PLXNB3

plexin B3, the group of Plexins|IPT domain containing

Basic information

Region (hg38): X:153764196-153779346

Previous symbols: [ "PLXN6" ]

Links

ENSG00000198753 ∙ NCBI:5365 ∙ OMIM:300214 ∙ HGNC:9105 ∙ Uniprot:Q9ULL4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLXNB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXNB3 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	12	12	25
missense			162	28	6	196
nonsense						0
start loss				1		1
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					2	2
non coding			4	1	1	6
Total	0	0	169	42	19

Variants in PLXNB3

This is a list of pathogenic ClinVar variants found in the PLXNB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-153765536-A-G			Likely benign (Dec 31, 2019)
X-153765540-G-A			Likely benign (May 01, 2023)
X-153765574-C-G			Likely benign (Apr 01, 2022)
X-153766260-G-A			Uncertain significance (Nov 01, 2023)
X-153766287-G-A		not specified	Uncertain significance (Jul 22, 2024)
X-153766292-G-T		not specified	Uncertain significance (Oct 07, 2024)
X-153766308-G-A		not specified	Uncertain significance (Mar 16, 2022)
X-153766888-C-T		not specified	Uncertain significance (Oct 20, 2024)
X-153766889-G-A		not specified	Uncertain significance (Mar 03, 2022)
X-153766910-G-A			Benign (Aug 08, 2017)
X-153766918-C-A		not specified	Uncertain significance (Dec 12, 2023)
X-153766918-C-G		not specified	Uncertain significance (Nov 09, 2021)
X-153766934-C-T		not specified	Uncertain significance (Apr 13, 2023)
X-153766970-C-T		not specified	Uncertain significance (Oct 28, 2024)
X-153767015-G-A		not specified	Uncertain significance (Oct 26, 2024)
X-153767020-A-G		not specified	Uncertain significance (Aug 02, 2023)
X-153767035-G-A		not specified	Uncertain significance (May 30, 2023)
X-153767047-C-T		PLXNB3-related Intellectual disability	Uncertain significance (Jul 30, 2021)
X-153767077-G-A		not specified	Uncertain significance (May 02, 2024)
X-153767080-G-A		not specified	Uncertain significance (Oct 26, 2024)
X-153767083-G-A		not specified	Likely benign (Feb 12, 2025)
X-153767090-T-G		not specified	Uncertain significance (Aug 13, 2021)
X-153767121-C-T			Likely benign (Oct 01, 2022)
X-153767131-C-T		not specified	Uncertain significance (May 26, 2024)
X-153767132-G-A		PLXNB3-related disorder	Likely benign (Feb 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLXNB3	protein_coding	protein_coding	ENST00000538966	35	15151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.232	0.768	125586	14	16	125616	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.227	805	823	0.978	0.0000752	12294
Missense in Polyphen		197	296.35	0.66474		4869
Synonymous	-4.49	496	384	1.29	0.0000375	4166
Loss of Function	5.30	13	55.7	0.234	0.00000385	921

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.0000988
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000340	0.000231
European (Non-Finnish)	0.000206	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000411	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration. Stimulates neurite outgrowth and mediates Ca(2+)/Mg(2+)-dependent cell aggregation. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. {ECO:0000269|PubMed:15218527, ECO:0000269|PubMed:20696765, ECO:0000269|PubMed:21706053}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Other semaphorin interactions;Semaphorin interactions;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.441
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.72

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.471
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plxnb3
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;homophilic cell adhesion via plasma membrane adhesion molecules;negative regulation of cell adhesion;regulation of cell shape;negative regulation of lamellipodium assembly;positive regulation of neuron projection development;regulation of cell migration;negative regulation of cell migration;negative regulation of GTPase activity;regulation of GTPase activity;positive regulation of axonogenesis;positive chemotaxis;cell chemotaxis;semaphorin-plexin signaling pathway;semaphorin-plexin signaling pathway involved in axon guidance
• Cellular component: semaphorin receptor complex;plasma membrane;integral component of plasma membrane;cell surface
• Molecular function: protein binding;semaphorin receptor activity;protein domain specific binding;Rho GDP-dissociation inhibitor binding;cell-cell adhesion mediator activity