SEMA3D (semaphorin 3D)

Gene

• Entrez ID: 223117
• Gene name: Semaphorin 3D
• Gene symbol: SEMA3D
• Synonyms (NCBI Gene): Sema-Z2, coll-2
• Chromosome: 7
• Chromosome location: 7q21.11
• Summary: This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal b

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1057519374	G>A	Pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT044883	hsa-miR-193a-3p	CLASH	23622248
MIRT531332	hsa-miR-590-3p	PAR-CLIP	22012620
MIRT531331	hsa-miR-1468-5p	PAR-CLIP	22012620
MIRT531330	hsa-miR-2053	PAR-CLIP	22012620
MIRT531329	hsa-miR-3646	PAR-CLIP	22012620
MIRT531328	hsa-miR-302f	PAR-CLIP	22012620
MIRT531327	hsa-miR-892c-5p	PAR-CLIP	22012620
MIRT531326	hsa-miR-203a-3p	PAR-CLIP	22012620
MIRT531325	hsa-miR-628-5p	PAR-CLIP	22012620
MIRT531332	hsa-miR-590-3p	PAR-CLIP	22012620
MIRT531331	hsa-miR-1468-5p	PAR-CLIP	22012620
MIRT531330	hsa-miR-2053	PAR-CLIP	22012620
MIRT531329	hsa-miR-3646	PAR-CLIP	22012620
MIRT531328	hsa-miR-302f	PAR-CLIP	22012620
MIRT531327	hsa-miR-892c-5p	PAR-CLIP	22012620
MIRT531326	hsa-miR-203a-3p	PAR-CLIP	22012620
MIRT531325	hsa-miR-628-5p	PAR-CLIP	22012620
MIRT1334874	hsa-miR-1272	CLIP-seq
MIRT1334875	hsa-miR-4305	CLIP-seq
MIRT1334876	hsa-miR-4477b	CLIP-seq
MIRT1334877	hsa-miR-4508	CLIP-seq
MIRT1334878	hsa-miR-4528	CLIP-seq
MIRT1334879	hsa-miR-4662a-5p	CLIP-seq
MIRT1334880	hsa-miR-4693-5p	CLIP-seq
MIRT1334881	hsa-miR-501-3p	CLIP-seq
MIRT1334882	hsa-miR-502-3p	CLIP-seq
MIRT1334883	hsa-miR-515-5p	CLIP-seq
MIRT1334884	hsa-miR-549	CLIP-seq
MIRT1334885	hsa-miR-711	CLIP-seq
MIRT1334878	hsa-miR-4528	CLIP-seq
MIRT2099022	hsa-miR-587	CLIP-seq
MIRT2099023	hsa-miR-889	CLIP-seq
MIRT2323817	hsa-miR-1279	CLIP-seq
MIRT2323818	hsa-miR-338-3p	CLIP-seq
MIRT2323819	hsa-miR-3671	CLIP-seq
MIRT2323820	hsa-miR-3674	CLIP-seq
MIRT2323821	hsa-miR-4422	CLIP-seq
MIRT2323822	hsa-miR-4676-5p	CLIP-seq
MIRT2323823	hsa-miR-570	CLIP-seq
MIRT2323824	hsa-miR-575	CLIP-seq
MIRT2459079	hsa-miR-1179	CLIP-seq
MIRT2459080	hsa-miR-339-5p	CLIP-seq
MIRT2459081	hsa-miR-4477a	CLIP-seq
MIRT2459082	hsa-miR-4503	CLIP-seq
MIRT2459083	hsa-miR-4778-5p	CLIP-seq
MIRT2619714	hsa-miR-1267	CLIP-seq
MIRT2619715	hsa-miR-24	CLIP-seq
MIRT2619716	hsa-miR-3161	CLIP-seq
MIRT2619717	hsa-miR-4251	CLIP-seq
MIRT2619718	hsa-miR-4284	CLIP-seq
MIRT2619719	hsa-miR-4420	CLIP-seq
MIRT2619720	hsa-miR-4517	CLIP-seq
MIRT2619721	hsa-miR-4666-5p	CLIP-seq
MIRT2619722	hsa-miR-4690-5p	CLIP-seq
MIRT2619723	hsa-miR-495	CLIP-seq
MIRT2619724	hsa-miR-539	CLIP-seq
MIRT2619725	hsa-miR-569	CLIP-seq
MIRT2619726	hsa-miR-659	CLIP-seq
MIRT2099023	hsa-miR-889	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001755	Process	Neural crest cell migration	IBA
GO:0005576	Component	Extracellular region	IEA
GO:0005615	Component	Extracellular space	IBA
GO:0005886	Component	Plasma membrane	IBA
GO:0007399	Process	Nervous system development	IEA
GO:0007411	Process	Axon guidance	IBA
GO:0030154	Process	Cell differentiation	IEA
GO:0030215	Function	Semaphorin receptor binding	IBA
GO:0030215	Function	Semaphorin receptor binding	IEA
GO:0030335	Process	Positive regulation of cell migration	IBA
GO:0030900	Process	Forebrain development	IEA
GO:0038191	Function	Neuropilin binding	IBA
GO:0045499	Function	Chemorepellent activity	IBA
GO:0050919	Process	Negative chemotaxis	IBA
GO:0071526	Process	Semaphorin-plexin signaling pathway	IBA

Other IDs

• MIM: 609907
• HGNC: 10726
• e!Ensembl: ENSG00000153993

Protein

• UniProt ID: O95025
• Protein name: Semaphorin-3D
• Protein function: Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin (By similarity).
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01403	Sema	72 → 513	Sema domain	Family

• Sequence:

  MNANKDERLKARSQDFHLFPALMMLSMTMLFLPVTGTLKQNIPRLKLTYKDLLLSNSCIP
  FLGSSEGLDFQTLLLDEERGRLLLGAKDHIFLLSLVDLNKNFKKIYWPAAKERVELCKLA
  GKDANTECANFIRVLQPYNKTHIYVCGTGAFHPICGYIDLGVYKEDIIFKLDTHNLESGR
  LKCPFDPQQPFASVMTDEYLYSGTASDFLGKDTAFTRSLGPTHDHHYIRTDISEHYWLNG
  AKFIGTFFIPDTYNPDDDKIYFFFRESSQEGSTSDKTILSRVGRVCKNDVGGQRSLINKW
  TTFLKARLICSIPGSDGADTYFDELQDIYLLPTRDERNPVVYGVFTTTSSIFKGSAVCVY
  SMADIRAVFNGPYAHKESADHRWVQYDGRIPYPRPGTCPSKTYDPLIKSTRDFPDDVISF
  IKRHSVMYKSVYPVAGGPTFKRINVDYRLTQIVVDHVIAEDGQYDVMFLGTDIGTVLKVV
  SISKEKWNMEEVVLEELQIFKHSSIILNMELSLKQQQLYIGSRDGLVQLSLHRCDTYGKA
  CADCCLARDPYCAWDGNACSRYAPTSKRRARRQDVKYGDPITQCWDIEDSISHETADEKV
  IFGIEFNSTFLECIPKSQQATIKWYIQRSGDEHREELKPDERIIKTEYGLLIRSLQKKDS
  GMYYCKAQEHTFIHTIVKLTLNVIENEQMENTQRAEHEEGKVKDLLAESRLRYKDYIQIL
  SSPNFSLDQYCEQMWHREKRRQRNKGGPKWKHMQEMKKKRNRRHHRDLDELPRAVAT

• Sequence length: 777

Pathways

KEGG:

Axon guidance

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Progressive sensorineural hearing impairment	Pathogenic	rs1057519374	RCV000416605	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SEMA3D-related disorder	Pathogenic	rs1057519374	RCV004748659	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Aganglionic megacolon	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HIRSCHSPRUNG DISEASE	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hirschsprung disease, susceptibility to, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDIOPATHIC OSTEONECROSIS OF THE FEMORAL HEAD	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SKELETAL DYSPLASIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Asthma	Asthma	Pubtator	26073756	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	28320475		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	28320475, 34573430	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Heart Defects	Congenital heart defects	BEFREE	25230848		★☆☆☆☆ Found in Text Mining only
Congenital Intestinal Aganglionosis	Congenital Intestinal Aganglionosis	ORPHANET_DG	25839327		★☆☆☆☆ Found in Text Mining only
Coronary heart disease	Coronary Heart Disease	BEFREE	25230848		★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	27077804		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	22936999		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	22936999		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	18781179	Inhibit	★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	21898659, 27469503, 28334784		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hirschsprung Disease	Hirschsprung disease	Pubtator	21898659, 23372769	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hirschsprung Disease	Hirschsprung Disease	ORPHANET_DG	25839327		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hirschsprung disease	Hirschsprung Disease	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hirschsprung Disease	Hirschsprung Disease	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperparathyroidism	Hyperparathyroidism	BEFREE	30979723		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intestinal Obstruction	Intestinal Obstruction	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intestinal Polyposis	Intestinal Polyposis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	28320475	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	26243191		★☆☆☆☆ Found in Text Mining only
Meniere Disease	Meniere Disease	BEFREE	27876815		★☆☆☆☆ Found in Text Mining only
Meniere Disease	Meniere disease	Pubtator	27876815	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	26243191, 28320475, 31163177		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	39743445	Associate	★☆☆☆☆ Found in Text Mining only
Osteoarthritis	Osteoarthritis	Pubtator	33782454	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	26243191		★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	BEFREE	26243191		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	20684831		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	20684831		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasm	Thyroid Neoplasm	HPO_DG			★☆☆☆☆ Found in Text Mining only