NPM3

protein-coding

nucleophosmin/nucleoplasmin 3

Gene summary

The protein encoded by this gene is related to the nuclear chaperone phosphoproteins, nucleoplasmin and nucleophosmin. This protein is strongly expressed in diverse cell types where it localizes primarily to the nucleus. Based on its similarity to nucleoplasmin and nucleophosmin, this protein likely functions as a molecular chaperone in the cell nucleus. [provided by RefSeq, Oct 2008]

MANE transcript

NM_006993.3

Inheritance

—

ClinVar variants

U:31

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr10:101,781,325-101,783,446

External References & Databases

Ensembl (ENSG00000107833)

Transcript & Mutation Effects

hg38 • Region Span ~2.1 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 NPM3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 28

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006993.3. 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			31 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	0	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006993.3	RefSeq	NP_008924.1	5	MANE Select
ENST00000370110.6	Ensembl	ENSP00000359128.5	5	MANE Select
ENST00000919538.1	Ensembl	ENSP00000589597.1	5	Standard
ENST00000919539.1	Ensembl	ENSP00000589598.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chromatin remodeling
rRNA processing
rRNA transcription

Molecular Function

chromatin binding
RNA binding
protein binding
histone binding

Cellular Component

nucleoplasm
nucleolus
cytoplasm
cytosol
actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370110
Coding exons: 5
Length: 2089
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 125747
p: 0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.346	117	107	1.09	0.00000576	1163
Missense (PolyPhen)		35	29.725	1.1775		374
Synonymous	-0.850	52	44.8	1.16	0.00000241	358
Loss of Function	1.64	3	8.00	0.375	3.45e-7	94

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00065	0.00065	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a chaperone.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.514
RVIS EVS: 0.01
RVIS percentile EVS: 54.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.914

Gene Damage Prediction

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