IMP3

protein-coding

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

Gene summary

This gene encodes the human homolog of the yeast Imp3 protein. The protein localizes to the nucleoli and interacts with the U3 snoRNP complex. The protein contains an S4 domain. [provided by RefSeq, Jul 2008]

Previous symbols:

MRPS4
C15orf12

MANE transcript

NM_018285.4

Inheritance

—

ClinVar variants

U:35

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 2.1

Max pathogenic AF

—

Genomic locus

chr15:75,639,085-75,648,706

External References & Databases

Ensembl (ENSG00000177971)

Transcript & Mutation Effects

hg38 • Region Span ~9.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IMP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 35

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018285.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			35 clinvar			35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	0	0	35

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018285.4	RefSeq	NP_060755.1	1	MANE Select
ENST00000403490.3	Ensembl	ENSP00000385217.1	1	MANE Select
ENST00000314852.2	Ensembl	ENSP00000326981.2	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

rRNA processing

Molecular Function

RNA binding
protein binding
rRNA binding
snoRNA binding

Cellular Component

nucleus
nucleoplasm
nucleolus
preribosome
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314852
Coding exons: 1
Length: 9622
Individuals with no LoFs: 125627
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125660
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.768	130	108	1.21	0.00000503	1153
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.00018	0.00016	rare
South Asian	0.00014	0.00013	rare
Other	0.00020	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

RVIS EVS: 0.15
RVIS percentile EVS: 64.11

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Indispensability pred.: E
Indispensability score: 0.927

Gene Damage Prediction

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