LEP

protein-coding

leptin, the group of Neuropeptides

Gene summary

This gene encodes a protein that is secreted by white adipocytes into the circulation and plays a major role in the regulation of energy homeostasis. Circulating leptin binds to the leptin receptor in the brain, which activates downstream signaling pathways that inhibit feeding and promote energy expenditure. This protein also has several endocrine functions, and is involved in the regulation of immune and inflammatory responses, hematopoiesis, angiogenesis, reproduction, bone formation and wound healing. Mutations in this gene and its regulatory regions cause severe obesity and morbid obesity with hypogonadism in human patients. A mutation in this gene has also been linked to type 2 diabetes mellitus development. [provided by RefSeq, Aug 2017]

Previous symbols:
  • OBS
  • OB

MANE transcript

NM_000230.3

Inheritance

AR

ClinVar variants

P:10U:39B:37

Top phenotype

Leptin deficiency or dysfunction

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr7:128,241,278-128,257,629

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~16.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

obesity due to congenital leptin deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013991

Submitter: Labcorp Genetics (formerly Invitae)

obesity due to congenital leptin deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013991

Submitter: Genomics England PanelApp

obesity due to congenital leptin deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013991

Submitter: PanelApp Australia

obesity due to congenital leptin deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013991

Submitter: Ambry Genetics

obesity due to congenital leptin deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013991

Submitter: Orphanet

Clinical Genomic Database (CGD)

Leptin deficiency or dysfunctionAR

Manifestation: Endocrine

Intervention: Endocrine

Rationale: Severely affected individuals may benefit from treatment with leptin

Comments: Heterozygotes may display milder forms of disease

Refs: 9202122; 9745435; 9500540; 10486419; 11281277; 11689931; 15070752; 17986612; 17206122; 19427251; 20382689; 22463805Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LEP variants in ClinVar

6 Conditions Cataloged
LEP-related disorderTotal: 59
not providedTotal: 37
Obesity due to congenital leptin deficiencyTotal: 12
not specifiedTotal: 10
Leptin dysfunctionTotal: 3
Monogenic diabetesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000230.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
33
clinvar
2
clinvar
38
missense
3
clinvar
3
clinvar
36
clinvar
2
clinvar
44
nonsense
1
clinvar
1
clinvar
2
start loss
0
frameshift
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
0
Total553935286

Highest pathogenic variant AF is 0.000041512234

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000230.3RefSeqNP_000221.12MANE Select
ENST00000308868.5EnsemblENSP00000312652.42MANE Select
ENST00000965599.1EnsemblENSP00000635658.12Standard
ENST00000965599.2EnsemblENSP00000635658.12Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
lepaDanio rerio

Structure: secondary motor neuron

Quality: branchiness

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Adipocytokine signaling pathway - Homo sapiens (human)
  • Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human)
  • Jak-STAT signaling pathway - Homo sapiens (human)
  • AMPK signaling pathway - Homo sapiens (human)
  • Neuroactive ligand-receptor interaction - Homo sapiens (human)

Biological Process

  • negative regulation of transcription by RNA polymerase II
  • angiogenesis
  • ovulation from ovarian follicle
  • response to hypoxia
  • placenta development

Molecular Function

  • hormone activity
  • peptide hormone receptor binding

Cellular Component

  • extracellular region
  • extracellular space
  • cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000308868
Coding exons
2
Length
16345
Individuals with no LoFs
125738
Homozygous LoFs
0
Heterozygous LoFs
9
Defined
125747
p
0.0000358
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.9106285.70.7230.000004411077
Missense (PolyPhen)1628.5180.56105388
Synonymous-2.415637.31.500.00000214343
Loss of Function1.8215.700.1752.48e-764

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000880.0000088rare
South Asian0.000230.00023rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Key player in the regulation of energy balance and body weight control. Once released into the circulation, has central and peripheral effects by binding LEPR, found in many tissues, which results in the activation of several major signaling pathways (PubMed:17344214, PubMed:15899045, PubMed:19688109). In the hypothalamus, acts as an appetite-regulating factor that induces a decrease in food intake and an increase in energy consumption by inducing anorexinogenic factors and suppressing orexigenic neuropeptides, also regulates bone mass and secretion of hypothalamo-pituitary-adrenal hormones. In the periphery, increases basal metabolism, influences reproductive function, regulates pancreatic beta-cell function and insulin secretion, is pro-angiogenic for endothelial cell and affects innate and adaptive immunity (By similarity) (PubMed:8589726, PubMed:11460888, PubMed:19688109, PubMed:24340098, PubMed:25060689). In the arcuate nucleus of the hypothalamus, activates by depolarization POMC neurons inducing FOS and SOCS3 expression to release anorexigenic peptides and inhibits by hyperpolarization NPY neurons inducing SOCS3 with a consequent reduction on release of orexigenic peptides (By similarity). In addition to its known satiety inducing effect, has a modulatory role in nutrient absorption. In the intestine, reduces glucose absorption by enterocytes by activating PKC and leading to a sequential activation of p38, PI3K and ERK signaling pathways which exerts an inhibitory effect on glucose absorption (PubMed:24340098). Acts as a growth factor on certain tissues, through the activation of different signaling pathways increases expression of genes involved in cell cycle regulation such as CCND1, via JAK2-STAT3 pathway, or VEGFA, via MAPK1/3 and PI3K-AKT1 pathways (By similarity) (PubMed:17344214). May also play an apoptotic role via JAK2-STAT3 pathway and up-regulation of BIRC5 expression (PubMed:18242580). Pro-angiogenic, has mitogenic activity on vascular endothelial cells and plays a role in matrix remodeling by regulating the expression of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) (PubMed:11460888). In innate immunity, modulates the activity and function of neutrophils by increasing chemotaxis and the secretion of oxygen radicals. Increases phagocytosis by macrophages and enhances secretion of pro- inflammatory mediators. Increases cytotoxic ability of NK cells (PubMed:12504075). Plays a pro-inflammatory role, in synergy with IL1B, by inducing NOS2 wich promotes the production of IL6, IL8 and Prostaglandin E2, through a signaling pathway that involves JAK2, PI3K, MAP2K1/MEK1 and MAPK14/p38 (PubMed:15899045, PubMed:19688109). In adaptive immunity, promotes the switch of memory T-cells towards T helper-1 cell immune responses (By similarity). Increases CD4(+)CD25(-) T-cell proliferation and reduces autophagy during TCR (T-cell receptor) stimulation, through MTOR signaling pathway activation and BCL2 up-regulation (PubMed:25060689). {ECO:0000250|UniProtKB:P41160, ECO:0000250|UniProtKB:P50596, ECO:0000269|PubMed:11460888, ECO:0000269|PubMed:12504075, ECO:0000269|PubMed:15899045, ECO:0000269|PubMed:17344214, ECO:0000269|PubMed:18242580, ECO:0000269|PubMed:19688109, ECO:0000269|PubMed:24340098, ECO:0000269|PubMed:25060689, ECO:0000269|PubMed:8589726, ECO:0000305|PubMed:15122202, ECO:0000305|PubMed:25232147}.;
Disease
DISEASE: Leptin deficiency (LEPD) [MIM:614962]: A rare disease characterized by low levels of serum leptin, severe hyperphagia and intractable obesity from an early age. {ECO:0000269|PubMed:25551525, ECO:0000269|PubMed:9500540}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.782

Intolerance Scores

LoFtool
0.373
RVIS EVS
0.06
RVIS percentile EVS
58.26

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.946

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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