EXOC3L4

Summary

EXOC3L4 (exocyst complex component 3 like 4, HGNC:20120) is a protein-coding gene on chromosome 14q32.32, encoding Exocyst complex component 3-like protein 4 (Q17RC7).

Predicted to enable SNARE binding activity. Predicted to be involved in exocyst localization and exocytosis. Predicted to be part of exocyst.

Source: NCBI Gene 91828 — RefSeq curated summary.

At a glance

• GWAS associations: 25
• Clinical variants (ClinVar): 168 total — 2 pathogenic
• MANE Select transcript: NM_001077594

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20120
Approved symbol	EXOC3L4
Name	exocyst complex component 3 like 4
Location	14q32.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205436
Ensembl biotype	protein_coding
OMIM	621085
Entrez	91828

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 22 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000380069, ENST00000559116, ENST00000559661, ENST00000559693, ENST00000560102, ENST00000560304, ENST00000560925, ENST00000687959, ENST00000688303, ENST00000865814, ENST00000865815, ENST00000865816, ENST00000865817, ENST00000865818, ENST00000865819, ENST00000865820, ENST00000865821, ENST00000865822, ENST00000865823, ENST00000865824, ENST00000953216, ENST00000953217, ENST00000953218, ENST00000953219, ENST00000953220, ENST00000953221

RefSeq mRNA: 3 — MANE Select: NM_001077594 NM_001077594, NM_001394941, NM_001394942

CCDS: CCDS32163

Canonical transcript exons

ENST00000688303 — 12 exons

Exon	Start	End
ENSE00001483647	103104738	103104838
ENSE00001483648	103104267	103104389
ENSE00001483651	103102118	103102772
ENSE00002547800	103094725	103094840
ENSE00003469318	103106785	103106899
ENSE00003527050	103108396	103108517
ENSE00003548478	103107631	103107783
ENSE00003632125	103107424	103107543
ENSE00003652255	103103941	103104052
ENSE00003656524	103104992	103105072
ENSE00003929751	103110031	103110559
ENSE00003931365	103100204	103100613

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 97.63.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	97.63	gold quality
liver	UBERON:0002107	90.47	gold quality
mucosa of transverse colon	UBERON:0004991	89.28	gold quality
small intestine Peyer’s patch	UBERON:0003454	87.34	gold quality
duodenum	UBERON:0002114	86.59	gold quality
small intestine	UBERON:0002108	85.99	gold quality
pancreatic ductal cell	CL:0002079	85.92	silver quality
spleen	UBERON:0002106	83.06	gold quality
transverse colon	UBERON:0001157	82.83	gold quality
body of stomach	UBERON:0001161	81.70	gold quality
buccal mucosa cell	CL:0002336	81.44	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	80.49	gold quality
mucosa of stomach	UBERON:0001199	80.10	gold quality
metanephros cortex	UBERON:0010533	79.67	gold quality
stomach	UBERON:0000945	79.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.43	gold quality
lymph node	UBERON:0000029	79.31	gold quality
adult mammalian kidney	UBERON:0000082	79.17	gold quality
vermiform appendix	UBERON:0001154	78.29	gold quality
fundus of stomach	UBERON:0001160	77.26	gold quality
intestine	UBERON:0000160	77.20	gold quality
cortex of kidney	UBERON:0001225	75.82	gold quality
gall bladder	UBERON:0002110	75.70	gold quality
colon	UBERON:0001155	74.93	gold quality
large intestine	UBERON:0000059	74.73	gold quality
jejunal mucosa	UBERON:0000399	74.66	gold quality
upper lobe of left lung	UBERON:0008952	74.45	gold quality
tendon of biceps brachii	UBERON:0008188	74.44	gold quality
caecum	UBERON:0001153	74.40	gold quality
kidney epithelium	UBERON:0004819	74.20	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.25

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting EXOC3L4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-6837-3P	98.42	66.71	1149
HSA-MIR-6804-5P	98.39	65.77	1084
HSA-MIR-4494	97.86	64.93	850
HSA-MIR-647	97.73	67.79	927
HSA-MIR-6859-3P	97.26	64.69	428

Literature-anchored findings (GeneRIF, showing 1)

• Rare variants in the splicing regulatory elements of EXOC3L4 are associated with Alzheimer’s disease. (PMID:30255815)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	exoc3l4	ENSDARG00000058180
danio_rerio	si:dkey-45k15.1	ENSDARG00000061714
mus_musculus	Exoc3l4	ENSMUSG00000021280
rattus_norvegicus	Exoc3l4	ENSRNOG00000010111

Paralogs (4): EXOC3L1 (ENSG00000179044), EXOC3 (ENSG00000180104), TNFAIP2 (ENSG00000185215), EXOC3L2 (ENSG00000283632)

Protein

Protein identifiers

Exocyst complex component 3-like protein 4 — Q17RC7 (reviewed: Q17RC7)

All UniProt accessions (4): Q17RC7, H0YNJ4, H0YNV0, H0YNV7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SEC6 family.

RefSeq proteins (3): NP_001071062, NP_001381870, NP_001381871 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010326	EXOC3/Sec6	Family
IPR042532	EXOC3/Sec6_C	Homologous_superfamily

Pfam: PF06046

UniProt features (12 total): sequence variant 5, region of interest 2, compositionally biased region 2, modified residue 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q17RC7-F1	78.98	0.54

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 52, 513

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, FOSTER_TOLERANT_MACROPHAGE_UP, GOBP_SECRETION, chr14q32, GOCC_EXOCYST, GOMF_SNARE_BINDING, CHEN_METABOLIC_SYNDROM_NETWORK, BRUINS_UVC_RESPONSE_LATE, GOBP_PROTEIN_CONTAINING_COMPLEX_LOCALIZATION, GOBP_EXOCYST_LOCALIZATION, HUANG_GATA2_TARGETS_DN, GOCC_VESICLE_TETHERING_COMPLEX, CBX5_TARGET_GENES, FOXN3_TARGET_GENES

GO Biological Process (2): exocytosis (GO:0006887), exocyst localization (GO:0051601)

GO Molecular Function (1): SNARE binding (GO:0000149)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
vesicle-mediated transport	1
secretion by cell	1
vesicle fusion to plasma membrane	1
protein-containing complex localization	1
protein binding	1
cell cortex	1
vesicle tethering complex	1

Protein interactions and networks

STRING

706 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EXOC3L4	OR7E24	Q6IFN5	562
EXOC3L4	ALS2CL	Q60I27	505
EXOC3L4	IQCJ	Q1A5X6	467
EXOC3L4	POU2AF2	Q8IXP5	446
EXOC3L4	EFNA2	O43921	434
EXOC3L4	EFNA4	P52798	423
EXOC3L4	GGT1	P19440	413
EXOC3L4	EXOC3L1	Q86VI1	407
EXOC3L4	CFAP263	Q9H0I3	402
EXOC3L4	EFNA5	P52803	400
EXOC3L4	HPDL	Q96IR7	395
EXOC3L4	CAPSL	Q8WWF8	395
EXOC3L4	TMEM39A	Q9NV64	391
EXOC3L4	APBA1	Q02410	388
EXOC3L4	TBC1D32	Q96NH3	377
EXOC3L4	TBC1D30	Q9Y2I9	377

IntAct

0 interactions, top by confidence:

BioGRID (4): EXOC3L4 (Affinity Capture-MS), EXOC3L4 (Affinity Capture-MS), EXOC3L4 (Affinity Capture-MS), EXOC3L4 (Affinity Capture-MS)

ESM2 similar proteins: A2AV37, A2BID5, A2VDR8, A7E2Y6, A7Z033, B4DZS4, O15068, O35821, O60645, O70576, O94812, P52630, P83436, Q01755, Q03169, Q08CY4, Q0P4Q0, Q0V8C2, Q14746, Q15021, Q17RC7, Q19262, Q1LXZ7, Q2TBH9, Q3T1G7, Q3TBD2, Q3UM29, Q5H9J9, Q5XI00, Q61333, Q62825, Q63406, Q64096, Q6DIA2, Q6GPP1, Q6KAR6, Q7T006, Q80TT2, Q80VA5, Q8K1H7

Diamond homologs: Q17RC7, Q2M3D2, Q6DIA2, Q0VCR8, Q86VI1, Q8BI71

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	139
Likely benign	14
Benign	3

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
57839	GRCh38/hg38 14q32.31-32.33(chr14:102210395-104449321)x1	Pathogenic
815679	GRCh37/hg19 14q32.31-32.33(chr14:103153637-107285437)x1	Pathogenic

SpliceAI

1910 predictions. Top by Δscore:

Variant	Effect	Δscore
14:103100611:CAG:C	donor_loss	1.0000
14:103100613:GGTAA:G	donor_loss	1.0000
14:103100614:G:GA	donor_loss	1.0000
14:103102768:GGCAG:G	donor_gain	1.0000
14:103102769:GCAG:G	donor_gain	1.0000
14:103102769:GCAGG:G	donor_gain	1.0000
14:103102770:CAGG:C	donor_loss	1.0000
14:103102773:G:C	donor_loss	1.0000
14:103104050:G:GT	donor_gain	1.0000
14:103104263:CCAG:C	acceptor_loss	1.0000
14:103104265:A:AC	acceptor_loss	1.0000
14:103104265:A:AG	acceptor_gain	1.0000
14:103104265:AG:A	acceptor_gain	1.0000
14:103104266:G:GT	acceptor_gain	1.0000
14:103104266:GG:G	acceptor_gain	1.0000
14:103104378:G:GT	donor_gain	1.0000
14:103104407:GGGC:G	donor_gain	1.0000
14:103104419:G:T	donor_gain	1.0000
14:103104736:A:AG	acceptor_gain	1.0000
14:103104737:G:GG	acceptor_gain	1.0000
14:103104834:CCCAG:C	donor_loss	1.0000
14:103104836:CAG:C	donor_loss	1.0000
14:103104837:AG:A	donor_loss	1.0000
14:103104838:GGT:G	donor_loss	1.0000
14:103104839:G:A	donor_loss	1.0000
14:103104987:CCCA:C	acceptor_loss	1.0000
14:103104988:CCA:C	acceptor_loss	1.0000
14:103104989:CAG:C	acceptor_loss	1.0000
14:103104990:A:AG	acceptor_gain	1.0000
14:103104990:AG:A	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000072844 (14:103101098 G>T), RS1000456285 (14:103092508 G>T), RS1000855439 (14:103107701 G>A,C), RS1001061676 (14:103101138 C>T), RS1001131814 (14:103102502 C>T), RS1001265957 (14:103110889 G>A), RS1001363898 (14:103108408 A>G), RS1001421396 (14:103106024 G>A), RS1001454542 (14:103093746 C>T), RS1001471839 (14:103106254 C>A,T), RS1001868445 (14:103102107 C>T), RS1002073488 (14:103098396 G>GA), RS1002094314 (14:103094496 G>A), RS1002120117 (14:103097424 G>A,T), RS1002360705 (14:103101804 T>C,G)

Disease associations

OMIM: gene MIM:621085 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

25 associations (top):

Study	Trait	p-value
GCST001277_24	Liver enzyme levels (gamma-glutamyl transferase)	6.000000e-29
GCST001307_3	Gamma glutamyl transferase levels	5.000000e-13
GCST001335_26	Mean platelet volume	5.000000e-11
GCST001337_45	Platelet count	2.000000e-10
GCST003129_9	Primary biliary cholangitis	6.000000e-19
GCST004599_174	Mean platelet volume	7.000000e-70
GCST004599_175	Mean platelet volume	2.000000e-18
GCST004603_156	Platelet count	5.000000e-39
GCST004607_105	Plateletcrit	7.000000e-09
GCST004616_58	Platelet distribution width	2.000000e-23
GCST005951_8	Body mass index	7.000000e-09
GCST005991_36	Platelet count	9.000000e-22
GCST006019_5	Gamma glutamyl transferase levels	1.000000e-78
GCST009652_27	Serum alkaline phosphatase levels	8.000000e-09
GCST011349_20	Gamma glutamyl transferase levels	2.000000e-88
GCST90002395_215	Mean platelet volume	5.000000e-172
GCST90002395_216	Mean platelet volume	2.000000e-13
GCST90002395_217	Mean platelet volume	1.000000e-20
GCST90002400_149	Plateletcrit	3.000000e-11
GCST90002401_85	Platelet distribution width	2.000000e-36
GCST90002402_202	Platelet count	8.000000e-79
GCST90002402_203	Platelet count	2.000000e-10
GCST90011900_109	Serum alkaline phosphatase levels	2.000000e-11
GCST90013406_147	Liver enzyme levels (alkaline phosphatase)	3.000000e-23
GCST90013407_2	Liver enzyme levels (gamma-glutamyl transferase)	1.000000e-300

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004532	serum gamma-glutamyl transferase measurement
EFO:0004309	platelet count
EFO:0007985	platelet crit
EFO:0007984	platelet component distribution width
EFO:0004340	body mass index
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation, increases expression	3
sodium arsenite	increases expression, decreases expression	2
Tobacco Smoke Pollution	decreases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
sotorasib	affects cotreatment, increases expression	1
methyleugenol	decreases expression	1
propionaldehyde	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, decreases expression	1
trametinib	affects cotreatment, increases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Folic Acid	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Triclosan	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression, increases methylation	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
S-Nitrosoglutathione	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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