NPM2

nucleophosmin/nucleoplasmin 2

Basic information

Region (hg38): 8:22024125-22036897

Links

ENSG00000158806 ∙ NCBI:10361 ∙ OMIM:608073 ∙ HGNC:7930 ∙ Uniprot:Q86SE8 ∙ 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 NPM2 gene.

• not_specified (37 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001286680.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	2	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPM2	protein_coding	protein_coding	ENST00000397940	8	12773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000906	0.945	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.223	123	116	1.06	0.00000615	1395
Missense in Polyphen		44	34.188	1.287		399
Synonymous	0.0951	43	43.8	0.982	0.00000235	382
Loss of Function	1.70	7	13.8	0.506	5.90e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000510	0.000510
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.000169	0.000163
South Asian	0.000143	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Core histones chaperone involved in chromatin reprogramming, specially during fertilization and early embryonic development. Probably involved in sperm DNA decondensation during fertilization. {ECO:0000269|PubMed:21863821}.

Recessive Scores

• pRec: 0.0900

Intolerance Scores

• loftool: 0.815
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.180
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.564

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npm2
• Phenotype: reproductive system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: npm2b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: blastocyst development;chromatin remodeling;regulation of exit from mitosis;single fertilization;oocyte differentiation;positive regulation of catalytic activity;positive regulation of DNA replication;positive regulation of meiotic nuclear division;protein homooligomerization
• Cellular component: cytoplasmic chromatin;nuclear chromatin;nucleus;nucleoplasm;nucleolus;cytoplasm
• Molecular function: chromatin binding;protein binding;enzyme binding;histone binding