LEPROT
Basic information
Region (hg38): 1:65420587-65436007
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (10 variants)
- Obesity_due_to_leptin_receptor_gene_deficiency (4 variants)
- not_provided (3 variants)
- Monogenic_Non-Syndromic_Obesity (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEPROT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017526.5. 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LEPROT | protein_coding | protein_coding | ENST00000371065 | 4 | 15421 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.438 | 0.535 | 125722 | 0 | 13 | 125735 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.708 | 55 | 71.9 | 0.765 | 0.00000369 | 835 |
| Missense in Polyphen | 11 | 22.436 | 0.49028 | 293 | ||
| Synonymous | 0.513 | 23 | 26.3 | 0.873 | 0.00000137 | 266 |
| Loss of Function | 1.76 | 1 | 5.42 | 0.184 | 2.28e-7 | 72 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000982 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000785 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Negatively regulates leptin receptor (LEPR) cell surface expression, and thus decreases response to leptin. Negatively regulates growth hormone (GH) receptor cell surface expression in liver. May play a role in liver resistance to GH during periods of reduced nutrient availability. {ECO:0000269|PubMed:18042720, ECO:0000269|PubMed:19907080}.;
Recessive Scores
- pRec
- 0.876
Intolerance Scores
- loftool
- 0.585
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.232
- hipred
- Y
- hipred_score
- 0.612
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.636
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Leprot
- Phenotype
- adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue 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); skeleton phenotype;
Gene ontology
- Biological process
- late endosome to vacuole transport via multivesicular body sorting pathway;negative regulation of JAK-STAT cascade;negative regulation of growth hormone receptor signaling pathway;positive regulation of protein targeting to mitochondrion;negative regulation of protein localization to cell surface
- Cellular component
- Golgi membrane;endosome;Golgi apparatus;endosome membrane;integral component of membrane
- Molecular function
- signaling receptor binding;protein binding