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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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NHLH2
nescient helix-loop-helix 2
Chromosome 1 · 1p13.1
NCBI Gene: 4808Ensembl: ENSG00000177551.6HGNC: HGNC:7818UniProt: Q02577
27PubMed Papers
21Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingprotein bindingtranscription coactivator bindingnucleushypogonadotropic hypogonadismhypogonadotropic hypogonadism 27 without anosmiaprimary thrombocytopeniaKallmann syndrome
✦AI Summary

NHLH2 is a basic helix-loop-helix transcription factor that functions as a master regulator of energy homeostasis and reproductive function 1. It binds E-box motifs in target gene promoters, including KISS1, PCSK1, and MC4R, acting as a transcriptional activator to coordinate hypothalamic neuropeptide expression 2. NHLH2 expression responds to energy availability signals, with high levels during energy surplus and reduced expression during food deprivation, positioning it centrally in leptin-responsive pathways that regulate prohormone convertase expression and downstream neuropeptide synthesis 1. The transcription factor is enriched in hypothalamic Kiss1 neurons, where it regulates kisspeptin and neurokinin B synthesis, controlling gonadotropin-releasing hormone release and reproductive timing in a sex-specific manner 2. NHLH2 is also expressed in pro-opiomelanocortin neurons, where it regulates motivated exercise behavior 3. Functionally, NHLH2 knockout mice exhibit adult-onset obesity with reduced exercise motivation and fertility defects. In humans, NHLH2 mutations cause hypogonadotropic hypogonadism without anosmia 4. Notably, NHLH2 mRNA stability is post-transcriptionally regulated by SNORD116, a non-coding RNA deleted in Prader-Willi syndrome, explaining reduced NHLH2 expression in PWS patients 5. Multiple missense variants cluster around the DNA-binding domain and may contribute to obesity and reproductive phenotypes 6.

Sources cited
1
NHLH2 is a transcription factor that regulates expression of prohormone convertases and downstream neuropeptides in response to energy availability signals
PMID: 17485352
2
NHLH2 is enriched in hypothalamic Kiss1 neurons and transcriptionally activates KISS1 and TAC3 promoters to regulate kisspeptin synthesis and reproductive timing
PMID: 34494548
3
NHLH2 is expressed in POMC neurons and regulates motivated exercise behavior; Nhlh2 knockout mice show reduced exercise behavior
PMID: 32168170
4
Two NHLH2 SNPs reduce mRNA stability and DNA binding; one is associated with obesity and both affect body weight and fertility phenotypes
PMID: 23026212
5
SNORD116 post-transcriptionally increases NHLH2 mRNA stability; SNORD116 deletion in Prader-Willi syndrome leads to reduced NHLH2 expression
PMID: 33856031
6
Over 300 missense variants exist in NHLH2; 37 predicted pathogenic variants cluster around the basic-helix-loop-helix and DNA binding domains
PMID: 36834605
7
NHLH2 core promoter CA-repeat variants are associated with late-onset neurocognitive disorder and show evidence of natural selection
PMID: 32877896
8
NHLH2 polymorphisms contribute to human motivation for exercise through transcriptional regulation of the MAO-A gene
PMID: 26196864
Disease Associationsⓘ21
hypogonadotropic hypogonadismOpen Targets
0.42Moderate
hypogonadotropic hypogonadism 27 without anosmiaOpen Targets
0.33Weak
primary thrombocytopeniaOpen Targets
0.11Weak
Kallmann syndromeOpen Targets
0.07Suggestive
Testicular regression syndromeOpen Targets
0.07Suggestive
ring chromosome YOpen Targets
0.07Suggestive
primary ovarian insufficiencyOpen Targets
0.06Suggestive
46,XX ovotesticular disorder of sex developmentOpen Targets
0.06Suggestive
partial androgen insensitivity syndromeOpen Targets
0.06Suggestive
46,XX gonadal dysgenesisOpen Targets
0.06Suggestive
Leydig cell hypoplasiaOpen Targets
0.06Suggestive
Isolated follicle stimulating hormone deficiencyOpen Targets
0.06Suggestive
46,XY partial gonadal dysgenesisOpen Targets
0.06Suggestive
sensory perception of smellOpen Targets
0.06Suggestive
46,XX testicular disorder of sex developmentOpen Targets
0.06Suggestive
46,XY disorder of sex development due to 5-alpha-reductase 2 deficiencyOpen Targets
0.06Suggestive
46,XY disorder of sex development due to isolated 17,20 lyase deficiencyOpen Targets
0.06Suggestive
hypogonadotropic hypogonadism 8 with or without anosmiaOpen Targets
0.06Suggestive
46,XY complete gonadal dysgenesisOpen Targets
0.06Suggestive
congenital adrenal hyperplasia due to 17-alpha-hydroxylase deficiencyOpen Targets
0.06Suggestive
Hypogonadotropic hypogonadism 27 without anosmiaUniProt
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
BTDShared pathway100%NHLH1Shared pathway100%ZIC5Shared pathway100%ZIC4Shared pathway100%SNTG2Shared pathway100%JRKLShared pathway100%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
3%
Lung
3%
Heart
0%
Ovary
0%
Liver
0%
Gene Interaction Network
Click a node to explore
NHLH2BTDNHLH1ZIC5ZIC4SNTG2JRKL
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q02577
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.78LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF1.04 [0.58–1.78]
RankingsWhere NHLH2 stands among ~20K protein-coding genes
  • #12,618of 20,598
    Most Researched27
  • #16,471of 17,882
    Most Constrained (LOEUF)1.78
Genes detectedNHLH2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Two single nucleotide polymorphisms in the human nescient helix-loop-helix 2 (NHLH2) gene reduce mRNA stability and DNA binding.
PMID: 23026212
Gene · 2013
1.00
2
In Silico Examination of Single Nucleotide Missense Mutations in
PMID: 36834605
Int J Mol Sci · 2023
0.90
3
Natural Selection at the NHLH2 Core Promoter Exceptionally Long CA-Repeat in Human and Disease-Only Genotypes in Late-Onset Neurocognitive Disorder.
PMID: 32877896
Gerontology · 2020
0.80
4
Energy balance pathways converging on the Nhlh2 transcription factor.
PMID: 17485352
Front Biosci · 2007
0.70
5
A Genetic Basis for Motivated Exercise.
PMID: 26196864
Exerc Sport Sci Rev · 2015
0.60