GeneBe

LHB

luteinizing hormone subunit beta, the group of Receptor ligands|Glycoprotein hormone subunits

Basic information

Region (hg38): 19:49015980-49017091

Links

ENSG00000104826 ∙ NCBI:3972 ∙ OMIM:152780 ∙ HGNC:6584 ∙ Uniprot:P01229 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • hypogonadotropic hypogonadism 23 with or without anosmia (Strong), mode of inheritance: AR
  • hypogonadotropic hypogonadism 23 with or without anosmia (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Hypogonadotropic hypogonadism 23 with or without anosmiaAREndocrineHomozygous/compound heterozygous males may not undergo spontaneous puberty, and treatment (eg, with HCG) can be beneficial; Females may be affected with infertility and oligo-amenorrhea, and medical treatment (eg, with HCG) may be beneficial; Monitoring of bone mineral density may be beneficial in order to allow early detection and treatment of diseaseEndocrine429481; 1727547; 7904610; 7714098; 9457942; 15602022; 19129711; 19890128; 22723313

ClinVar

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

  • not_provided (35 variants)
  • not_specified (28 variants)
  • Isolated_lutropin_deficiency (9 variants)
  • LHB-related_disorder (3 variants)
  • Variant_of_unknown_significance (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000894.3. 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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
3
clinvar
 10
missense
2
clinvar
28
clinvar
8
clinvar
3
clinvar
 41
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total 4 0 29 15 6

Highest pathogenic variant AF is 0.00000685146

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LHBprotein_codingprotein_codingENST00000221421 31102
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.002250.542125625071256320.0000279
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.62310891.31.180.00000660886
Missense in Polyphen3739.080.94679404
Synonymous-1.034738.81.210.00000270312
Loss of Function0.22844.520.8841.95e-748

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009050.0000904
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.00004680.0000462
European (Non-Finnish)0.00002650.0000264
Middle Eastern0.00005450.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Promotes spermatogenesis and ovulation by stimulating the testes and ovaries to synthesize steroids.;
Pathway
GnRH signaling pathway - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Intracellular Signalling Through LHCGR Receptor and Luteinizing Hormone/Choriogonadotropin;T-Cell antigen Receptor (TCR) Signaling Pathway;Signaling by GPCR;Signal Transduction;Peptide hormone metabolism;Metabolism of lipids;Post-translational protein modification;Reactions specific to the complex N-glycan synthesis pathway;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Metabolism;G alpha (s) signalling events;Mineralocorticoid biosynthesis;Hormone ligand-binding receptors;Androgen biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;GPCR signaling-G alpha i;Glycoprotein hormones;GPCR downstream signalling;Steroid hormones;Peptide hormone biosynthesis (Consensus)

Recessive Scores

pRec
0.477

Intolerance Scores

loftool
0.375
rvis_EVS
0.75
rvis_percentile_EVS
86.65

Haploinsufficiency Scores

pHI
0.168
hipred
N
hipred_score
0.112
ghis
0.421

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.141

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lhb
Phenotype
reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype;

Zebrafish Information Network

Gene name
lhb
Affected structure
postovulatory follicle
Phenotype tag
abnormal
Phenotype quality
absent

Gene ontology

Biological process
progesterone biosynthetic process;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;male gonad development;hormone-mediated signaling pathway;regulation of signaling receptor activity;peptide hormone processing
Cellular component
extracellular region;extracellular space;cytoplasm;Golgi lumen
Molecular function
signaling receptor binding;hormone activity