NPM2
Basic information
Region (hg38): 8:22024125-22036897
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 1 | |||||
| missense | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 1 |
Variants in NPM2
This is a list of pathogenic ClinVar variants found in the NPM2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-22025656-G-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 8-22025771-T-C | not specified | Uncertain significance (Oct 26, 2021) | ||
| 8-22033137-T-C | not specified | Uncertain significance (Aug 30, 2021) | ||
| 8-22033157-C-T | not specified | Uncertain significance (Apr 26, 2023) | ||
| 8-22033179-G-C | not specified | Uncertain significance (Mar 08, 2024) | ||
| 8-22033196-G-A | not specified | Uncertain significance (Mar 20, 2023) | ||
| 8-22033218-G-A | not specified | Uncertain significance (Oct 02, 2023) | ||
| 8-22034113-A-C | Benign (Apr 10, 2018) | |||
| 8-22034201-A-G | not specified | Likely benign (Jun 21, 2023) | ||
| 8-22034210-G-C | not specified | Uncertain significance (Jan 10, 2023) | ||
| 8-22034220-G-T | not specified | Uncertain significance (Jun 03, 2022) | ||
| 8-22034267-G-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 8-22034535-A-G | not specified | Uncertain significance (Apr 01, 2024) | ||
| 8-22036498-G-T | not specified | Uncertain significance (Mar 29, 2023) | ||
| 8-22036651-C-T | not specified | Uncertain significance (May 14, 2024) | ||
| 8-22036656-G-A | not specified | Uncertain significance (Jun 11, 2021) |
GnomAD
Source:
| 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:
- 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