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GeneBe

SEMA6B

semaphorin 6B, the group of Semaphorins

Basic information

Region (hg38): 19:4542592-4581776

Previous symbols: [ "SEMAN" ]

Links

ENSG00000167680NCBI:10501OMIM:608873HGNC:10739Uniprot:Q9H3T3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • epilepsy, progressive myoclonic, 11 (Moderate), mode of inheritance: AD
  • epilepsy, progressive myoclonic, 11 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Epilepsy, progressive myoclonic, 11ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic32169168
As with other conditions involving seizures, optimal seizure control is beneficial, and awareness of genetic causes may help with medication selection

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA6B gene.

  • not provided (62 variants)
  • Inborn genetic diseases (62 variants)
  • Epilepsy, progressive myoclonic, 11 (17 variants)
  • SEMA6B-related condition (2 variants)
  • See cases (2 variants)
  • Autism (1 variants)
  • Intellectual disability (1 variants)
  • Myoclonic-astatic epilepsy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA6B 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
16
clinvar
4
clinvar
20
missense
3
clinvar
59
clinvar
24
clinvar
2
clinvar
88
nonsense
2
clinvar
2
clinvar
1
clinvar
5
start loss
0
frameshift
5
clinvar
2
clinvar
4
clinvar
11
inframe indel
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
non coding
6
clinvar
6
Total 7 8 65 40 13

Variants in SEMA6B

This is a list of pathogenic ClinVar variants found in the SEMA6B region.

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

Position Type Phenotype Significance ClinVar
19-4543626-T-C Uncertain significance (Jun 01, 2023)2649065
19-4543675-C-A Inborn genetic diseases • SEMA6B-related condition Benign/Likely benign (Mar 09, 2022)2355486
19-4543701-G-A Inborn genetic diseases Uncertain significance (Dec 14, 2023)3159912
19-4543713-C-T Uncertain significance (Jan 10, 2023)2571978
19-4543717-T-A Inborn genetic diseases Uncertain significance (Jun 01, 2021)2375066
19-4543741-G-A Likely benign (Mar 01, 2022)2649066
19-4543744-T-G Inborn genetic diseases Uncertain significance (Feb 24, 2022)2373044
19-4543752-G-T Inborn genetic diseases Uncertain significance (May 18, 2022)2290449
19-4543776-C-A Inborn genetic diseases Uncertain significance (Nov 09, 2023)3159911
19-4543791-G-A SEMA6B-related condition Uncertain significance (Apr 18, 2023)2629489
19-4543825-C-T Inborn genetic diseases Uncertain significance (Nov 17, 2022)2326433
19-4543829-G-C Likely benign (Jul 06, 2018)756525
19-4543855-T-C Inborn genetic diseases Likely benign (Jul 20, 2021)2238461
19-4543896-G-C Epilepsy, progressive myoclonic, 11 • Inborn genetic diseases Conflicting classifications of pathogenicity (Dec 21, 2022)1709918
19-4543904-C-G Likely benign (Dec 31, 2019)792322
19-4543910-G-T Inborn genetic diseases Uncertain significance (Sep 01, 2021)2350112
19-4543920-G-A Uncertain significance (Sep 03, 2022)2096279
19-4543926-C-A Inborn genetic diseases Benign/Likely benign (Feb 01, 2024)2212749
19-4543951-G-A not specified Uncertain significance (Mar 29, 2024)3233952
19-4543953-C-G Inborn genetic diseases Likely benign (Apr 07, 2023)2534537
19-4543954-C-T Inborn genetic diseases Uncertain significance (Jul 25, 2023)2613849
19-4543956-T-G Inborn genetic diseases Uncertain significance (Sep 14, 2021)2249023
19-4543963-T-G Inborn genetic diseases Uncertain significance (Sep 14, 2021)2249022
19-4543966-G-A Uncertain significance (Jan 14, 2022)1697105
19-4543972-C-T Uncertain significance (Sep 01, 2022)2649067

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA6Bprotein_codingprotein_codingENST00000586582 1617221
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.06230.9381257270161257430.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.223104410.7030.00003155538
Missense in Polyphen126201.140.626432263
Synonymous-0.3852192121.030.00001731999
Loss of Function3.97934.00.2650.00000189368

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008690.0000869
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.00009380.0000462
European (Non-Finnish)0.00008990.0000879
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a role in both peripheral and central nervous system development. {ECO:0000250}.;
Pathway
Axon guidance - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

pHI
0.254
hipred
Y
hipred_score
0.563
ghis
0.654

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.245

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema6b
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);

Gene ontology

Biological process
neural crest cell migration;positive regulation of cell migration;negative regulation of axon extension involved in axon guidance;negative chemotaxis;semaphorin-plexin signaling pathway
Cellular component
extracellular space;integral component of plasma membrane
Molecular function
semaphorin receptor binding;chemorepellent activity