PLXNA4

plexin A4, the group of Plexins|IPT domain containing

Basic information

Region (hg38): 7:132123339-132648688

Previous symbols: [ "PLXNA4A", "PLXNA4B" ]

Links

ENSG00000221866 ∙ NCBI:91584 ∙ OMIM:604280 ∙ HGNC:9102 ∙ Uniprot:Q9HCM2 ∙ 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 PLXNA4 gene.

• PLXNA4-related condition (77 variants)
• Inborn genetic diseases (33 variants)
• not provided (26 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXNA4 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	8	6	17
missense			96	2	6	104
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding			4	1		5
Total	0	0	103	11	12

Variants in PLXNA4

This is a list of pathogenic ClinVar variants found in the PLXNA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-132130473-C-T		PLXNA4-related disorder	Likely benign (Aug 24, 2021)
7-132130474-G-A		PLXNA4-related disorder	Likely benign (Mar 10, 2022)
7-132130494-C-T		PLXNA4-related disorder	Uncertain significance (Dec 21, 2023)
7-132130515-T-G		PLXNA4-related disorder	Likely benign (Dec 20, 2021)
7-132130528-A-C		PLXNA4-related disorder	Uncertain significance (Feb 22, 2024)
7-132130551-A-G		PLXNA4-related disorder	Benign (Jul 19, 2022)
7-132130553-C-T		PLXNA4-related disorder	Uncertain significance (Dec 29, 2023)
7-132130556-G-A		PLXNA4-related disorder	Benign (Apr 29, 2020)
7-132130578-C-T		PLXNA4-related disorder	Likely benign (Apr 20, 2022)
7-132130579-G-A		PLXNA4-related disorder	Likely benign (Sep 03, 2021)
7-132130584-G-A		PLXNA4-related disorder	Benign (Jul 19, 2022)
7-132133064-G-T		PLXNA4-related disorder	Likely benign (May 26, 2021)
7-132133074-G-A		PLXNA4-related disorder	Likely benign (Sep 22, 2021)
7-132133091-T-C		PLXNA4-related disorder	Benign (Jul 19, 2022)
7-132133099-T-C		PLXNA4-related disorder	Uncertain significance (Dec 30, 2023)
7-132133125-C-T		PLXNA4-related disorder	Uncertain significance (Dec 26, 2023)
7-132133148-G-A		PLXNA4-related disorder	Likely benign (Nov 10, 2021)
7-132133163-G-A		PLXNA4-related disorder	Likely benign (Dec 09, 2021)
7-132140674-C-T		PLXNA4-related disorder	Uncertain significance (Dec 15, 2023)
7-132140685-C-A		PLXNA4-related disorder	Likely benign (Aug 31, 2021)
7-132140733-G-A		PLXNA4-related disorder	Likely benign (May 28, 2021)
7-132140772-C-T		PLXNA4-related disorder	Likely benign (Oct 11, 2021)
7-132140815-C-T		PLXNA4-related disorder	Likely benign (Jan 30, 2023)
7-132140816-G-A		PLXNA4-related disorder	Likely benign (Apr 11, 2022)
7-132145144-C-T		PLXNA4-related disorder	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLXNA4	protein_coding	protein_coding	ENST00000359827	31	525357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000119	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.80	788	1.15e+3	0.685	0.0000722	12422
Missense in Polyphen		291	562.39	0.51744		6094
Synonymous	-2.89	568	487	1.17	0.0000331	3723
Loss of Function	7.32	12	84.8	0.142	0.00000439	983

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Coreceptor for SEMA3A. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. 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}.
• Pathway: Axon guidance - Homo sapiens (human);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: 0.113

Intolerance Scores

• loftool: 0.191
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.21

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.736
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plxna4
• Phenotype: vision/eye 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); cellular phenotype

Gene ontology

• Biological process: negative regulation of cell adhesion;regulation of cell shape;facial nerve structural organization;glossopharyngeal nerve morphogenesis;trigeminal nerve structural organization;vagus nerve morphogenesis;postganglionic parasympathetic fiber development;chemorepulsion of branchiomotor axon;anterior commissure morphogenesis;regulation of cell migration;regulation of GTPase activity;sympathetic nervous system development;regulation of axon extension involved in axon guidance;positive regulation of axonogenesis;regulation of negative 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
• Molecular function: semaphorin receptor activity