CARTPT
Basic information
Region (hg38): 5:71719275-71721048
Links
Phenotypes
GenCC
Source:
- inherited obesity (Limited), mode of inheritance: AD
- inherited obesity (Limited), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (12 variants)
- not_provided (2 variants)
- Obesity (1 variants)
- Pheochromocytoma/paraganglioma_syndrome_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARTPT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004291.4. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CARTPT | protein_coding | protein_coding | ENST00000296777 | 3 | 1886 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0937 | 0.779 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.343 | 53 | 60.5 | 0.876 | 0.00000318 | 728 |
| Missense in Polyphen | 25 | 29.316 | 0.85277 | 367 | ||
| Synonymous | 0.525 | 25 | 28.6 | 0.875 | 0.00000162 | 245 |
| Loss of Function | 1.16 | 2 | 4.71 | 0.425 | 2.09e-7 | 60 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Satiety factor closely associated with the actions of leptin and neuropeptide y; this anorectic peptide inhibits both normal and starvation-induced feeding and completely blocks the feeding response induced by neuropeptide Y and regulated by leptin in the hypothalamus. It promotes neuronal development and survival in vitro. {ECO:0000269|PubMed:9590691}.;
Recessive Scores
- pRec
- 0.169
Intolerance Scores
- loftool
- 0.452
- rvis_EVS
- 0.33
- rvis_percentile_EVS
- 73.11
Haploinsufficiency Scores
- pHI
- 0.364
- hipred
- Y
- hipred_score
- 0.589
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.513
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cartpt
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- activation of MAPKK activity;cellular glucose homeostasis;signal transduction;G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;cell-cell signaling;chemical synaptic transmission;adult feeding behavior;cellular response to starvation;regulation of signaling receptor activity;negative regulation of appetite;positive regulation of epinephrine secretion;circadian regulation of gene expression;negative regulation of osteoclast differentiation;positive regulation of blood pressure;negative regulation of bone resorption;regulation of insulin secretion;positive regulation of transmission of nerve impulse;negative regulation of glucagon secretion;somatostatin secretion
- Cellular component
- extracellular space;secretory granule
- Molecular function
- molecular_function;neuropeptide hormone activity;protein binding