PLXNB1

plexin B1, the group of Plexins|IPT domain containing

Basic information

Region (hg38): 3:48403853-48430086

Previous symbols: [ "PLXN5" ]

Links

ENSG00000164050 ∙ NCBI:5364 ∙ OMIM:601053 ∙ HGNC:9103 ∙ Uniprot:O43157 ∙ 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 PLXNB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXNB1 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				19	13	32
missense			113	11	8	132
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding				1		1
Total	0	0	113	31	21

Variants in PLXNB1

This is a list of pathogenic ClinVar variants found in the PLXNB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48404496-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-48405718-G-T		PLXNB1-related disorder	Likely benign (Jan 16, 2020)
3-48407039-C-T		not specified	Likely benign (Mar 19, 2024)
3-48407049-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-48409367-T-C		not specified	Uncertain significance (May 24, 2023)
3-48409368-G-C		not specified	Uncertain significance (Nov 08, 2021)
3-48409421-C-G		not specified	Uncertain significance (Sep 22, 2023)
3-48409421-C-T		not specified	Uncertain significance (Dec 15, 2023)
3-48409644-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-48409676-C-T		not specified	Uncertain significance (May 15, 2024)
3-48409677-G-A		not specified	Uncertain significance (Jun 14, 2022)
3-48409685-C-T		not specified	Uncertain significance (Oct 03, 2023)
3-48409686-T-C		not specified	Uncertain significance (Dec 21, 2022)
3-48409714-G-A		PLXNB1-related disorder	Benign (Feb 22, 2019)
3-48409966-C-T		not specified	Uncertain significance (Dec 05, 2022)
3-48409972-C-T		not specified	Uncertain significance (Sep 29, 2023)
3-48410020-T-A		not specified	Uncertain significance (Dec 26, 2023)
3-48410040-G-A		PLXNB1-related disorder	Benign (Jul 31, 2019)
3-48410323-C-T		not specified	Uncertain significance (Dec 18, 2023)
3-48410326-G-A		not specified	Uncertain significance (Feb 17, 2024)
3-48410353-C-T		not specified	Uncertain significance (Dec 02, 2022)
3-48410881-G-A		PLXNB1-related disorder	Benign/Likely benign (Feb 21, 2019)
3-48410908-C-G		PLXNB1-related disorder	Benign (Jul 31, 2019)
3-48411029-T-G		not specified	Uncertain significance (Oct 05, 2023)
3-48412277-G-A		PLXNB1-related disorder	Benign (Sep 12, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLXNB1	protein_coding	protein_coding	ENST00000358536	36	26334

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000383	1.00	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.23	966	1.29e+3	0.747	0.0000830	13536
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000484	0.000483
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.000230	0.000217
Finnish	0.000285	0.000277
European (Non-Finnish)	0.000220	0.000211
Middle Eastern	0.000230	0.000217
South Asian	0.000131	0.000131
Other	0.000177	0.000163

dbNSFP

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}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Signaling by GPCR;Signal Transduction;Sema4D mediated inhibition of cell attachment and migration;Sema4D induced cell migration and growth-cone collapse;Sema4D in semaphorin signaling;Semaphorin interactions;Axon guidance;G alpha (12/13) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.481
• rvis_EVS: -2.51
• rvis_percentile_EVS: 0.93

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.747
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plxnb1
• Phenotype: cellular phenotype; reproductive system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype

Zebrafish Information Network

• Gene name: plxnb1b
• Affected structure: CaP motoneuron
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• 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;cell migration;regulation of cell migration;negative regulation of osteoblast proliferation;intracellular signal transduction;regulation of GTPase activity;positive regulation of GTPase activity;ossification involved in bone maturation;neuron projection morphogenesis;positive regulation of axonogenesis;regulation of cytoskeleton organization;semaphorin-plexin signaling pathway;semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis;semaphorin-plexin signaling pathway involved in axon guidance
• Cellular component: semaphorin receptor complex;extracellular region;plasma membrane;integral component of plasma membrane
• Molecular function: transmembrane signaling receptor activity;GTPase activator activity;protein binding;semaphorin receptor activity;semaphorin receptor binding;GTPase activating protein binding;signaling receptor activity