GeneBe

CCS

copper chaperone for superoxide dismutase

Basic information

Region (hg38): 11:66593153-66606019

Links

ENSG00000173992 ∙ NCBI:9973 ∙ OMIM:603864 ∙ HGNC:1613 ∙ Uniprot:O14618 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCS gene.

  • not_specified (35 variants)
  • not_provided (1 variants)
  • Neurodegeneration (1 variants)
  • CCS-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005125.2. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
35
clinvar
1
clinvar
 36
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 0 0 36 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCSprotein_codingprotein_codingENST00000533244 813199
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
8.63e-80.3051256680801257480.000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4001561710.9140.00001071756
Missense in Polyphen5458.2980.92628563
Synonymous1.165668.20.8210.00000442557
Loss of Function0.5281214.10.8487.67e-7149

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005280.000526
Ashkenazi Jewish0.0002350.000198
East Asian0.0003290.000326
Finnish0.00009530.0000924
European (Non-Finnish)0.0004170.000413
Middle Eastern0.0003290.000326
South Asian0.0002180.000196
Other0.0006660.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: Delivers copper to copper zinc superoxide dismutase (SOD1).;
Pathway
Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS);Copper homeostasis;Detoxification of Reactive Oxygen Species;Cellular responses to stress;Cellular responses to external stimuli (Consensus)

Recessive Scores

pRec
0.326

Intolerance Scores

loftool
0.339
rvis_EVS
-0.23
rvis_percentile_EVS
37.32

Haploinsufficiency Scores

pHI
0.0676
hipred
N
hipred_score
0.368
ghis
0.547

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.847

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ccs
Phenotype
endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; reproductive system phenotype;

Gene ontology

Biological process
superoxide metabolic process;protein maturation by copper ion transfer;removal of superoxide radicals;metal ion transport;cellular response to oxidative stress;positive regulation of oxidoreductase activity;oxidation-reduction process
Cellular component
extracellular space;nucleus;cytoplasm;cytosol
Molecular function
superoxide dismutase activity;copper ion binding;protein binding;zinc ion binding;protein disulfide oxidoreductase activity;superoxide dismutase copper chaperone activity;cadherin binding