Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	64218
Gene name Gene Name - the full gene name approved by the HGNC.	Semaphorin 4A
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SEMA4A
Synonyms (NCBI Gene) Gene synonyms aliases	CORD10, RP35, SEMAB, SEMB
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q22
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass t

Show/Hide all(8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs41265017	G>A	Pathogenic, benign, likely-benign	Coding sequence variant, missense variant
rs145993678	A>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs149652495	T>C	Likely-pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant
rs149711133	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant, synonymous variant, 5 prime UTR variant, coding sequence variant
rs267607033	G>C	Pathogenic	Missense variant, coding sequence variant
rs267607034	T>G	Pathogenic	Missense variant, coding sequence variant
rs756475595	A>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1028250483	C>T	Likely-pathogenic	Coding sequence variant, missense variant

Show/Hide all(14)

miRTarBase ID	miRNA	Experiments	Reference
MIRT755953	hsa-miR-218-5p	Luciferase reporter assay, qRT-PCR, RNA-seq	38785931
MIRT1335038	hsa-miR-122	CLIP-seq
MIRT1335039	hsa-miR-3180-5p	CLIP-seq
MIRT1335040	hsa-miR-3622b-5p	CLIP-seq
MIRT1335041	hsa-miR-3659	CLIP-seq
MIRT1335042	hsa-miR-4433	CLIP-seq
MIRT1335043	hsa-miR-4653-3p	CLIP-seq
MIRT1335044	hsa-miR-665	CLIP-seq
MIRT1335045	hsa-miR-759	CLIP-seq
MIRT2323842	hsa-miR-1343	CLIP-seq
MIRT2323843	hsa-miR-3192	CLIP-seq
MIRT2323844	hsa-miR-4746-3p	CLIP-seq
MIRT2323845	hsa-miR-548u	CLIP-seq
MIRT2323846	hsa-miR-617	CLIP-seq

Show/Hide all(30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001525	Process	Angiogenesis	IEA
GO:0001755	Process	Neural crest cell migration	IBA
GO:0002250	Process	Adaptive immune response	IEA
GO:0002292	Process	T cell differentiation involved in immune response	IEA
GO:0002376	Process	Immune system process	IEA
GO:0005515	Function	Protein binding	IPI	17318185
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0007399	Process	Nervous system development	IEA
GO:0007409	Process	Axonogenesis	IEA
GO:0007411	Process	Axon guidance	IBA
GO:0008360	Process	Regulation of cell shape	IEA
GO:0010594	Process	Regulation of endothelial cell migration	IEA
GO:0016020	Component	Membrane	IEA
GO:0016525	Process	Negative regulation of angiogenesis	IEA
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:0038191	Function	Neuropilin binding	IBA
GO:0045063	Process	T-helper 1 cell differentiation	IEA
GO:0045499	Function	Chemorepellent activity	IBA
GO:0050919	Process	Negative chemotaxis	IBA
GO:0071526	Process	Semaphorin-plexin signaling pathway	IBA
GO:0071526	Process	Semaphorin-plexin signaling pathway	IEA
GO:1904891	Process	Positive regulation of excitatory synapse assembly	IEA
GO:1904891	Process	Positive regulation of excitatory synapse assembly	ISS
GO:1905704	Process	Positive regulation of inhibitory synapse assembly	IEA
GO:1905704	Process	Positive regulation of inhibitory synapse assembly	ISS

MIM	HGNC	e!Ensembl
607292	10729	ENSG00000196189

Protein

UniProt ID

Q9H3S1

Protein name

Semaphorin-4A (Semaphorin-B) (Sema B)

Protein function

Cell surface receptor for PLXNB1, PLXNB2, PLXNB3 and PLXND1 that plays an important role in cell-cell signaling (By similarity). Regulates glutamatergic and GABAergic synapse development (By similarity). Promotes the development of inhibitory sy

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01403	Sema	66 → 476	Sema domain	Family
PF01437	PSI	496 → 548	Plexin repeat	Family

Sequence

MALPALGLDPWSLLGLFLFQLLQLLLPTTTAGGGGQGPMPRVRYYAGDERRALSFFHQKG
LQDFDTLLLSGDGNTLYVGAREAILALDIQDPGVPRLKNMIPWPASDRKKSECAFKKKSN
ETQCFNFIRVLVSYNVTHLYTCGTFAFSPACTFIELQDSYLLPISEDKVMEGKGQSPFDP
AHKHTAVLVDGMLYSGTMNNFLGSEPILMRTLGSQPVLKTDNFLRWLHHDASFVAAIPST
QVVYFFFEETASEFDFFERLHTSRVARVCKNDVGGEKLLQKKWTTFLKAQLLCTQPGQLP
FNVIRHAVLLPADSPTAPHIYAVFTSQWQVGGTRSSAVCAFSLLDIERVFKGKYKELNKE
TSRWTTYRGPETNPRPGSCSVGPSSDKALTFMKDHFLMDEQVVGTPLLVKSGVEYTRLAV
ETAQGLDGHSHLVMYLGTTTGSLHKAVVSGDSSAHLVEEIQLFPDPEPVRNLQLAPTQGA
VFVGFSGGVWRVPRANCSVYESCVDCVLARDPHCAWDPESRTCCLLSAPNLNSWKQDMER
GNPEWACASGPMSRSLRPQSRPQIIKEVLAVPNSILELPCPHLSALASYYWSHGPAAVPE
ASSTVYNGSLLLIVQDGVGGLYQCWATENGFSYPVISYWVDSQDQTLALDPELAGIPREH
VKVPLTRVSGGAALAAQQSYWPHFVTVTVLFALVLSGALIILVASPLRALRARGKVQGCE
TLRPGEKAPLSREQHLQSPKECRTSASDVDADNNCLGTEVA

Sequence length

761

Interactions

View interactions

	KEGG		Reactome
	Axon guidance		Other semaphorin interactions

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Retinitis Pigmentosa	retinitis pigmentosa 35, retinitis pigmentosa	rs267607034, rs1653548589	N/A
Helicoid Peripapillary Chorioretinal Degeneration	helicoid peripapillary chorioretinal degeneration	rs1249149946	N/A

Show/Hide Unknown Diseases (9)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Breast cancer	Breast cancer	N/A	N/A	GWAS
Colorectal Cancer	familial colorectal cancer type X	N/A	N/A	GenCC
colorectal cancer	Colorectal cancer	N/A	N/A	ClinVar
Cone Dystrophy	cone-rod dystrophy	N/A	N/A	GenCC
Cone-rod dystrophy	Cone-Rod Dystrophy, Recessive, cone-rod dystrophy 10	N/A	N/A	ClinVar, GenCC
Lynch Syndrome	Lynch syndrome	N/A	N/A	GenCC
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
Parkinson disease	Parkinson disease	N/A	N/A	GWAS
retinal dystrophy	Retinal dystrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (31)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	27484806
Amaurosis congenita of Leber type 1	Associate	16199541
Arthritis	Associate	26542940
Arthritis Rheumatoid	Stimulate	26303122
Arthritis Rheumatoid	Associate	26542940, 31876207, 32971928
Autoimmune Diseases	Associate	31876207, 32971928
Breast Neoplasms	Inhibit	28607365
Breast Neoplasms	Stimulate	30270262
Cerebral Small Vessel Diseases	Associate	31430377
Colitis Ulcerative	Inhibit	25978359
Color Vision Defects	Associate	28805479
Colorectal Neoplasms	Associate	25307848
Communicable Diseases	Associate	26303122
Cone Rod Dystrophies	Associate	16199541
Crohn Disease	Inhibit	25978359
Drug Related Side Effects and Adverse Reactions	Stimulate	29457657
HIV Seropositivity	Associate	29457657
Hypoxia	Associate	30270262
Hypoxia Brain	Stimulate	30270262
Inflammation	Associate	25978359
Inflammatory Bowel Diseases	Associate	25978359
Lung Neoplasms	Associate	37901456
Lupus Erythematosus Systemic	Associate	31876207
Multiple Sclerosis	Associate	29457657, 32971928
Neoplasms	Associate	30270262
Retinal Degeneration	Associate	16199541, 28805479
Retinal Diseases	Associate	16199541
Retinitis Pigmentosa	Associate	16199541, 28805479
Scleroderma Systemic	Associate	32971928
Squamous Cell Carcinoma of Head and Neck	Stimulate	34099645
Triple Negative Breast Neoplasms	Associate	28607365

SEMA4A (semaphorin 4A)