CP
Basic information
Region (hg38): 3:149162410-149221829
Links
Phenotypes
GenCC
Source:
- aceruloplasminemia (Strong), mode of inheritance: AR
- aceruloplasminemia (Definitive), mode of inheritance: AR
- aceruloplasminemia (Supportive), mode of inheritance: AR
- aceruloplasminemia (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Aceruloplasminemia | AR | Biochemical | In Aceruloplasminemia, medical management can be beneficial (eg, with iron chelating agents to decrease serum ferritin, brain and liver iron stores, and prevent progression of neurologic signs/symptoms; Combined IV desferrioxamine and fresh-frozen plasma can decrease liver iron content; repetitive FFP treatment can improve neurologic manifestations; antioxidants and oral zinc and deferasirox may prevent tissue damage to the liver and pancreas | Biochemical; Endocrine; Gastrointestinal; Neurologic; Ophthalmologic | 3574673; 1458725; 7820540; 7539672; 9066364; 20301666 |
ClinVar
This is a list of variants' phenotypes submitted to
- Deficiency of ferroxidase (24 variants)
- not provided (6 variants)
- CP-related disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CP gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 87 | 95 | ||||
missense | 219 | 16 | 243 | |||
nonsense | 11 | 12 | ||||
start loss | 1 | |||||
frameshift | 11 | 15 | ||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 8 | |||||
splice region | 12 | 15 | 3 | 30 | ||
non coding | 14 | 59 | 72 | 145 | ||
Total | 26 | 13 | 243 | 162 | 79 |
Highest pathogenic variant AF is 0.0000329
Variants in CP
This is a list of pathogenic ClinVar variants found in the CP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-149162442-CAG-C | Benign (Jul 09, 2018) | |||
3-149162672-C-T | Likely benign (Jul 12, 2023) | |||
3-149162679-C-T | Likely benign (Jun 14, 2023) | |||
3-149162681-G-C | Likely benign (Jul 13, 2023) | |||
3-149162681-GTTTTTAAGGTGC-G | Likely pathogenic (Oct 20, 2022) | |||
3-149162689-G-A | Likely pathogenic (Sep 08, 2021) | |||
3-149162709-A-G | Inborn genetic diseases | Uncertain significance (Mar 28, 2024) | ||
3-149162710-A-G | Likely benign (May 23, 2021) | |||
3-149162712-A-G | Inborn genetic diseases | Uncertain significance (Dec 30, 2023) | ||
3-149162713-T-C | Likely benign (Dec 01, 2018) | |||
3-149162714-AC-A | Pathogenic (Apr 11, 2023) | |||
3-149162719-T-A | Likely benign (Dec 18, 2023) | |||
3-149162730-T-C | Inborn genetic diseases | Uncertain significance (Apr 09, 2022) | ||
3-149162734-A-G | Likely benign (Jun 16, 2023) | |||
3-149162737-CTT-C | Hermansky-Pudlak syndrome 3 | Pathogenic/Likely pathogenic (Jan 18, 2024) | ||
3-149162739-T-C | Uncertain significance (Mar 26, 2021) | |||
3-149162752-G-A | Likely benign (Jan 22, 2024) | |||
3-149162758-G-A | Likely benign (Sep 10, 2021) | |||
3-149162761-A-G | Hermansky-Pudlak syndrome | Likely benign (Jan 22, 2024) | ||
3-149162767-C-G | Hermansky-Pudlak syndrome | Likely benign (Sep 05, 2023) | ||
3-149162768-CCA-C | Hermansky-Pudlak syndrome 3 | Likely pathogenic (Mar 22, 2024) | ||
3-149162775-T-C | Hermansky-Pudlak syndrome 3 • Hermansky-Pudlak syndrome • HPS3-related disorder | Conflicting classifications of pathogenicity (Jan 28, 2024) | ||
3-149162775-TG-T | Hermansky-Pudlak syndrome 3 | Likely pathogenic (Mar 30, 2022) | ||
3-149162776-G-T | Likely benign (Jun 20, 2020) | |||
3-149162784-A-G | Uncertain significance (Oct 21, 2020) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CP | protein_coding | protein_coding | ENST00000264613 | 19 | 59646 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.20e-10 | 1.00 | 114812 | 0 | 10936 | 125748 | 0.0445 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.223 | 550 | 565 | 0.974 | 0.0000281 | 7076 |
Missense in Polyphen | 152 | 195.24 | 0.77853 | 2418 | ||
Synonymous | -1.09 | 221 | 201 | 1.10 | 0.0000109 | 1926 |
Loss of Function | 3.66 | 25 | 54.1 | 0.462 | 0.00000262 | 689 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0682 | 0.0685 |
Ashkenazi Jewish | 0.0373 | 0.0368 |
East Asian | 0.0349 | 0.0351 |
Finnish | 0.0397 | 0.0395 |
European (Non-Finnish) | 0.0553 | 0.0556 |
Middle Eastern | 0.0349 | 0.0351 |
South Asian | 0.0326 | 0.0325 |
Other | 0.0490 | 0.0493 |
dbNSFP
Source:
- Function
- FUNCTION: Ceruloplasmin is a blue, copper-binding (6-7 atoms per molecule) glycoprotein. It has ferroxidase activity oxidizing Fe(2+) to Fe(3+) without releasing radical oxygen species. It is involved in iron transport across the cell membrane. Provides Cu(2+) ions for the ascorbate-mediated deaminase degradation of the heparan sulfate chains of GPC1. May also play a role in fetal lung development or pulmonary antioxidant defense (By similarity). {ECO:0000250}.;
- Disease
- DISEASE: Note=Ceruloplasmin levels are decreased in Wilson disease, in which copper cannot be incorporated into ceruloplasmin in liver because of defects in the copper-transporting ATPase 2.;
- Pathway
- Porphyrin and chlorophyll metabolism - Homo sapiens (human);Ferroptosis - Homo sapiens (human);Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Methionine and cysteine metabolism;Metal ion SLC transporters;Iron uptake and transport;HIF-1-alpha transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.673
Intolerance Scores
- loftool
- 0.0942
- rvis_EVS
- 0.25
- rvis_percentile_EVS
- 69.7
Haploinsufficiency Scores
- pHI
- 0.433
- hipred
- Y
- hipred_score
- 0.652
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.928
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cp
- Phenotype
- immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- cp
- Affected structure
- otolith
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- copper ion transport;iron ion transport;cellular iron ion homeostasis;post-translational protein modification;cellular protein metabolic process;iron ion homeostasis;oxidation-reduction process
- Cellular component
- extracellular region;extracellular space;lysosomal membrane;endoplasmic reticulum lumen;plasma membrane;extracellular exosome;blood microparticle
- Molecular function
- ferroxidase activity;copper ion binding;oxidoreductase activity;chaperone binding