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GeneBe

SEMA4B

semaphorin 4B, the group of Semaphorins

Basic information

Region (hg38): 15:90160603-90229679

Previous symbols: [ "SEMAC" ]

Links

ENSG00000185033NCBI:10509OMIM:617029HGNC:10730Uniprot:Q9NPR2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA4B gene.

  • Inborn genetic diseases (48 variants)
  • not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA4B 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
1
clinvar
1
missense
46
clinvar
3
clinvar
49
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 46 4 0

Variants in SEMA4B

This is a list of pathogenic ClinVar variants found in the SEMA4B region.

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

Position Type Phenotype Significance ClinVar
15-90201604-G-A not specified Uncertain significance (Nov 03, 2022)2362457
15-90201649-C-T not specified Uncertain significance (Nov 09, 2021)2389254
15-90201663-C-A not specified Uncertain significance (Jul 19, 2023)2613107
15-90201679-T-A not specified Uncertain significance (Jun 01, 2023)2554712
15-90217463-G-C not specified Uncertain significance (Jul 20, 2021)2403723
15-90217468-G-C not specified Uncertain significance (Feb 05, 2024)3159768
15-90217508-G-A not specified Uncertain significance (May 31, 2023)2509810
15-90217828-A-G not specified Uncertain significance (Oct 18, 2021)2255598
15-90219793-C-T not specified Uncertain significance (Dec 28, 2022)2410451
15-90219820-C-A not specified Uncertain significance (Jan 17, 2024)3159778
15-90219834-C-T Likely benign (Nov 01, 2022)2645703
15-90219854-G-A not specified Uncertain significance (Jan 31, 2024)3159779
15-90220982-A-G not specified Uncertain significance (Dec 13, 2023)3159780
15-90220986-T-C not specified Uncertain significance (Oct 13, 2023)3159781
15-90221017-G-C Likely benign (Nov 01, 2022)2645704
15-90221024-G-A not specified Likely benign (Jul 15, 2021)2217880
15-90221048-C-T not specified Uncertain significance (Feb 16, 2023)2486283
15-90221387-A-G not specified Uncertain significance (Oct 04, 2022)2315671
15-90221444-C-T not specified Uncertain significance (Oct 26, 2022)3159782
15-90223562-G-A not specified Uncertain significance (Jan 30, 2024)3159783
15-90223592-C-T not specified Uncertain significance (May 25, 2022)2372633
15-90223614-C-T not specified Uncertain significance (Feb 27, 2023)2489475
15-90223632-G-A not specified Uncertain significance (Oct 29, 2021)2374018
15-90223670-G-A not specified Uncertain significance (Jun 29, 2023)2608365
15-90223676-A-T not specified Uncertain significance (Apr 13, 2022)2284203

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA4Bprotein_codingprotein_codingENST00000411539 1469076
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0005410.9991246110441246550.000177
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9564304900.8780.00003105329
Missense in Polyphen152207.30.733232245
Synonymous-1.282362121.110.00001421695
Loss of Function3.831338.80.3350.00000216394

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003490.000346
Ashkenazi Jewish0.000.00
East Asian0.0002230.000223
Finnish0.0005580.000557
European (Non-Finnish)0.0001640.000159
Middle Eastern0.0002230.000223
South Asian0.00006710.0000654
Other0.0001650.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. {ECO:0000250}.;
Pathway
Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.101

Intolerance Scores

loftool
0.841
rvis_EVS
-0.04
rvis_percentile_EVS
50.54

Haploinsufficiency Scores

pHI
0.135
hipred
Y
hipred_score
0.706
ghis
0.432

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.809

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema4b
Phenotype
homeostasis/metabolism phenotype; hematopoietic system phenotype; renal/urinary system phenotype; immune system phenotype;

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;plasma membrane;integral component of plasma membrane
Molecular function
semaphorin receptor binding;neuropilin binding;chemorepellent activity