CCS
protein-codingcopper chaperone for superoxide dismutase
Gene summary
Copper chaperone for superoxide dismutase specifically delivers Cu to copper/zinc superoxide dismutase and may activate copper/zinc superoxide dismutase through direct insertion of the Cu cofactor. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0017762
Submitter: ClinGen
The *CCS* gene was first reported in relation to an autosomal recessive disorder of copper metabolism in 2012 (Huppker et al., PMID: 22508683). There has not been further evidence in the literature associating this gene with a specific phenotype. The proband described in this paper was a child from a consanguineous family who was found to have homozygous mutations in two genes: *SLC33A1* and *CCS*. His phenotype was mostly consistent with Huppke-Brendel syndrome (caused by bi-allelic pathogenic variants in *SLC33A1* with an unclear contribution from the missense variants in *CCS* reported in this paper. Currently, there are no OMIM phenotypes associated with this gene. A gene-disease relationship in the published case report was postulated by protein expression analysis through Western blotting on the proband’s fibroblasts, which showed that CCS protein levels were about 40% of those in controls, and that SOD1 enzyme activity was significantly decreased (Huppker et al., PMID: 22508683). This evidence was not scored in the present curation due to an alternative explanation for the described phenotype. In summary, there is limited evidence supporting the relationship between *CCS* and the autosomal recessive disorder of copper metabolism. This classification was approved by the ClinGen IEM GCEP on the meeting date [September, 27, 2024] (SOP Version 10).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CCS variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005125.2. 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 | 2 | |||
| missense | 39 | 1 | 40 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 44 | 2 | 0 | 46 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005116.1 | 8 | MANE Select | |
| Ensembl | ENSP00000436318.1 | 8 | MANE Select | |
| Ensembl | ENSP00000307870.4 | 7 | Standard | |
| Ensembl | ENSP00000307870.4 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human)
- Amyotrophic lateral sclerosis (ALS)
- Copper homeostasis
- Detoxification of Reactive Oxygen Species
- Cellular responses to stress
Biological Process
- superoxide metabolic process
- protein maturation by copper ion transfer
- removal of superoxide radicals
- metal ion transport
- cellular response to oxidative stress
Molecular Function
- superoxide dismutase activity
- copper ion binding
- protein binding
- zinc ion binding
- protein disulfide oxidoreductase activity
Cellular Component
- extracellular space
- nucleus
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000533244
- Coding exons
- 8
- Length
- 13199
- Individuals with no LoFs
- 125668
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 80
- Defined
- 125748
- p
- 0.000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.400 | 156 | 171 | 0.914 | 0.0000107 | 1756 |
| Missense (PolyPhen) | 54 | 58.298 | 0.92628 | 563 | ||
| Synonymous | 1.16 | 56 | 68.2 | 0.821 | 0.00000442 | 557 |
| Loss of Function | 0.528 | 12 | 14.1 | 0.848 | 7.67e-7 | 149 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00028 | 0.00026 | rare |
| Ashkenazi Jewish | 0.00024 | 0.00020 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.00042 | 0.00041 | rare |
| South Asian | 0.00022 | 0.00020 | rare |
| Other | 0.00067 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Delivers copper to copper zinc superoxide dismutase (SOD1).;
Recessive Scores
- pRec
- 0.326
Intolerance Scores
- LoFtool
- 0.339
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 37.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.847
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |