EXOC3L2

gene
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Also known as FLJ36147XTP7

Summary

EXOC3L2 (exocyst complex component 3 like 2, HGNC:30162) is a protein-coding gene on chromosome 19q13.32, encoding Exocyst complex component 3-like protein 2 (Q2M3D2).

The protein encoded by this gene is upregulated by vascular endothelial growth factor A and interacts with exocyst complex component 4. The encoded protein may be part of an exocyst complex that plays a role in cell membrane dynamics. Mutations in this gene may be associated with Alzheimer’s disease.

Source: NCBI Gene 90332 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): brain malformation renal syndrome (Strong, GenCC)
  • GWAS associations: 25
  • Clinical variants (ClinVar): 105 total — 5 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 28
  • MANE Select transcript: NM_001382422

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30162
Approved symbolEXOC3L2
Nameexocyst complex component 3 like 2
Location19q13.32
Locus typegene with protein product
StatusApproved
AliasesFLJ36147, XTP7
Ensembl geneENSG00000283632
Ensembl biotypeprotein_coding
OMIM616927
Entrez90332

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000413988, ENST00000857198, ENST00000952151

RefSeq mRNA: 1 — MANE Select: NM_001382422 NM_001382422

CCDS: CCDS92642

Canonical transcript exons

ENST00000413988 — 12 exons

ExonStartEnd
ENSE000011125934523176345231874
ENSE000011588674521237045213357
ENSE000027748684523852345239061
ENSE000028088874524534145245407
ENSE000037992794523419345234826
ENSE000038021574522477845224913
ENSE000038037484521752845217683
ENSE000038058024522766245227772
ENSE000038071744521607345216194
ENSE000038073674521819745218319
ENSE000038093204522797445228074
ENSE000038107604522816545228266

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 96.31.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2963 / max 63.2392, expressed in 277 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1814461.2963277

Top tissues by expression

217 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002396.31gold quality
secondary oocyteCL:000065591.91gold quality
buccal mucosa cellCL:000233690.46gold quality
cardia of stomachUBERON:000116288.12gold quality
substantia nigra pars reticulataUBERON:000196687.63silver quality
renal medullaUBERON:000036287.08gold quality
lateral nuclear group of thalamusUBERON:000273686.70silver quality
vena cavaUBERON:000408786.62silver quality
subthalamic nucleusUBERON:000190686.55silver quality
pylorusUBERON:000116686.10silver quality
substantia nigra pars compactaUBERON:000196585.81silver quality
lateral globus pallidusUBERON:000247685.77gold quality
nasal cavity epitheliumUBERON:000538485.73silver quality
ventral tegmental areaUBERON:000269185.66silver quality
dorsal plus ventral thalamusUBERON:000189785.60silver quality
skeletal muscle tissue of biceps brachiiUBERON:000450285.20silver quality
metanephros cortexUBERON:001053385.13gold quality
right lobe of thyroid glandUBERON:000111984.78gold quality
pericardiumUBERON:000240784.78gold quality
metanephrosUBERON:000008184.43gold quality
inferior vagus X ganglionUBERON:000536384.08silver quality
medulla oblongataUBERON:000189683.77silver quality
superior vestibular nucleusUBERON:000722783.24silver quality
ponsUBERON:000098882.79silver quality
adult mammalian kidneyUBERON:000008282.71gold quality
tongueUBERON:000172382.64silver quality
superior surface of tongueUBERON:000737182.62silver quality
body of tongueUBERON:001187682.50silver quality
tracheaUBERON:000312682.11silver quality
left lobe of thyroid glandUBERON:000112082.10gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-135922yes533.46
E-ANND-3yes3.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

41 targeting EXOC3L2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4425100.0067.591049
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-1915-3P99.5866.791988
HSA-MIR-6832-5P99.5864.821132
HSA-MIR-444199.4966.563216
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-318299.4068.152454
HSA-MIR-429199.2068.882969
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-92299.0267.231838
HSA-MIR-427099.0266.261987
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-939-3P98.9765.072347
HSA-MIR-214-3P98.7168.122128
HSA-MIR-76198.7168.072051
HSA-MIR-6840-3P98.6865.951923

Literature-anchored findings (GeneRIF, showing 5)

  • exoc3l2 silencing inhibits VEGF receptor 2 phosphorylation and VEGFA-directed migration of cultured endothelial cells. (PMID:21566143)
  • This study suggests that the rs597668 polymorphism near EXOC3L2 may not play a major role in the susceptibility to late-onset Alzheimer’s disease in the Northern Han Chinese population. (PMID:22381399)
  • This meta-analysis assesses an association between rs597668 polymorphism in EXOC3L2 and Alzheimer’s disease. (PMID:23663385)
  • EXOC3L2 rs597668 variant is associated with Alzheimer’s disease susceptibility. (PMID:28423615)
  • We propose that biallelic EXOC3L2 mutations lead to a novel syndrome that affects hindbrain development, kidney and possibly the bone marrow. (PMID:30327448)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioexoc3l2aENSDARG00000008414
danio_rerioexoc3l2bENSDARG00000030782
mus_musculusExoc3l2ENSMUSG00000011263
rattus_norvegicusExoc3l2ENSRNOG00000017448

Paralogs (4): EXOC3L1 (ENSG00000179044), EXOC3 (ENSG00000180104), TNFAIP2 (ENSG00000185215), EXOC3L4 (ENSG00000205436)

Protein

Protein identifiers

Exocyst complex component 3-like protein 2Q2M3D2 (reviewed: Q2M3D2)

Alternative names: HBV X-transactivated gene 7 protein, HBV XAg-transactivated protein 7

All UniProt accessions (1): Q2M3D2

UniProt curated annotations — full annotation on UniProt →

Disease relevance. Brain malformation renal syndrome (BMRS) [MIM:620943] An autosomal recessive syndrome characterized by brain abnormalities, Dandy-Walker malformation, and renal dysplasia. Dandy-Walker malformation features agenesis/hypoplasia of the cerebellar vermis, cystic dilatation of the fourth ventricle and enlargement of posterior fossa. The disease may be caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the SEC6 family.

RefSeq proteins (1): NP_001369351* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR010326EXOC3/Sec6Family
IPR042532EXOC3/Sec6_CHomologous_superfamily

Pfam: PF06046

UniProt features (9 total): region of interest 3, sequence variant 3, chain 1, coiled-coil region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2M3D2-F174.260.40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 134 (showing top): BENPORATH_ES_WITH_H3K27ME3, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, ROVERSI_GLIOMA_COPY_NUMBER_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, GOBP_SECRETION, CUI_TCF21_TARGETS_2_DN, GOCC_EXOCYST, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, LEE_BMP2_TARGETS_DN, GOCC_VESICLE_TETHERING_COMPLEX, ZNF282_TARGET_GENES, MIR15A_5P, MIR195_5P, MIR15B_5P

GO Biological Process (1): exocytosis (GO:0006887)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): exocyst (GO:0000145)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
vesicle-mediated transport1
secretion by cell1
vesicle fusion to plasma membrane1
binding1
cell cortex1
vesicle tethering complex1

Protein interactions and networks

STRING

692 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EXOC3L2PDE7BQ9NP56678
EXOC3L2PICALMQ13492661
EXOC3L2EXOC4Q96A65647
EXOC3L2MARK4Q96L34609
EXOC3L2BLOC1S3Q6QNY0598
EXOC3L2BIN1O00499597
EXOC3L2CLUP10909544
EXOC3L2MS4A6EQ96DS6517
EXOC3L2TNK1Q13470507
EXOC3L2ABCA7Q8IZY2506
EXOC3L2SEPTIN9Q9UHD8506
EXOC3L2CD2APQ9Y5K6471
EXOC3L2APOEP02649448
EXOC3L2SORL1Q92673447
EXOC3L2TOMM40O96008445

IntAct

23 interactions, top by confidence:

ABTypeScore
EXOC3L2TNFSF18psi-mi:“MI:0915”(physical association)0.560
MRPL12EXOC3L2psi-mi:“MI:0915”(physical association)0.560
BIKEXOC3L2psi-mi:“MI:0915”(physical association)0.560
EXOC3L2psi-mi:“MI:0915”(physical association)0.560
EXOC3L2GPR148psi-mi:“MI:0915”(physical association)0.560
EXOC3L2HSPA8psi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
EXOC3L2SIAH1psi-mi:“MI:0914”(association)0.350
PCDH20CAPN5psi-mi:“MI:0914”(association)0.350
TUBBVWA8psi-mi:“MI:0914”(association)0.350
UBR2NIPSNAP2psi-mi:“MI:0914”(association)0.350
MDC1SMCHD1psi-mi:“MI:2364”(proximity)0.270
EXOC3L2MRPL12psi-mi:“MI:0915”(physical association)0.000
EXOC3L2BIKpsi-mi:“MI:0915”(physical association)0.000
EXOC3L2psi-mi:“MI:0915”(physical association)0.000
EXOC3L2GPR148psi-mi:“MI:0915”(physical association)0.000

BioGRID (16): SIAH1 (Affinity Capture-MS), MIPEP (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), EXOC4 (Affinity Capture-Western), EXOC3L2 (Proximity Label-MS), EXOC3L2 (Two-hybrid), EXOC3L2 (Two-hybrid), EXOC3L2 (Two-hybrid), EXOC3L2 (Two-hybrid), EXOC3L2 (Two-hybrid), EXOC3L2 (Two-hybrid), EXOC3L2 (Positive Genetic), MIPEP (Affinity Capture-MS), SIAH1 (Affinity Capture-MS), EXOC3L2 (Negative Genetic)

ESM2 similar proteins: A0A8I5KY20, A2A9T0, A2IDD5, B0BNK9, B8ZZ34, C9JI98, C9JLR9, F5GYI3, O18734, P0CG25, P84157, Q0IIA6, Q0PHV7, Q0X0E2, Q13387, Q1RMK9, Q2M3D2, Q2TAM9, Q3ZCQ3, Q4VA45, Q673H1, Q69YZ2, Q6NS60, Q6P6N5, Q6PJ61, Q7Z6J2, Q80ZJ8, Q810I0, Q86SX3, Q86UD0, Q86XT2, Q8BNN1, Q8IUW3, Q8N4Y2, Q8N6N2, Q8QZV0, Q8R4T5, Q8TF61, Q8VCR9, Q8WXF8

Diamond homologs: A2AV37, O60645, Q0V8C2, Q0VCR8, Q2M3D2, Q62825, Q6KAR6, Q86VI1, Q8BI71, Q17RC7, Q6DIA2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

105 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic5
Likely pathogenic1
Uncertain significance62
Likely benign21
Benign10

Top pathogenic / likely-pathogenic (6)

Variant IDHGVSClassification
1027393NC_000019.9:g.(45728172_45730919)_(45731525_45735020)delPathogenic
1252026NM_001382422.1(EXOC3L2):c.1301T>A (p.Leu434Gln)Pathogenic
3340131EXOC3L2, LEU41GLNPathogenic
3340132EXOC3L2, ARG72TERPathogenic
3340134EXOC3L2, EX3-5DEL (SCV001519072)Pathogenic
3235909NM_001382422.1(EXOC3L2):c.1972dup (p.Gln658fs)Likely pathogenic

SpliceAI

891 predictions. Top by Δscore:

VariantEffectΔscore
19:45213354:CTGC:Cacceptor_gain1.0000
19:45213355:TGC:Tacceptor_gain1.0000
19:45213356:GC:Gacceptor_gain1.0000
19:45213357:CC:Cacceptor_gain1.0000
19:45213357:CCTG:Cacceptor_loss1.0000
19:45213358:C:CCacceptor_gain1.0000
19:45216068:CTCAC:Cdonor_loss1.0000
19:45216069:TCACC:Tdonor_loss1.0000
19:45216070:CACCT:Cdonor_loss1.0000
19:45216071:A:AGdonor_loss1.0000
19:45216072:C:Gdonor_loss1.0000
19:45216190:GACTC:Gacceptor_gain1.0000
19:45216191:ACTC:Aacceptor_gain1.0000
19:45216191:ACTCC:Aacceptor_gain1.0000
19:45216192:CTC:Cacceptor_gain1.0000
19:45216192:CTCC:Cacceptor_gain1.0000
19:45216192:CTCCT:Cacceptor_gain1.0000
19:45216193:TC:Tacceptor_gain1.0000
19:45216193:TCCT:Tacceptor_gain1.0000
19:45216194:CC:Cacceptor_gain1.0000
19:45216195:C:Aacceptor_loss1.0000
19:45216195:C:CCacceptor_gain1.0000
19:45216198:C:CTacceptor_gain1.0000
19:45217523:CTGA:Cdonor_loss1.0000
19:45217524:TGA:Tdonor_loss1.0000
19:45217525:GAC:Gdonor_loss1.0000
19:45217526:A:ACdonor_gain1.0000
19:45217527:C:CCdonor_gain1.0000
19:45217527:CCAG:Cdonor_gain1.0000
19:45217679:AGCGC:Aacceptor_gain1.0000

AlphaMissense

5011 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:45218289:A:GW191R0.998
19:45218289:A:TW191R0.998
19:45218287:C:AW191C0.997
19:45218287:C:GW191C0.997
19:45217537:G:CF270L0.995
19:45217537:G:TF270L0.995
19:45217539:A:GF270L0.995
19:45217539:A:TF270I0.994
19:45217665:G:CH228D0.994
19:45213334:A:TL322H0.992
19:45216097:A:GL306S0.992
19:45217538:A:GF270S0.992
19:45227983:A:GF95S0.992
19:45216154:A:GL287S0.991
19:45213220:A:GF360S0.990
19:45227982:G:CF95L0.990
19:45227982:G:TF95L0.990
19:45227984:A:GF95L0.990
19:45213219:A:CF360L0.989
19:45213219:A:TF360L0.989
19:45213221:A:GF360L0.989
19:45213220:A:CF360C0.988
19:45216118:A:TI299N0.988
19:45216120:G:CS298R0.988
19:45216120:G:TS298R0.988
19:45216122:T:GS298R0.988
19:45217550:A:GL266P0.988
19:45217571:A:GL259P0.988
19:45217539:A:CF270V0.987
19:45217667:A:GL227P0.987

dbSNP variants (sampled 300 via entrez): RS1000026004 (19:45216897 C>T), RS1000424724 (19:45225835 C>T), RS1000433164 (19:45246646 A>G,T), RS1000471139 (19:45214653 C>T), RS1000511579 (19:45231173 C>T), RS1000598048 (19:45244739 C>T), RS1000826049 (19:45238701 G>A), RS1000875981 (19:45242367 C>T), RS1000880315 (19:45226101 G>T), RS1000949929 (19:45238520 C>T), RS1000991360 (19:45242721 G>A), RS1001078940 (19:45215897 C>T), RS1001124255 (19:45237017 A>T), RS1001185061 (19:45228598 C>G), RS1001344003 (19:45234516 A>G,T)

Disease associations

OMIM: gene MIM:616927 | disease phenotypes: MIM:249000, MIM:620943

GenCC curated gene-disease

DiseaseClassificationInheritance
brain malformation renal syndromeStrongAutosomal recessive

Mondo (2): Meckel syndrome (MONDO:0018921), brain malformation renal syndrome (MONDO:0975799)

Orphanet (1): Meckel syndrome (Orphanet:564)

HPO phenotypes

28 total (28 of 28 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000092Renal tubular atrophy
HP:0000659Peters anomaly
HP:0000793Membranoproliferative glomerulonephritis
HP:0001305Dandy-Walker malformation
HP:0001320Cerebellar vermis hypoplasia
HP:0001562Oligohydramnios
HP:0001873Thrombocytopenia
HP:0001875Decreased total neutrophil count
HP:0001876Pancytopenia
HP:0001903Anemia
HP:0002089Pulmonary hypoplasia
HP:0002198Dilated fourth ventricle
HP:0003577Congenital onset
HP:0003774Stage 5 chronic kidney disease
HP:0004719Hyperechogenic kidneys
HP:0005445Enlarged posterior fossa
HP:0005528Bone marrow hypocellularity
HP:0007063Aplasia of the inferior half of the cerebellar vermis
HP:0011344Severe global developmental delay
HP:0025700Anhydramnios
HP:0030674Antenatal onset
HP:0031412Abnormal telomere morphology
HP:0034198Second trimester onset
HP:0040012Chromosome breakage
HP:0100307Cerebellar hemisphere hypoplasia
HP:0100333Unilateral cleft lip
HP:0100334Unilateral cleft palate

GWAS associations

25 associations (top):

StudyTraitp-value
GCST000337_21Quantitative traits2.000000e-06
GCST000337_22Quantitative traits4.000000e-07
GCST001337_36Platelet count4.000000e-10
GCST002422_1Alzheimer’s disease9.000000e-116
GCST003219_43Advanced age-related macular degeneration3.000000e-07
GCST004599_154Mean platelet volume6.000000e-78
GCST005194_29Coronary artery disease1.000000e-10
GCST005557_4Serum uric acid levels3.000000e-07
GCST005950_15Body mass index x sex x age interaction (4df test)2.000000e-10
GCST005951_56Body mass index1.000000e-06
GCST005952_8Body mass index (age>50)9.000000e-12
GCST005954_4Body mass index x age interaction2.000000e-07
GCST006701_3Parental longevity (father’s attained age)9.000000e-09
GCST006979_682Heel bone mineral density2.000000e-10
GCST007320_22Alzheimer’s disease or family history of Alzheimer’s disease2.000000e-22
GCST007320_41Alzheimer’s disease or family history of Alzheimer’s disease5.000000e-13
GCST007320_46Alzheimer’s disease or family history of Alzheimer’s disease4.000000e-12
GCST007827_3Alzheimer’s disease or HDL levels (pleiotropy)1.000000e-97
GCST007827_8Alzheimer’s disease or HDL levels (pleiotropy)3.000000e-36
GCST90002384_455Hemoglobin1.000000e-13
GCST90002395_417Mean platelet volume2.000000e-166
GCST90002401_295Platelet distribution width9.000000e-80
GCST90002402_566Platelet count2.000000e-52
GCST90002403_302Red blood cell count1.000000e-13
GCST90002407_629White blood cell count5.000000e-09

EFO canonical traits (15, from GWAS)

EFO IDTrait name
EFO:0004458C-reactive protein measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004309platelet count
EFO:1001492atrophic macular degeneration
EFO:0004761uric acid measurement
EFO:0004340body mass index
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0007796parental longevity
EFO:0009270heel bone mineral density
EFO:0009268family history of Alzheimer’s disease
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004509hemoglobin measurement
EFO:0007984platelet component distribution width
EFO:0004305erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation2
sodium arseniteincreases expression1
aflatoxin B2decreases methylation1
maleic acidincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression, affects response to substance, increases expression1
CGP 52608affects binding, increases reaction1
nutlin 3affects cotreatment, increases expression1
abrineincreases expression1
licochalcone Bincreases expression1
jinfukangaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Fulvestrantincreases methylation1
Arsenicaffects methylation1
Camptothecinincreases expression1
Cisplatinaffects cotreatment, decreases expression1
Dactinomycinaffects cotreatment, increases expression1
Hydralazineaffects cotreatment, increases expression1
Lipopolysaccharidesaffects response to substance, increases expression, affects cotreatment, decreases expression1
Plant Extractsdecreases expression, affects cotreatment1
Triclosandecreases expression1
Valproic Acidincreases expression, affects cotreatment1

Clinical trials (associated diseases)

1 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT01401998Not specifiedRECRUITINGARPKD Database Study