IMP4

IMP U3 small nucleolar ribonucleoprotein 4, the group of MPP10 subcomplex

Basic information

Region (hg38): 2:130342876-130347967

Links

ENSG00000136718 ∙ NCBI:92856 ∙ OMIM:612981 ∙ HGNC:30856 ∙ Uniprot:Q96G21 ∙ 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 IMP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMP4 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in IMP4

This is a list of pathogenic ClinVar variants found in the IMP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-130343144-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-130343150-G-T		not specified	Uncertain significance (Jun 11, 2024)
2-130343166-G-C		not specified	Uncertain significance (Apr 15, 2024)
2-130344632-A-G		not specified	Uncertain significance (Mar 07, 2024)
2-130344635-G-A		not specified	Uncertain significance (Dec 27, 2023)
2-130344656-G-A		not specified	Uncertain significance (Sep 29, 2023)
2-130344659-G-A		not specified	Uncertain significance (Mar 23, 2022)
2-130344677-A-G		not specified	Uncertain significance (Mar 25, 2024)
2-130345570-C-G		not specified	Uncertain significance (Jan 29, 2024)
2-130345586-C-T		not specified	Uncertain significance (Jun 22, 2021)
2-130345637-G-A		not specified	Uncertain significance (Jun 13, 2024)
2-130345663-G-C		not specified	Uncertain significance (Mar 02, 2023)
2-130345790-G-A		not specified	Uncertain significance (Dec 06, 2021)
2-130345791-T-C		not specified	Uncertain significance (Aug 04, 2023)
2-130345812-C-T		not specified	Uncertain significance (Mar 04, 2024)
2-130345815-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-130345846-G-A		not specified	Uncertain significance (Jun 11, 2021)
2-130345890-C-T		not specified	Uncertain significance (May 02, 2024)
2-130346062-C-G		not specified	Uncertain significance (Aug 17, 2021)
2-130346070-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-130346208-G-A		not specified	Uncertain significance (May 02, 2024)
2-130346226-C-G		not specified	Uncertain significance (Oct 05, 2022)
2-130346247-G-A		not specified	Uncertain significance (Nov 14, 2023)
2-130346250-G-A		not specified	Uncertain significance (Jul 13, 2022)
2-130346259-C-T		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IMP4	protein_coding	protein_coding	ENST00000259239	9	5586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.86e-7	0.926	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.362	182	196	0.927	0.0000134	1848
Missense in Polyphen		38	47.965	0.79225		468
Synonymous	0.152	77	78.7	0.978	0.00000518	607
Loss of Function	1.75	13	21.8	0.596	0.00000169	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000925	0.000925
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000925	0.000925
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP). Required for the early cleavages during pre-18S ribosomal RNA processing. {ECO:0000269|PubMed:12655004}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.816
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.139
• hipred: Y
• hipred_score: 0.702
• ghis: 0.532

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Imp4

Gene ontology

• Biological process: rRNA processing
• Cellular component: fibrillar center;nucleoplasm;nucleolus;preribosome;small-subunit processome;Mpp10 complex
• Molecular function: protein binding;snoRNA binding