CALU
protein-codingcalumenin, the group of CREC family
Gene summary
The product of this gene is a calcium-binding protein localized in the endoplasmic reticulum (ER) and it is involved in such ER functions as protein folding and sorting. This protein belongs to a family of multiple EF-hand proteins (CERC) that include reticulocalbin, ERC-55, and Cab45 and the product of this gene. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~34.1 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 CALU variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001219.5. 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 | 2 | 1 | 3 | |||
| missense | 29 | 29 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 1 | 32 | 1 | 0 | 34 |
Highest pathogenic variant AF is 6.8411805e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001210.1 | 6 | MANE Select | |
| Ensembl | ENSP00000249364.4 | 6 | MANE Select | |
| RefSeq | NP_001124146.1 | 6 | Standard | |
| RefSeq | NP_001186600.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Warfarin Pathway, Pharmacodynamics
- NOTCH1 regulation of human endothelial cell calcification
- Post-translational protein phosphorylation
- Post-translational protein modification
- Metabolism of proteins
Biological Process
- biological_process
- post-translational protein modification
- cellular protein metabolic process
Molecular Function
- calcium ion binding
- protein binding
Cellular Component
- extracellular region
- endoplasmic reticulum
- endoplasmic reticulum lumen
- endoplasmic reticulum membrane
- Golgi apparatus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000542996
- Coding exons
- 7
- Length
- 32516
- Individuals with no LoFs
- 125543
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125550
- p
- 0.0000279
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.31 | 128 | 177 | 0.724 | 0.00000896 | 2211 |
| Missense (PolyPhen) | 48 | 75.917 | 0.63227 | 966 | ||
| Synonymous | 0.0400 | 60 | 60.4 | 0.993 | 0.00000305 | 514 |
| Loss of Function | 2.42 | 6 | 16.6 | 0.360 | 8.72e-7 | 203 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in regulation of vitamin K-dependent carboxylation of multiple N-terminal glutamate residues. Seems to inhibit gamma-carboxylase GGCX. Binds 7 calcium ions with a low affinity (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.420
Intolerance Scores
- LoFtool
- 0.422
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.824
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |