NPM3
Basic information
Region (hg38): 10:101781325-101783446
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (24 variants)
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. These statistics are base on transcript: NM_000006993.3. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 24 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 24 | 0 | 0 |
GnomAD
Source:
| 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:
- 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