HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SEMA3D
semaphorin 3D
Chromosome 7 · 7q21.11
NCBI Gene: 223117Ensembl: ENSG00000153993.15HGNC: HGNC:10726UniProt: O95025
28PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
plasma membraneneuropilin bindingchemorepellent activityneural crest cell migrationalcohol drinkingProgressive sensorineural hearing impairmentHirschsprung diseasediverticular disease
✦AI Summary

SEMA3D (semaphorin 3D) is an axon guidance molecule that functions as a chemorepellent signal regulating neuronal growth cone collapse and neural migration. Beyond its classical neurobiological role, SEMA3D has emerged as a multifunctional protein with significant disease relevance in cancer and inner ear disorders. In pancreatic ductal adenocarcinoma (PDA), SEMA3D operates through dual tumor and nerve-derived sources. Tumor-derived SEMA3D binds to neuropilin receptors (particularly PLXND1) on dorsal root ganglion neurons, promoting perineural invasion and metastasis 1. Mechanistically, SEMA3D indirectly reprograms macrophages through KRASMUT-dependent ARF6 signaling in PDA cells, increasing lactate production that stimulates M2 macrophage polarization via GPCR132, thereby creating a pro-tumorigenic microenvironment 2. In contrast, SEMA3D shows tumor-suppressive functions in papillary thyroid carcinoma, where downregulation is associated with poor prognosis, and exogenous SEMA3D inhibits cancer cell proliferation and migration through MAPK/ERK pathway inhibition 3. Genetically, SEMA3D variants are implicated in familial Meniere's disease with variable expressivity and incomplete penetrance, linked to sensorineural hearing loss and vertigo 45. Additionally, SEMA3D represents a recurrent HPV integration hotspot in cervical carcinogenesis 6, suggesting context-dependent roles in cancer development.

Sources cited
1
SEMA3D secretion is regulated by ANXA2, binds PLXND1 receptor on dorsal root ganglion neurons, and promotes PDA cell invasion, perineural invasion, and metastasis
PMID: 31163177
2
Tumor and nerve-derived SEMA3D promotes PDA progression through macrophage reprogramming via KRASMUT-dependent ARF6 signaling and lactate-GPCR132 sensing, resulting in M2 polarization
PMID: 39413197
3
SEMA3D is downregulated in papillary thyroid carcinoma and its overexpression inhibits cell proliferation and migration through MAPK/ERK pathway inhibition
PMID: 35190928
4
Heterozygous SEMA3D variants segregate with autosomal dominant familial Meniere's disease phenotype and are expressed in the human cochlea
PMID: 27876815
5
SEMA3D variants are associated with familial Meniere's disease as part of the genetic heterogeneity in this inner ear disorder
PMID: 31874721
6
SEMA3D is a recurrent HPV integration hotspot (4.9% frequency) in cervical carcinomas and intraepithelial neoplasias
PMID: 25581428
7
Rare SEMA3D variants have been identified through exome sequencing in familial Meniere disease
PMID: 29095749
8
SEMA3D is among the genes associated with familial Meniere's disease, part of the genetic architecture underlying this inner ear disorder
PMID: 30430003
Disease Associationsⓘ20
alcohol drinkingOpen Targets
0.38Weak
Progressive sensorineural hearing impairmentOpen Targets
0.34Weak
Hirschsprung diseaseOpen Targets
0.29Weak
diverticular diseaseOpen Targets
0.28Weak
glaucomaOpen Targets
0.26Weak
androgenetic alopeciaOpen Targets
0.25Weak
Abnormality of the skeletal systemOpen Targets
0.24Weak
sinoatrial node disorderOpen Targets
0.20Weak
female reproductive system diseaseOpen Targets
0.20Weak
ocular hypotensionOpen Targets
0.19Weak
ovarian neoplasmOpen Targets
0.19Weak
polycystic ovary syndromeOpen Targets
0.19Weak
multinodular goiterOpen Targets
0.18Weak
HirsutismOpen Targets
0.18Weak
Tension-type headacheOpen Targets
0.18Weak
abscessOpen Targets
0.17Weak
tonsillitisOpen Targets
0.17Weak
upper respiratory tract disorderOpen Targets
0.17Weak
HypercholesterolemiaOpen Targets
0.17Weak
cellulitisOpen Targets
0.17Weak
Pathogenic Variants1
NM_001384900.1(SEMA3D):c.1738C>T (p.Pro580Ser)Pathogenic
Progressive sensorineural hearing impairment|SEMA3D-related disorder
★☆☆☆2016→ Residue 580
View on ClinVar ↗
Related Genes
PLXNA1Protein interaction100%NRP2Protein interaction100%NRP1Protein interaction100%PLXND1Protein interaction100%PLXNA3Protein interaction100%SEMA3GShared pathway86%
Tissue Expression6 tissues
Heart
100%
Brain
65%
Lung
51%
Ovary
50%
Liver
17%
Bone Marrow
1%
Gene Interaction Network
Click a node to explore
SEMA3DPLXNA1NRP2NRP1PLXND1PLXNA3SEMA3G
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt O95025
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.07LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.81 [0.61–1.07]
RankingsWhere SEMA3D stands among ~20K protein-coding genes
  • #12,440of 20,598
    Most Researched28
  • #5,280of 5,498
    Most Pathogenic Variants1
  • #10,882of 17,882
    Most Constrained (LOEUF)1.07
Genes detectedSEMA3D
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Axon Guidance Molecules Promote Perineural Invasion and Metastasis of Orthotopic Pancreatic Tumors in Mice.
PMID: 31163177
Gastroenterology · 2019
1.00
2
Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism.
PMID: 25581428
Nat Genet · 2015
0.90
3
Semaphorin 3D promotes pancreatic ductal adenocarcinoma progression and metastasis through macrophage reprogramming.
PMID: 39413197
Sci Adv · 2024
0.80
4
Genetics of vestibular syndromes.
PMID: 29095749
Curr Opin Neurol · 2018
0.70
5
Genetic architecture of Meniere's disease.
PMID: 31874721
Hear Res · 2020
0.60