SEMA3B

protein-coding

semaphorin 3B, the group of Immunoglobulin like domain containing|Semaphorins|MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]

Previous symbols:

SEMAA

MANE transcript

NM_001290060.2

Inheritance

—

ClinVar variants

U:231B:104

Top phenotype

SEMA3B-related disorder

Max pathogenic AF

—

Genomic locus

chr3:50,267,558-50,277,546

External References & Databases

Ensembl (ENSG00000012171)

Transcript & Mutation Effects

hg38 • Region Span ~10.0 kb

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GenCC 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 SEMA3B variants in ClinVar

4 Conditions Cataloged

SEMA3B-related disorderTotal: 323

not specifiedTotal: 42

not providedTotal: 1

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001290060.2. 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			17 clinvar	76 clinvar	2 clinvar	95
missense			187 clinvar	24 clinvar		211
nonsense			6 clinvar	1 clinvar		7
start loss						0
frameshift			8 clinvar		1 clinvar	9
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	0	231	101	3	335

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001290060.2	RefSeq	NP_001276989.1	17	MANE Select
ENST00000616701.5	Ensembl	ENSP00000484146.1	17	MANE Select
NM_001005914.3	RefSeq	NP_001005914.1	17	Standard
NM_001290061.1	RefSeq	NP_001276990.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Axon guidance - Homo sapiens (human)
Vitamin D Receptor Pathway

Biological Process

neural crest cell migration
cell-cell signaling
axon guidance
positive regulation of cell migration
negative regulation of axon extension involved in axon guidance

Molecular Function

semaphorin receptor binding
neuropilin binding
chemorepellent activity

Cellular Component

extracellular space
endoplasmic reticulum
integral component of plasma membrane

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. {ECO:0000250}.;

Recessive Scores

pRec: 0.147

Essentials

Indispensability pred.: N
Indispensability score: 0.288