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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SEMA3A
semaphorin 3A
Chromosome 7 Β· 7q21.11
NCBI Gene: 10371Ensembl: ENSG00000075213.12HGNC: HGNC:10723UniProt: Q14563
202PubMed Papers
21Diseases
0Drugs
4Pathogenic Variants
RESEARCH IMPACT
Trending
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
olfactory bulb developmentnegative regulation of neuron projection developmentregulation of axon extension involved in axon guidanceneural crest cell migrationKallmann syndromeAbnormality of the skeletal systemalcohol drinkingopen-angle glaucoma
✦AI Summary

SEMA3A (semaphorin 3A) is a secreted axon guidance cue that functions primarily as a chemorepellent molecule in neuronal development and tissue homeostasis. The protein binds to neuropilin-1/plexin-A1 receptor complexes to inhibit axonal growth cone motility and guide neuronal migration 1. In the nervous system, SEMA3A plays critical roles in olfactory system development and pubertal control, with mutations causing hypogonadotropic hypogonadism with or without anosmia 2. Beyond neurodevelopment, SEMA3A functions in tissue homeostasis through context-dependent mechanisms. In articular cartilage, SEMA3A maintains the aneural state and prevents chondrocyte hypertrophy via PI3K pathway activation, protecting against osteoarthritis progression 3. During bone remodeling under mechanical loads, sensory nerve-derived SEMA3A promotes osteogenic differentiation while facilitating nerve withdrawal through ROCK2 pathway regulation 1. In lymphatic development, SEMA3A mutations impair vessel maturation and dendritic cell recruitment 2. SEMA3A also regulates immune responses by promoting M2 macrophage polarization through the Sema3A/XIAP/PAX6 pathway, supporting tissue repair 4. Clinically, dysregulated SEMA3A expression associates with pathological conditions: high SEMA3A promotes aggressive basal-like pancreatic cancer phenotypes and macrophage infiltration 5, while reduced SEMA3A contributes to thin endometrium-associated infertility 6. These findings suggest SEMA3A modulation as a potential therapeutic target across diverse diseases.

Sources cited
1
SEMA3A secreted by sensory nerves induces bone formation under mechanical loads and facilitates nerve withdrawal
PMID: 38238300
2
SEMA3A inhibits neurite ingrowth and prevents chondrocyte hypertrophy in osteoarthritis through PI3K pathway activation
PMID: 39746903
3
SEMA3A mutations cause lymphatic vessel development abnormalities and impair dendritic cell recruitment
PMID: 33190429
4
SEMA3A promotes aggressive pancreatic cancer phenotype through NRP1-mediated signaling and macrophage polarization
PMID: 38670629
5
Aberrant SEMA3 signaling contributes to insufficient endometrial proliferation in thin endometrium
PMID: 35169075
6
SEMA3A mediates sensory innervation-dependent immunoregulation through M2 macrophage polarization via the Sema3A/XIAP/PAX6 pathway
PMID: 40117376
Disease Associationsβ“˜21
Kallmann syndromeOpen Targets
0.53Moderate
Abnormality of the skeletal systemOpen Targets
0.49Moderate
alcohol drinkingOpen Targets
0.41Moderate
open-angle glaucomaOpen Targets
0.40Moderate
Brugada syndromeOpen Targets
0.38Weak
congenital heart diseaseOpen Targets
0.37Weak
skeletal dysplasiaOpen Targets
0.37Weak
urethral syndromeOpen Targets
0.34Weak
glaucomaOpen Targets
0.33Weak
primary angle closure glaucomaOpen Targets
0.32Weak
COVID-19Open Targets
0.32Weak
JaundiceOpen Targets
0.30Weak
carpal tunnel syndromeOpen Targets
0.29Weak
alcohol dependenceOpen Targets
0.29Weak
ventricular fibrillationOpen Targets
0.28Weak
cardiac arrhythmiaOpen Targets
0.28Weak
diabetic ketoacidosisOpen Targets
0.28Weak
major depressive disorderOpen Targets
0.28Weak
poisoningOpen Targets
0.27Weak
male infertility with azoospermia or oligozoospermia due to single gene mutationOpen Targets
0.27Weak
Hypogonadotropic hypogonadism 16 with or without anosmiaUniProt
Pathogenic Variants4
NM_006080.3(SEMA3A):c.333+2T>CLikely pathogenic
Hypogonadotropic hypogonadism 16 with or without anosmia
β˜…β˜†β˜†β˜†2021
NM_006080.3(SEMA3A):c.1531C>T (p.Gln511Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2016β†’ Residue 511
NM_006080.3(SEMA3A):c.607dup (p.Arg203fs)Likely pathogenic
SEMA3A-related disorder
β˜†β˜†β˜†β˜†2024β†’ Residue 203
NM_006080.3(SEMA3A):c.1591C>T (p.Arg531Ter)Likely pathogenic
SEMA3A-related disorder
β˜†β˜†β˜†β˜†2024β†’ Residue 531
View on ClinVar β†—
Related Genes
PLXND1Protein interaction95%DPYSL3Protein interaction85%PLXNB1Protein interaction84%CRMP1Protein interaction84%DPYSL2Protein interaction83%PLXNA1Protein interaction83%
Tissue Expression6 tissues
Brain
100%
Lung
65%
Heart
58%
Bone Marrow
25%
Ovary
16%
Liver
9%
Gene Interaction Network
Click a node to explore
SEMA3APLXND1DPYSL3PLXNB1CRMP1DPYSL2PLXNA1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q14563
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.45Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.31 [0.21–0.45]
RankingsWhere SEMA3A stands among ~20K protein-coding genes
  • #2,087of 20,598
    Most Researched202 Β· top quartile
  • #3,699of 5,498
    Most Pathogenic Variants4
  • #2,531of 17,882
    Most Constrained (LOEUF)0.45 Β· top quartile
Genes detectedSEMA3A
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
Deciphering the endometrial niche of human thin endometrium at single-cell resolution.
PMID: 35169075
Proc Natl Acad Sci U S A Β· 2022
1.00
2
Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC.
PMID: 38670629
Gut Β· 2024
0.90
3
Sema3A secreted by sensory nerve induces bone formation under mechanical loads.
PMID: 38238300
Int J Oral Sci Β· 2024
0.80
4
Genetic architecture of the structural connectome.
PMID: 38438384
Nat Commun Β· 2024
0.72
5
Neuronal guidance factor Sema3A inhibits neurite ingrowth and prevents chondrocyte hypertrophy in the degeneration of knee cartilage in mice, monkeys and humans.
PMID: 39746903
Bone Res Β· 2025
0.70