PLXNA4 plexin A4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLXNA4provided by HGNC
Official Full Name: plexin A4provided by HGNC
Primary source: HGNC:HGNC:9102
See related: Ensembl:ENSG00000221866 MIM:604280; AllianceGenome:HGNC:9102
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PLEXA4; PLXNA4A; PLXNA4B; FAYV2820; PRO34003
Summary: Predicted to enable semaphorin receptor activity. Predicted to be involved in nervous system development; regulation of cell migration; and semaphorin-plexin signaling pathway. Predicted to act upstream of or within nervous system development; regulation of axon extension involved in axon guidance; and regulation of negative chemotaxis. Predicted to be located in membrane. Predicted to be part of semaphorin receptor complex. Predicted to be active in cerebellar climbing fiber to Purkinje cell synapse and plasma membrane. [provided by Alliance of Genome Resources, Apr 2025]
Expression: Broad expression in fat (RPKM 7.3), brain (RPKM 3.4) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q32.3

Exon count:: 41

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (132123340..132648688, complement)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (133444537..133970190, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (131808099..132333447, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Induction of PLXNA4 Gene during Neural Differentiation in Human Umbilical-Cord-Derived Mesenchymal Stem Cells by Low-Intensity Sub-Sonic Vibration.
Title: Induction of PLXNA4 Gene during Neural Differentiation in Human Umbilical-Cord-Derived Mesenchymal Stem Cells by Low-Intensity Sub-Sonic Vibration.
An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism.
Title: An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism.
A Genome-wide Association Study for Concussion Risk.
Title: A Genome-wide Association Study for Concussion Risk.
In the absence of neuropilins, plexin-A4 formed complexes with plexin-D1, and was required in addition to plexin-D1 to enable Sema3C-induced signal transduction.
Title: Complexes of plexin-A4 and plexin-D1 convey semaphorin-3C signals to induce cytoskeletal collapse in the absence of neuropilins.
B7-H4Ig binds to Sema3a, which acts as a functional bridge to stimulate an Nrp-1/Plexin A4 heterodimer.
Title: B7-H4 Modulates Regulatory CD4(+) T Cell Induction and Function via Ligation of a Semaphorin 3a/Plexin A4/Neuropilin-1 Complex.
Both CLU and PLXNA4 have been genetically associated with Alzheimer disease (AD) risk and our data thus provide a direct relationship between two AD risk genes. Our data suggest that increasing the levels of PLXNA4 or targeting CLU-PLXNA4 interactions may have therapeutic value in AD.
Title: Identification of plexin A4 as a novel clusterin receptor links two Alzheimer's disease risk genes.
Data indicate that plexin A1-4 (PLXNA1-4) mediation of neuroanatomical traits can be detected using in vivo neuroimaging techniques.
Title: PlexinA polymorphisms mediate the developmental trajectory of human corpus callosum microstructure.
There is a significant association between Alzheimer's disease risk and SNPs in PLXNA4.
Title: PLXNA4 is associated with Alzheimer disease and modulates tau phosphorylation.
Rare variants in PLXNA4 and Parkinson's disease.
Title: Rare variants in PLXNA4 and Parkinson's disease.
Plexin-A4 promotes tumor progression and tumor angiogenesis by enhancement of VEGF and bFGF signaling.
Title: Plexin-A4 promotes tumor progression and tumor angiogenesis by enhancement of VEGF and bFGF signaling.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of lung function decline in adults with and without asthma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
Heritability and genetic association analysis of cognition in the&#x000a0;Diabetes Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
The genetic architecture of economic and political preferences. EBI GWAS Catalog EBI GWAS CatalogPubMed
The molecular genetic architecture of self-employment. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:4585040 (e-PCR)
- UniSTS:45323

SHGC-81312 (e-PCR)
- UniSTS:102677

GDB:1318448 (e-PCR)
- UniSTS:2105

SHGC-172821 (e-PCR)
- UniSTS:184634

SHGC-172834 (e-PCR)
- UniSTS:184635

GDB:4585113 (e-PCR)
- UniSTS:1853

D7S512 (e-PCR)
- UniSTS:87400

D7S1804 (e-PCR)
- UniSTS:77681

G09882 (e-PCR)
- UniSTS:53873

SHGC-144776 (e-PCR)
- UniSTS:172411

STS-M78506 (e-PCR)
- UniSTS:54155

MARC_9713-9714:996688545:1 (e-PCR)
- UniSTS:269978

GDB:4585449 (e-PCR)
- UniSTS:48284

GDB:4585279 (e-PCR)
- UniSTS:26781

UniSTS:10408 (e-PCR)
- UniSTS:10408

GDB:4585426 (e-PCR)
- UniSTS:79536

A002T25 (e-PCR)
- UniSTS:5814

GDB:4585001 (e-PCR)
- UniSTS:11967

SHGC-143876 (e-PCR)
- UniSTS:184520

GDB:4585647 (e-PCR)
- UniSTS:3278

D7S556E (e-PCR)
- UniSTS:17622

GDB:4585531 (e-PCR)
- UniSTS:37853

1248 (e-PCR)
- UniSTS:35308

GDB:4585401 (e-PCR)
- UniSTS:38137

G17193 (e-PCR)
- UniSTS:32762

AFMa240wc9 (e-PCR)
- UniSTS:38910

Clone Names

FLJ35026, FLJ38287, KIAA1550, DKFZp434G0625, DKFZp566O0546

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables semaphorin receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor activity	IEA Inferred from Electronic Annotation more info
enables signaling receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within anterior commissure morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon guidance	IEA Inferred from Electronic Annotation more info
involved_in branchiomotor neuron axon guidance	IEA Inferred from Electronic Annotation more info
involved_in branchiomotor neuron axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell surface receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chemorepulsion of branchiomotor axon	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cranial nerve morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic heart tube development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within facial nerve morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in facial nerve structural organization	IEA Inferred from Electronic Annotation more info
involved_in facial nerve structural organization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within glossopharyngeal nerve morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in maintenance of synapse structure	IEA Inferred from Electronic Annotation more info
involved_in motor neuron axon guidance	IEA Inferred from Electronic Annotation more info
involved_in motor neuron axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative chemotaxis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuron projection morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within postganglionic parasympathetic fiber development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of axon extension involved in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in regulation of axon extension involved in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of chemotaxis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of negative chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within semaphorin-plexin signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in semaphorin-plexin signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in semaphorin-plexin signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in semaphorin-plexin signaling pathway	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within sympathetic nervous system development	IEA Inferred from Electronic Annotation more info
involved_in sympathetic neuron axon guidance	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in telencephalon development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within trigeminal nerve morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in trigeminal nerve structural organization	IEA Inferred from Electronic Annotation more info
involved_in trigeminal nerve structural organization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within vagus nerve morphogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cerebellar climbing fiber to Purkinje cell synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
part_of semaphorin receptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of semaphorin receptor complex	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: plexin-A4

Names: epididymis secretory sperm binding protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001105543.2 → NP_001099013.1 plexin-A4 isoform 3 precursor

See identical proteins and their annotated locations for NP_001099013.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has a different 3' terminal exon, and is missing many coding exons found in variant 1. It thus encodes a shorter isoform (3) with the same N-terminus, but a different C-terminus compared to isoform 1.

Source sequence(s)

AC011625, AK123428, DR003088

Consensus CDS

CCDS43647.1

UniProtKB/TrEMBL

A0A384NYW6

Related

ENSP00000392772.2, ENST00000423507.6

Conserved Domains (1) summary

cl15693
Location:39 → 458

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
NM_001393897.1 → NP_001380826.1 plexin-A4 isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC009364, AC009785, AC018643

Consensus CDS

CCDS43646.1

UniProtKB/Swiss-Prot

A4D1N6, E9PAM2, Q6UWC6, Q6ZW89, Q8N969, Q8ND00, Q8NEN3, Q9HCM2, Q9NTD4

Related

ENSP00000352882.3, ENST00000359827.7

Conserved Domains (10) summary

cd11274
Location:39 → 511

Sema_plexin_A4; The Sema domain, a protein interacting module, of Plexin A4

smart00423
Location:510 → 548

PSI; domain found in Plexins, Semaphorins and Integrins

cd00603
Location:1142 → 1222

IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...

cd01179
Location:955 → 1038

IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01180
Location:858 → 953

IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01181
Location:1040 → 1140

IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

pfam01437
Location:804 → 856

PSI; Plexin repeat

pfam08337
Location:1311 → 1864

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:564 → 654

TIG_plexin; TIG domain

pfam18020
Location:708 → 802

TIG_2; TIG domain found in plexin
NM_020911.2 → NP_065962.1 plexin-A4 isoform 1 precursor

See identical proteins and their annotated locations for NP_065962.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AA253415, AB046770, AC018643, AK123428, CD243425, DR003088

Consensus CDS

CCDS43646.1

UniProtKB/Swiss-Prot

A4D1N6, E9PAM2, Q6UWC6, Q6ZW89, Q8N969, Q8ND00, Q8NEN3, Q9HCM2, Q9NTD4

Related

ENSP00000323194.4, ENST00000321063.9

Conserved Domains (10) summary

cd11274
Location:39 → 511

Sema_plexin_A4; The Sema domain, a protein interacting module, of Plexin A4

smart00423
Location:510 → 548

PSI; domain found in Plexins, Semaphorins and Integrins

cd00603
Location:1142 → 1222

IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...

cd01179
Location:955 → 1038

IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01180
Location:858 → 953

IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01181
Location:1040 → 1140

IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

pfam01437
Location:804 → 856

PSI; Plexin repeat

pfam08337
Location:1311 → 1864

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:564 → 654

TIG_plexin; TIG domain

pfam18020
Location:708 → 802

TIG_2; TIG domain found in plexin
NM_181775.4 → NP_861440.2 plexin-A4 isoform 2 precursor

See identical proteins and their annotated locations for NP_861440.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) has different 5' and 3' terminal exons, and is missing many coding exons found in variant 1. It thus encodes a shorter isoform (2) with the same N-terminus, but a different C-terminus compared to isoform 1.

Source sequence(s)

AL137352, BC028744

Consensus CDS

CCDS5826.1

UniProtKB/TrEMBL

A0A384NYW6

Related

ENSP00000367800.5, ENST00000378539.5

Conserved Domains (1) summary

cl15693
Location:39 → 469

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

132123340..132648688 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017012779.1 → XP_016868268.1 plexin-A4 isoform X2
XM_006716171.5 → XP_006716234.1 plexin-A4 isoform X1

See identical proteins and their annotated locations for XP_006716234.1

UniProtKB/Swiss-Prot

A4D1N6, E9PAM2, Q6UWC6, Q6ZW89, Q8N969, Q8ND00, Q8NEN3, Q9HCM2, Q9NTD4

Related

ENSP00000619008.1, ENST00000948949.1

Conserved Domains (10) summary

cd11274
Location:39 → 511

Sema_plexin_A4; The Sema domain, a protein interacting module, of Plexin A4

smart00423
Location:510 → 548

PSI; domain found in Plexins, Semaphorins and Integrins

cd00603
Location:1142 → 1222

IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...

cd01179
Location:955 → 1038

IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01180
Location:858 → 953

IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01181
Location:1040 → 1140

IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

pfam01437
Location:804 → 856

PSI; Plexin repeat

pfam08337
Location:1311 → 1864

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:564 → 654

TIG_plexin; TIG domain

pfam18020
Location:708 → 802

TIG_2; TIG domain found in plexin
XM_047421017.1 → XP_047276973.1 plexin-A4 isoform X1

UniProtKB/Swiss-Prot

A4D1N6, E9PAM2, Q6UWC6, Q6ZW89, Q8N969, Q8ND00, Q8NEN3, Q9HCM2, Q9NTD4
XM_011516676.3 → XP_011514978.1 plexin-A4 isoform X3

Conserved Domains (7) summary

cd11274
Location:39 → 511

Sema_plexin_A4; The Sema domain, a protein interacting module, of Plexin A4

cd00603
Location:1142 → 1222

IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...

cd01179
Location:955 → 1038

IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01180
Location:858 → 953

IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01181
Location:1040 → 1140

IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

pfam01437
Location:509 → 555

PSI; Plexin repeat

cl02569
Location:1311 → 1339

RasGAP; Ras GTPase Activating Domain
XM_047421018.1 → XP_047276974.1 plexin-A4 isoform X5
XM_047421019.1 → XP_047276975.1 plexin-A4 isoform X4

UniProtKB/TrEMBL

A0A384NYW6