PLXNA2

plexin A2, the group of Plexins|IPT domain containing

Basic information

Region (hg38): 1:208022242-208244384

Previous symbols: [ "PLXN2" ]

Links

ENSG00000076356 ∙ NCBI:5362 ∙ OMIM:601054 ∙ HGNC:9100 ∙ Uniprot:O75051 ∙ 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 PLXNA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXNA2 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			3	174	12	189
missense		1	297	11	13	322
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			3			3
splice region			5	20	3	28
non coding				58	16	74
Total	0	1	305	243	41

Variants in PLXNA2

This is a list of pathogenic ClinVar variants found in the PLXNA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-208027253-A-G		not specified • PLXNA2-related disorder	Uncertain significance (Jan 03, 2024)
1-208027270-GAGCTGCTCCACCTTATAAGCC-G		PLXNA2-related disorder	Uncertain significance (Jun 13, 2024)
1-208027295-C-T		PLXNA2-related disorder	Uncertain significance (Jun 12, 2024)
1-208027296-G-A		PLXNA2-related disorder	Uncertain significance (Aug 18, 2023)
1-208027301-C-T			Uncertain significance (Nov 04, 2022)
1-208027304-C-T		PLXNA2-related disorder	Uncertain significance (Sep 24, 2024)
1-208027310-T-A		PLXNA2-related disorder	Uncertain significance (Jun 27, 2022)
1-208027314-C-T			Uncertain significance (Aug 22, 2022)
1-208027317-C-G		not specified	Uncertain significance (Apr 20, 2023)
1-208027330-C-G		PLXNA2-related disorder	Likely benign (Aug 29, 2023)
1-208027332-C-T			Uncertain significance (Mar 29, 2022)
1-208027344-G-A		PLXNA2-related disorder	Likely benign (Apr 17, 2023)
1-208027347-C-T			Likely benign (Jun 24, 2021)
1-208027996-G-T			Likely benign (Dec 02, 2021)
1-208027999-C-T		PLXNA2-related disorder	Likely benign (Aug 20, 2024)
1-208028006-C-T		PLXNA2-related disorder	Likely benign (Nov 23, 2021)
1-208028046-T-C		PLXNA2-related disorder	Uncertain significance (Oct 25, 2022)
1-208028059-G-A			Likely benign (May 18, 2018)
1-208028064-T-G			Uncertain significance (Mar 27, 2023)
1-208028074-C-T		PLXNA2-related disorder • not specified	Uncertain significance (Oct 20, 2022)
1-208028077-C-T		PLXNA2-related disorder	Uncertain significance (Sep 27, 2023)
1-208028078-G-A		PLXNA2-related disorder	Likely benign (Oct 19, 2022)
1-208028086-G-A		PLXNA2-related disorder	Uncertain significance (Aug 25, 2022)
1-208028094-T-C		PLXNA2-related disorder	Uncertain significance (Dec 27, 2023)
1-208028096-G-A		PLXNA2-related disorder	Likely benign (Mar 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLXNA2	protein_coding	protein_coding	ENST00000367033	31	222079

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000108	1.00	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.93	889	1.17e+3	0.759	0.0000756	12378
Missense in Polyphen		389	594.17	0.6547		6245
Synonymous	-0.431	514	502	1.02	0.0000340	3853
Loss of Function	5.94	28	88.3	0.317	0.00000461	955

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000365	0.000365
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000238	0.000220
Middle Eastern	0.000163	0.000163
South Asian	0.000168	0.000163
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Coreceptor for SEMA3A and SEMA6A. Necessary for signaling by SEMA6A and class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down- stream signaling events in the cytoplasm (By similarity). {ECO:0000250, ECO:0000269|PubMed:10520995}.
• Pathway: Axon guidance - Homo sapiens (human);Spinal Cord Injury;Ectoderm Differentiation;Developmental Biology;SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion;Sema3A PAK dependent Axon repulsion;Other semaphorin interactions;Semaphorin interactions;Axon guidance;CRMPs in Sema3A signaling (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.424
• rvis_EVS: -1.48
• rvis_percentile_EVS: 3.64

Haploinsufficiency Scores

• pHI: 0.401
• hipred: Y
• hipred_score: 0.668
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.422

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plxna2
• Phenotype: immune system phenotype; 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); vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: plxna2
• Affected structure: optic cup
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: somitogenesis;negative regulation of cell adhesion;regulation of cell shape;neural tube development;cerebellar granule cell precursor tangential migration;regulation of cell migration;regulation of GTPase activity;positive regulation of axonogenesis;centrosome localization;pharyngeal system development;limb bud formation;semaphorin-plexin signaling pathway;semaphorin-plexin signaling pathway involved in axon guidance
• Cellular component: semaphorin receptor complex;plasma membrane;integral component of plasma membrane
• Molecular function: protein binding;semaphorin receptor activity;identical protein binding