SEMA5A

semaphorin 5A, the group of MicroRNA protein coding host genes|Semaphorins

Basic information

Region (hg38): 5:9035032-9546075

Previous symbols: [ "SEMAF" ]

Links

ENSG00000112902 ∙ NCBI:9037 ∙ OMIM:609297 ∙ HGNC:10736 ∙ Uniprot:Q13591 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA5A gene.

• not provided (63 variants)
• Inborn genetic diseases (50 variants)
• Intellectual disability (1 variants)
• Infantile epilepsy syndrome (1 variants)
• SEMA5A-related condition (1 variants)
• SEMA5A-associated Neurodevelopmental syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA5A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				26	19	45
missense			52	5	2	59
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				5	1	6
non coding			1	3		4
Total	0	0	54	34	21

Variants in SEMA5A

This is a list of pathogenic ClinVar variants found in the SEMA5A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-9042965-G-C		not specified	Uncertain significance (Oct 12, 2021)
5-9042993-G-A			Likely benign (Aug 04, 2017)
5-9043024-A-G			Likely benign (May 15, 2018)
5-9044388-C-T		SEMA5A-related disorder	Likely benign (Dec 31, 2019)
5-9044439-G-A		SEMA5A-related disorder	Benign/Likely benign (Apr 01, 2023)
5-9044454-G-A			Likely benign (Dec 31, 2019)
5-9044470-G-A		SEMA5A-related disorder	Likely benign (May 04, 2022)
5-9044475-G-A			Benign (Dec 31, 2019)
5-9044494-C-T		SEMA5A-related disorder	Benign (Feb 20, 2019)
5-9044499-G-A			Likely benign (May 24, 2018)
5-9044513-C-T		not specified	Uncertain significance (Dec 15, 2022)
5-9044534-C-T		not specified	Uncertain significance (Mar 29, 2022)
5-9044535-G-A		SEMA5A-related disorder	Benign (May 09, 2019)
5-9044550-C-G			Uncertain significance (-)
5-9044558-C-G		not specified	Uncertain significance (Feb 15, 2023)
5-9050412-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-9050431-C-T		not specified	Uncertain significance (Nov 17, 2022)
5-9050434-T-C		not specified	Uncertain significance (Dec 15, 2022)
5-9050437-T-C			Benign (Oct 01, 2023)
5-9050465-A-G			Benign/Likely benign (Dec 01, 2022)
5-9051863-C-T			Likely benign (Jun 27, 2018)
5-9051865-G-C			Benign (Jun 08, 2018)
5-9051899-C-T		not specified	Uncertain significance (May 09, 2023)
5-9051901-C-T		SEMA5A-related disorder	Benign (Dec 31, 2019)
5-9051905-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA5A	protein_coding	protein_coding	ENST00000382496	21	511050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000154	1.00	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	573	670	0.855	0.0000433	7038
Missense in Polyphen		228	268.21	0.85008		2751
Synonymous	-1.33	298	270	1.10	0.0000185	2055
Loss of Function	4.79	20	60.1	0.333	0.00000292	647

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000414
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.000230	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bifunctional axonal guidance cue regulated by sulfated proteoglycans; attractive effects result from interactions with heparan sulfate proteoglycans (HSPGs), while the inhibitory effects depend on interactions with chondroitin sulfate proteoglycans (CSPGs) (By similarity). Ligand for receptor PLXNB3. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. May promote angiogenesis by increasing endothelial cell proliferation and migration and inhibiting apoptosis. {ECO:0000250, ECO:0000269|PubMed:15218527, ECO:0000269|PubMed:19850054, ECO:0000269|PubMed:20696765, ECO:0000269|PubMed:21706053}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Post-translational protein modification;Metabolism of proteins;Other semaphorin interactions;Semaphorin interactions;Axon guidance;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.632
• rvis_EVS: -2.89
• rvis_percentile_EVS: 0.58

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.725
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.352

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sema5a
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype

Zebrafish Information Network

• Gene name: sema5a
• Affected structure: CaP motoneuron
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: neural crest cell migration;positive regulation of endothelial cell proliferation;blood vessel endothelial cell proliferation involved in sprouting angiogenesis;cell adhesion;negative regulation of cell adhesion;cell-cell signaling;nervous system development;axonal fasciculation;diencephalon development;positive regulation of cell migration;positive regulation of actin filament depolymerization;positive regulation of angiogenesis;positive regulation of axon extension involved in axon guidance;negative regulation of axon extension involved in axon guidance;positive chemotaxis;negative chemotaxis;positive regulation of protein kinase B signaling;cell chemotaxis;semaphorin-plexin signaling pathway;positive regulation of canonical Wnt signaling pathway;signal clustering;negative regulation of endothelial cell apoptotic process;positive regulation of endothelial cell chemotaxis
• Cellular component: plasma membrane;membrane;integral component of membrane;extracellular exosome
• Molecular function: semaphorin receptor binding;chondroitin sulfate proteoglycan binding;heparan sulfate proteoglycan binding;chemorepellent activity;syndecan binding