SEMA4B
protein-codingsemaphorin 4B, the group of Semaphorins
Gene summary
Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Predicted to be involved in several processes, including axon guidance; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be located in membrane and synapse. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
- SEMAC
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~69.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SEMA4B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198925.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 4 | |||
| missense | 140 | 9 | 149 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 147 | 10 | 0 | 157 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_945119.1 | 14 | MANE Select | |
| Ensembl | ENSP00000394720.2 | 14 | MANE Select | |
| RefSeq | NP_001310958.1 | 12 | Standard | |
| RefSeq | NP_001310959.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Axon guidance - Homo sapiens (human)
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
Molecular Function
- semaphorin receptor binding
- neuropilin binding
- chemorepellent activity
Cellular Component
- extracellular space
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000411539
- Coding exons
- 14
- Length
- 69076
- Individuals with no LoFs
- 124611
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 44
- Defined
- 124655
- p
- 0.000177
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.956 | 430 | 490 | 0.878 | 0.0000310 | 5329 |
| Missense (PolyPhen) | 152 | 207.3 | 0.73323 | 2245 | ||
| Synonymous | -1.28 | 236 | 212 | 1.11 | 0.0000142 | 1695 |
| Loss of Function | 3.83 | 13 | 38.8 | 0.335 | 0.00000216 | 394 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00026 | rare |
| Latino/Admixed American | 0.000088 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00056 | 0.00056 | rare |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.000067 | 0.000065 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- LoFtool
- 0.841
- RVIS EVS
- -0.04
- RVIS percentile EVS
- 50.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.809
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |