CARTPT

CART prepropeptide

Basic information

Region (hg38): 5:71719275-71721048

Links

ENSG00000164326 ∙ NCBI:9607 ∙ OMIM:602606 ∙ HGNC:24323 ∙ Uniprot:Q16568 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inherited obesity (Limited), mode of inheritance: AD
• inherited obesity (Limited), mode of inheritance: Unknown

ClinVar

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

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.

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				1		1
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					7	7
Total	0	0	7	2	7

Variants in CARTPT

This is a list of pathogenic ClinVar variants found in the CARTPT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-71719300-A-G		not specified	Uncertain significance (Nov 14, 2023)
5-71719324-C-A		not specified	Uncertain significance (Dec 10, 2024)
5-71719384-G-T		not specified	Uncertain significance (Oct 25, 2023)
5-71719387-G-A			Likely benign (May 04, 2018)
5-71719624-C-T			Benign (Nov 10, 2018)
5-71719676-A-G			Benign (Nov 10, 2018)
5-71719903-G-C		Obesity	Uncertain significance (Apr 18, 2018)
5-71719923-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-71719932-T-A		not specified	Uncertain significance (Jul 14, 2023)
5-71720534-G-A			Likely benign (Sep 11, 2018)
5-71720598-C-T		not specified	Uncertain significance (Sep 20, 2022)
5-71720621-C-G			Benign (Nov 10, 2018)
5-71720635-CA-C			Benign (Jun 18, 2021)
5-71720654-A-G			Benign (Jun 18, 2021)
5-71720692-G-A			Benign (Jun 19, 2021)
5-71720741-C-A			Benign (Jun 19, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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