NPM3

nucleophosmin/nucleoplasmin 3

Basic information

Region (hg38): 10:101781325-101783446

Links

ENSG00000107833 ∙ NCBI:10360 ∙ OMIM:606456 ∙ HGNC:7931 ∙ Uniprot:O75607 ∙ 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 NPM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPM3 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in NPM3

This is a list of pathogenic ClinVar variants found in the NPM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-101781746-C-A		not specified	Uncertain significance (Jul 02, 2024)
10-101781773-G-C		not specified	Uncertain significance (Feb 07, 2023)
10-101781848-A-G		not specified	Uncertain significance (Aug 15, 2023)
10-101781849-T-C		not specified	Uncertain significance (Oct 08, 2024)
10-101782342-C-T		not specified	Uncertain significance (May 25, 2022)
10-101782344-A-G		not specified	Uncertain significance (Apr 06, 2023)
10-101782346-A-T		not specified	Uncertain significance (Oct 20, 2024)
10-101782491-G-A		not specified	Uncertain significance (Oct 20, 2021)
10-101782519-C-T		not specified	Uncertain significance (Jun 28, 2022)
10-101782572-T-A		not specified	Uncertain significance (Mar 01, 2025)
10-101782856-C-T		not specified	Uncertain significance (Nov 08, 2022)
10-101782910-C-T		not specified	Uncertain significance (Jul 27, 2024)
10-101783300-G-C		not specified	Uncertain significance (Dec 22, 2023)
10-101783311-C-T		not specified	Uncertain significance (Jan 18, 2023)
10-101783336-G-A		not specified	Uncertain significance (Nov 17, 2022)
10-101783338-G-C		not specified	Uncertain significance (Aug 02, 2021)
10-101783369-C-A		not specified	Uncertain significance (Nov 14, 2023)
10-101783369-C-T		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPM3	protein_coding	protein_coding	ENST00000370110	5	2089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0695	0.878	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.346	117	107	1.09	0.00000576	1163
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000653	0.000653
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000653	0.000653
South Asian	0.0000329	0.0000327
Other	0.000164	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.740
• hipred: Y
• hipred_score: 0.518
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npm3
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: chromatin remodeling;rRNA processing;rRNA transcription
• Cellular component: nucleoplasm;nucleolus;cytoplasm;cytosol;actin cytoskeleton
• Molecular function: chromatin binding;RNA binding;protein binding;histone binding