IMP3

IMP U3 small nucleolar ribonucleoprotein 3, the group of MPP10 subcomplex

Basic information

Region (hg38): 15:75639085-75648706

Previous symbols: [ "MRPS4", "C15orf12" ]

Links

ENSG00000177971 ∙ NCBI:55272 ∙ OMIM:612980 ∙ HGNC:14497 ∙ Uniprot:Q9NV31 ∙ 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 IMP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMP3 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in IMP3

This is a list of pathogenic ClinVar variants found in the IMP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75639697-C-A		not specified	Uncertain significance (May 09, 2024)
15-75639708-A-G		not specified	Uncertain significance (Jun 29, 2023)
15-75639744-A-G		not specified	Uncertain significance (Apr 13, 2022)
15-75639783-G-A		not specified	Uncertain significance (May 17, 2023)
15-75639793-C-T		not specified	Uncertain significance (Oct 04, 2022)
15-75639799-G-A		not specified	Uncertain significance (Jan 21, 2025)
15-75639817-G-C		not specified	Uncertain significance (Jun 29, 2023)
15-75639832-T-C		not specified	Uncertain significance (Jan 19, 2022)
15-75639864-G-A		not specified	Uncertain significance (May 01, 2022)
15-75639875-G-C		not specified	Uncertain significance (Dec 13, 2023)
15-75639900-G-A		not specified	Uncertain significance (Sep 27, 2022)
15-75639936-G-A		not specified	Uncertain significance (Dec 27, 2022)
15-75639940-C-T		not specified	Uncertain significance (Jan 16, 2024)
15-75639945-G-A		not specified	Uncertain significance (Feb 04, 2025)
15-75639954-C-T		not specified	Uncertain significance (Jan 22, 2024)
15-75639984-A-G		not specified	Uncertain significance (Nov 07, 2023)
15-75639993-G-A		not specified	Uncertain significance (May 17, 2023)
15-75640002-C-G		not specified	Uncertain significance (Feb 11, 2025)
15-75640020-T-A		not specified	Uncertain significance (Mar 07, 2025)
15-75640039-C-T		not specified	Uncertain significance (Nov 29, 2023)
15-75640096-C-A		not specified	Uncertain significance (Sep 26, 2022)
15-75640098-G-C		not specified	Uncertain significance (Apr 23, 2024)
15-75640125-T-C		not specified	Uncertain significance (Aug 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IMP3	protein_coding	protein_coding	ENST00000314852	1	9622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-7	0.0357	125627	0	33	125660	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.768	130	108	1.21	0.00000503	1153
Missense in Polyphen		39	38.297	1.0184		425
Synonymous	-1.91	69	51.6	1.34	0.00000240	409
Loss of Function	-1.99	8	3.80	2.10	1.63e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000283	0.000272
Finnish	0.0000489	0.0000462
European (Non-Finnish)	0.000181	0.000158
Middle Eastern	0.000283	0.000272
South Asian	0.000139	0.000131
Other	0.000195	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: 0.118

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.512
• hipred: Y
• hipred_score: 0.769
• ghis: 0.559

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Imp3

Gene ontology

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