Menu
GeneBe

SEMA5A

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

Basic information

Region (hg38): 5:9035032-9546075

Previous symbols: [ "SEMAF" ]

Links

ENSG00000112902NCBI:9037OMIM:609297HGNC:10736Uniprot:Q13591AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
19
clinvar
45
missense
52
clinvar
5
clinvar
2
clinvar
59
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
5
1
6
non coding
1
clinvar
3
clinvar
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)2254789
5-9042993-G-A Likely benign (Aug 04, 2017)715979
5-9043024-A-G Likely benign (May 15, 2018)744036
5-9044388-C-T SEMA5A-related condition Likely benign (Dec 31, 2019)734449
5-9044439-G-A SEMA5A-related condition Benign/Likely benign (Apr 01, 2023)2655293
5-9044454-G-A Likely benign (Dec 31, 2019)745365
5-9044470-G-A SEMA5A-related condition Likely benign (May 04, 2022)3038259
5-9044475-G-A Benign (Dec 31, 2019)782995
5-9044494-C-T SEMA5A-related condition Benign (Feb 20, 2019)3041731
5-9044499-G-A Likely benign (May 24, 2018)748888
5-9044513-C-T not specified Uncertain significance (Dec 15, 2022)2362865
5-9044534-C-T not specified Uncertain significance (Mar 29, 2022)2280007
5-9044535-G-A SEMA5A-related condition Benign (May 09, 2019)3059430
5-9044550-C-G Uncertain significance (-)91956
5-9044558-C-G not specified Uncertain significance (Feb 15, 2023)2484396
5-9050412-C-T not specified Uncertain significance (Aug 12, 2021)3159866
5-9050431-C-T not specified Uncertain significance (Nov 17, 2022)3159865
5-9050434-T-C not specified Uncertain significance (Dec 15, 2022)2370179
5-9050437-T-C Benign (Oct 01, 2023)2655294
5-9050465-A-G Benign/Likely benign (Dec 01, 2022)777593
5-9051863-C-T Likely benign (Jun 27, 2018)755064
5-9051865-G-C Benign (Jun 08, 2018)767994
5-9051899-C-T not specified Uncertain significance (May 09, 2023)2546047
5-9051901-C-T SEMA5A-related condition Benign (Dec 31, 2019)733345
5-9051905-C-T not specified Uncertain significance (Sep 20, 2023)3159864

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA5Aprotein_codingprotein_codingENST00000382496 21511050
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00001541.001257100381257480.000151
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.335736700.8550.00004337038
Missense in Polyphen228268.210.850082751
Synonymous-1.332982701.100.00001852055
Loss of Function4.792060.10.3330.00000292647

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004150.000414
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0001390.000139
European (Non-Finnish)0.0001330.000132
Middle Eastern0.0001090.000109
South Asian0.0002300.000163
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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