SEMA5B

protein-coding

semaphorin 5B, the group of Semaphorins

Gene summary

This gene encodes a member of the semaphorin protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

Previous symbols:

SEMAG

MANE transcript

NM_001031702.4

Inheritance

—

ClinVar variants

U:190B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr3:122,909,082-123,028,605

External References & Databases

Ensembl (ENSG00000082684)

Transcript & Mutation Effects

hg38 • Region Span ~119.5 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 SEMA5B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 180

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031702.4. 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 clinvar		1 clinvar	4
missense			184 clinvar	4 clinvar		188
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	190	4	1	195

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031702.4	RefSeq	NP_001026872.2	22	MANE Select
ENST00000357599.8	Ensembl	ENSP00000350215.3	22	MANE Select
NM_001256346.2	RefSeq	NP_001243275.1	22	Standard
NM_001256347.1	RefSeq	NP_001243276.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Axon guidance - Homo sapiens (human)
Post-translational protein modification
Metabolism of proteins
O-glycosylation of TSR domain-containing proteins
O-linked glycosylation

Biological Process

neural crest cell migration
positive regulation of cell migration
axon extension
negative regulation of axon extension involved in axon guidance
detection of light stimulus involved in visual perception

Molecular Function

semaphorin receptor binding
chemorepellent activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000451055
Coding exons: 23
Length: 119412
Individuals with no LoFs: 125656
Homozygous LoFs: 0
Heterozygous LoFs: 92
Defined: 125748
p: 0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.50	625	740	0.845	0.0000486	7682
Missense (PolyPhen)		239	314.17	0.76073		3136
Synonymous	0.0341	314	315	0.998	0.0000218	2444
Loss of Function	4.09	27	61.6	0.438	0.00000325	633

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00042	0.00040	rare
Ashkenazi Jewish	0.00024	0.00020	rare
East Asian	0.00023	0.00022	rare
Finnish	0.00068	0.00055	rare
European (Non-Finnish)	0.00037	0.00034	rare
South Asian	0.00059	0.00052	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as positive axonal guidance cues. {ECO:0000250}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.668
RVIS EVS: -0.45
RVIS percentile EVS: 23.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.131

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium