PLXNB1

protein-coding

plexin B1, the group of Plexins|IPT domain containing

Gene summary

Enables semaphorin receptor activity. Involved in several processes, including negative regulation of cell adhesion; regulation of cell shape; and semaphorin-plexin signaling pathway. Located in plasma membrane. Part of semaphorin receptor complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PLXN5

MANE transcript

NM_001130082.3

Inheritance

—

ClinVar variants

U:296B:64

Top phenotype

PLXNB1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr3:48,403,854-48,430,086

External References & Databases

Ensembl (ENSG00000164050)

Transcript & Mutation Effects

hg38 • Region Span ~26.2 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 PLXNB1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 271

PLXNB1-related disorderTotal: 55

not providedTotal: 18

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130082.3. 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			8 clinvar	19 clinvar	16 clinvar	43
missense			273 clinvar	21 clinvar	8 clinvar	302
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			12 clinvar			12
Total	0	0	296	40	24	360

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001130082.3	RefSeq	NP_001123554.1	36	MANE Select
ENST00000296440.11	Ensembl	ENSP00000296440.6	36	MANE Select
NM_002673.6	RefSeq	NP_002664.2	36	Standard
ENST00000358536.8	Ensembl	ENSP00000351338.4	36	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
plxnb1b	Danio rerio	Structure: CaP motoneuron Quality: decreased length abnormal

Gene / Model

Organism

Observed Phenotype

plxnb1b

Danio rerio

Structure: CaP motoneuron

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Axon guidance - Homo sapiens (human)
Developmental Biology
Signaling by GPCR
Signal Transduction
Sema4D mediated inhibition of cell attachment and migration

Biological Process

negative regulation of cell adhesion
signal transduction
G protein-coupled receptor signaling pathway
regulation of cell shape
positive regulation of phosphatidylinositol 3-kinase signaling

Molecular Function

transmembrane signaling receptor activity
GTPase activator activity
protein binding
semaphorin receptor activity
semaphorin receptor binding

Cellular Component

semaphorin receptor complex
extracellular region
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358536
Coding exons: 36
Length: 26334
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125748
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.23	966	1.29e+3	0.747	0.0000830	13536
Missense (PolyPhen)		408	625.19	0.6526		6878
Synonymous	-0.133	549	545	1.01	0.0000355	4579
Loss of Function	6.40	25	90.7	0.275	0.00000453	1008

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00023	0.00022	rare
Finnish	0.00029	0.00028	rare
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.00013	0.00013	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor for SEMA4D. Plays a role in RHOA activation and subsequent changes of the actin cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. {ECO:0000269|PubMed:12196628, ECO:0000269|PubMed:12198496, ECO:0000269|PubMed:15210733, ECO:0000269|PubMed:19843518, ECO:0000269|PubMed:20877282, ECO:0000269|PubMed:21912513}.;

Recessive Scores

pRec: 0.119

Intolerance Scores

LoFtool: 0.481
RVIS EVS: -2.51
RVIS percentile EVS: 0.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.905

Gene Damage Prediction

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