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GeneBe

SEMA6A

semaphorin 6A, the group of Semaphorins

Basic information

Region (hg38): 5:116443554-116574823

Previous symbols: [ "SEMAQ" ]

Links

ENSG00000092421NCBI:57556OMIM:605885HGNC:10738Uniprot:Q9H2E6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA6A gene.

  • Inborn genetic diseases (44 variants)
  • not provided (12 variants)
  • Delayed puberty, self-limited (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA6A 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
2
clinvar
5
clinvar
7
missense
1
clinvar
44
clinvar
4
clinvar
49
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 1 44 6 5

Variants in SEMA6A

This is a list of pathogenic ClinVar variants found in the SEMA6A region.

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

Position Type Phenotype Significance ClinVar
5-116446678-C-T not specified Uncertain significance (Oct 27, 2021)2257541
5-116446689-A-C not specified Uncertain significance (May 23, 2023)2550649
5-116446698-G-A not specified Uncertain significance (Nov 15, 2021)2382717
5-116446708-G-C not specified Uncertain significance (Aug 08, 2022)2305523
5-116446792-G-A not specified Uncertain significance (Aug 12, 2021)2358517
5-116446797-T-G Benign/Likely benign (Oct 01, 2023)718147
5-116446912-T-A not specified Uncertain significance (Aug 02, 2022)2305055
5-116446915-C-G Likely benign (Jan 18, 2018)712532
5-116446915-C-T not specified Uncertain significance (Sep 27, 2021)2252186
5-116446933-G-A not specified Uncertain significance (Jun 07, 2023)2558483
5-116446955-C-G not specified Uncertain significance (Apr 07, 2023)2534919
5-116446999-G-A not specified Uncertain significance (Mar 05, 2024)3159892
5-116447028-G-T not specified Uncertain significance (Dec 27, 2023)3159891
5-116447034-G-A Likely benign (Jul 20, 2018)713698
5-116447034-G-T not specified Uncertain significance (Feb 05, 2024)3159890
5-116447097-A-G not specified Uncertain significance (Mar 23, 2022)2279638
5-116447128-T-C not specified Uncertain significance (Dec 13, 2021)2266532
5-116447142-A-C not specified Uncertain significance (Mar 07, 2024)3159889
5-116447178-A-G not specified Uncertain significance (Nov 15, 2021)2261740
5-116447205-T-C not specified Uncertain significance (Nov 14, 2023)3159888
5-116447217-A-G not specified Uncertain significance (Jul 16, 2021)2238163
5-116447244-G-A not specified Uncertain significance (Jun 11, 2021)2406282
5-116447251-G-A not specified Uncertain significance (Oct 27, 2021)2368406
5-116447283-G-A not specified Uncertain significance (Nov 09, 2021)2260146
5-116447284-A-G not specified Uncertain significance (Nov 09, 2021)2260145

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA6Aprotein_codingprotein_codingENST00000343348 18131319
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.0002441246300151246450.0000602
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7475435940.9140.00003536744
Missense in Polyphen209278.270.751083108
Synonymous-1.232692441.100.00001652028
Loss of Function5.39441.40.09650.00000196541

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009450.0000935
Ashkenazi Jewish0.00009940.0000994
East Asian0.0001110.000111
Finnish0.00004650.0000464
European (Non-Finnish)0.00007250.0000708
Middle Eastern0.0001110.000111
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Cell surface receptor for PLXNA2 that plays an important role in cell-cell signaling. Required for normal granule cell migration in the developing cerebellum. Promotes reorganization of the actin cytoskeleton and plays an important role in axon guidance in the developing central nervous system. Can act as repulsive axon guidance cue. Has repulsive action towards migrating granular neurons. May play a role in channeling sympathetic axons into the sympathetic chains and controlling the temporal sequence of sympathetic target innervation (By similarity). {ECO:0000250}.;
Pathway
Axon guidance - Homo sapiens (human);Spinal Cord Injury;Developmental Biology;Other semaphorin interactions;Semaphorin interactions;Axon guidance (Consensus)

Recessive Scores

pRec
0.470

Intolerance Scores

loftool
0.133
rvis_EVS
-0.06
rvis_percentile_EVS
48.91

Haploinsufficiency Scores

pHI
0.565
hipred
Y
hipred_score
0.785
ghis
0.463

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.878

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema6a
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;

Zebrafish Information Network

Gene name
sema6a
Affected structure
optic cup
Phenotype tag
abnormal
Phenotype quality
decreased occurrence

Gene ontology

Biological process
neural crest cell migration;apoptotic process;cytoskeleton organization;cell surface receptor signaling pathway;nervous system development;axon guidance;animal organ morphogenesis;negative regulation of angiogenesis;positive regulation of cell migration;cellular response to vascular endothelial growth factor stimulus;negative regulation of axon extension involved in axon guidance;negative chemotaxis;negative regulation of ERK1 and ERK2 cascade;semaphorin-plexin signaling pathway;negative regulation of cell adhesion involved in sprouting angiogenesis;negative regulation of vascular endothelial growth factor signaling pathway;negative regulation of sprouting angiogenesis;positive regulation of neuron migration
Cellular component
extracellular space;integral component of plasma membrane;integral component of membrane;axon
Molecular function
protein binding;semaphorin receptor binding;chemorepellent activity