NUBP1
Basic information
Region (hg38): 16:10743786-10769351
Previous symbols: [ "NBP1" ]
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 NUBP1 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 42 | 44 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 42 | 4 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUBP1 | protein_coding | protein_coding | ENST00000283027 | 11 | 25566 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.73e-14 | 0.0102 | 125691 | 0 | 56 | 125747 | 0.000223 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.943 | 222 | 186 | 1.19 | 0.0000101 | 2086 |
| Missense in Polyphen | 89 | 71.556 | 1.2438 | 764 | ||
| Synonymous | -1.03 | 85 | 73.8 | 1.15 | 0.00000466 | 604 |
| Loss of Function | -0.404 | 19 | 17.2 | 1.11 | 7.30e-7 | 212 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000268 | 0.000268 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000262 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000327 | 0.000325 |
| Middle Eastern | 0.000262 | 0.000217 |
| South Asian | 0.000211 | 0.000196 |
| Other | 0.000349 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery (PubMed:18573874). Required for maturation of extramitochondrial Fe-S proteins (PubMed:18573874). The NUBP1-NUBP2 heterotetramer forms a Fe-S scaffold complex, mediating the de novo assembly of an Fe-S cluster and its transfer to target apoproteins (PubMed:18573874). Implicated in the regulation of centrosome duplication (By similarity). Negatively regulates cilium formation and structure (By similarity). {ECO:0000250|UniProtKB:Q9R060, ECO:0000269|PubMed:18573874}.;
Recessive Scores
- pRec
- 0.0825
Intolerance Scores
- loftool
- 0.742
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.54
Haploinsufficiency Scores
- pHI
- 0.355
- hipred
- N
- hipred_score
- 0.294
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.782
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nubp1
- Phenotype
- respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- regulation of cell growth;cellular iron ion homeostasis;negative regulation of centrosome duplication;iron-sulfur cluster assembly;cell projection organization;centrosome localization;protein localization to cell cortex
- Cellular component
- nucleus;centriole;cytosol;plasma membrane;cilium
- Molecular function
- nucleotide binding;protein binding;ATP binding;metal ion binding;iron-sulfur cluster binding;4 iron, 4 sulfur cluster binding