1	14	-	-

Phenotypes

GenCC

Source: genCC

• microcephaly (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MSI1 gene.

• not_specified (34 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_002442.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			36			36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	39	0	1

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
		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

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

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