NUCB1
protein-codingnucleobindin 1, the group of EF-hand domain containing
Gene summary
This gene encodes a member of a small calcium-binding EF-hand protein family. The encoded protein is thought to have a key role in Golgi calcium homeostasis and Ca(2+)-regulated signal transduction events. [provided by RefSeq, Jun 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NUCB1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006184.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 73 | 5 | 78 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 9 | 9 | ||||
| Total | 0 | 0 | 83 | 5 | 0 | 88 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006175.2 | 12 | MANE Select | |
| Ensembl | ENSP00000385923.3 | 12 | MANE Select | |
| Ensembl | ENSP00000385211.1 | 12 | Standard | |
| Ensembl | ENSP00000385211.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- miR-targeted genes in epithelium - TarBase
- miR-targeted genes in lymphocytes - TarBase
- miR-targeted genes in muscle cell - TarBase
- Post-translational protein phosphorylation
- Post-translational protein modification
Biological Process
- post-translational protein modification
- cellular protein metabolic process
- response to cisplatin
- regulation of protein targeting
Molecular Function
- G-protein alpha-subunit binding
- DNA binding
- calcium ion binding
- protein binding
Cellular Component
- extracellular space
- nucleus
- early endosome
- endoplasmic reticulum lumen
- rough endoplasmic reticulum
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000405315
- Coding exons
- 12
- Length
- 23323
- Individuals with no LoFs
- 125700
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 47
- Defined
- 125747
- p
- 0.000187
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.933 | 251 | 296 | 0.847 | 0.0000192 | 3011 |
| Missense (PolyPhen) | 68 | 87.033 | 0.78132 | 897 | ||
| Synonymous | 0.659 | 111 | 120 | 0.923 | 0.00000727 | 892 |
| Loss of Function | 2.17 | 16 | 28.5 | 0.561 | 0.00000162 | 284 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00023 | 0.00022 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Major calcium-binding protein of the Golgi. May have a role in calcium homeostasis (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.232
Intolerance Scores
- LoFtool
- 0.632
- RVIS EVS
- -0.89
- RVIS percentile EVS
- 10.43
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |