AGRP
agouti related neuropeptide, the group of Neuropeptides
Basic information
Region (hg38): 16:67482571-67483547
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Respiratory infections, recurrent, and failure to thrive with or without diarrhea | AR | Allergy/Immunology/Infectious; Cardiovascular; Pulmonary | The condition can involve recurrent respiratory infections, and awareness may allow preventative and treatment measures may be beneficial; Cardiovascular anomalies have been described, and awareness may early diagnosis and management | Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Pulmonary | 34952832 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGRP 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 | 3 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 3 |
Variants in AGRP
This is a list of pathogenic ClinVar variants found in the AGRP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-67482644-G-A | not specified | Uncertain significance (May 11, 2022) | ||
| 16-67482658-A-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 16-67482677-G-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 16-67482702-G-C | Benign (May 31, 2017) | |||
| 16-67482740-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 16-67482749-C-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 16-67482771-T-C | Obesity | Uncertain significance (Dec 10, 2021) | ||
| 16-67483042-C-T | Obesity, late-onset • Leanness, inherited • Inherited obesity | Benign (Apr 04, 2024) | ||
| 16-67483061-T-G | not specified | Uncertain significance (Nov 09, 2022) | ||
| 16-67483099-G-A | not specified | Uncertain significance (May 24, 2023) | ||
| 16-67483276-C-T | Benign (Jun 09, 2021) | |||
| 16-67483286-A-C | not specified | Uncertain significance (May 12, 2024) | ||
| 16-67483330-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
| 16-67483385-G-A | not specified | Likely benign (Jan 19, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AGRP | protein_coding | protein_coding | ENST00000290953 | 3 | 1243 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000699 | 0.530 | 125731 | 0 | 9 | 125740 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.449 | 70 | 81.4 | 0.860 | 0.00000532 | 826 |
| Missense in Polyphen | 27 | 33.243 | 0.81219 | 313 | ||
| Synonymous | 0.526 | 29 | 32.8 | 0.883 | 0.00000185 | 287 |
| Loss of Function | 0.331 | 5 | 5.87 | 0.852 | 3.28e-7 | 64 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000110 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in weight homeostasis. Involved in the control of feeding behavior through the central melanocortin system. Acts as alpha melanocyte-stimulating hormone antagonist by inhibiting cAMP production mediated by stimulation of melanocortin receptors within the hypothalamus and adrenal gland. Has very low activity with MC5R (By similarity). Is an inverse agonist for MC3R and MC4R being able to suppress their constitutive activity. It promotes MC3R and MC4R endocytosis in an arrestin-dependent manner. {ECO:0000250, ECO:0000269|PubMed:10371151, ECO:0000269|PubMed:11145747, ECO:0000269|PubMed:15927146, ECO:0000269|PubMed:17041250, ECO:0000269|PubMed:9892020}.;
- Disease
- DISEASE: Obesity (OBESITY) [MIM:601665]: A condition characterized by an increase of body weight beyond the limitation of skeletal and physical requirements, as the result of excessive accumulation of body fat. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Adipocytokine signaling pathway - Homo sapiens (human);Syndecan-3-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.353
Intolerance Scores
- loftool
- 0.471
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.19
Haploinsufficiency Scores
- pHI
- 0.702
- hipred
- N
- hipred_score
- 0.170
- ghis
- 0.403
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.926
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Agrp
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype;
Zebrafish Information Network
- Gene name
- agrp
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- neuropeptide signaling pathway;circadian rhythm;feeding behavior;adult feeding behavior;hormone-mediated signaling pathway;regulation of signaling receptor activity;response to insulin;eating behavior;long-day photoperiodism;maternal process involved in female pregnancy;regulation of feeding behavior;positive regulation of feeding behavior
- Cellular component
- extracellular space;Golgi lumen;neuronal cell body
- Molecular function
- signaling receptor binding;neuropeptide hormone activity