CCS

protein-coding

copper 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

NM_005125.2

Inheritance

—

ClinVar variants

U:44B:2

Top phenotype

Neurodegeneration

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr11:66,593,153-66,606,019

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~12.9 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

disorder of copper metabolismNO_KNOWN

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

4 Conditions Cataloged
not specifiedTotal: 38
not providedTotal: 1
NeurodegenerationTotal: 1
CCS-related disorderTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
39
clinvar
1
clinvar
40
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total00442046
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005125.2RefSeqNP_005116.18MANE Select
ENST00000533244.6EnsemblENSP00000436318.18MANE Select
ENST00000310190.8EnsemblENSP00000307870.47Standard
ENST00000310190.9EnsemblENSP00000307870.47Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4001561710.9140.00001071756
Missense (PolyPhen)5458.2980.92628563
Synonymous1.165668.20.8210.00000442557
Loss of Function0.5281214.10.8487.67e-7149

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000280.00026rare
Ashkenazi Jewish0.000240.00020rare
East Asian0.000330.00033rare
Finnish0.0000950.000092rare
European (Non-Finnish)0.000420.00041rare
South Asian0.000220.00020rare
Other0.000670.00065rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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