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

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Progressive sensorineural hearing impairment	Pathogenic	rs1057519374	RCV000416605
SEMA3D-related disorder	Pathogenic	rs1057519374	RCV004748659

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Aganglionic megacolon	Conflicting classifications of pathogenicity	rs141893504	RCV000627055
Hirschsprung disease, susceptibility to, 1	Uncertain significance	rs549337695	RCV000201294
Thymoma	Likely benign	rs142039244	RCV005902649

Associations from Text Mining
Disease Name	Relationship Type	References
Asthma	Associate	26073756
Colorectal Neoplasms	Associate	28320475, 34573430
Glioma	Inhibit	18781179
Hirschsprung Disease	Associate	21898659, 23372769
Lymphatic Metastasis	Associate	28320475
Meniere Disease	Associate	27876815
Neoplasm Metastasis	Associate	28320475
Neoplasms	Associate	28320475, 29074988, 37315831
Obesity	Associate	39743445
Osteoarthritis	Associate	33782454
Weight Loss	Associate	39743445