GOLPH3L

Summary

GOLPH3L (golgi phosphoprotein 3 like, HGNC:24882) is a protein-coding gene on chromosome 1q21.3, encoding Golgi phosphoprotein 3-like (Q9H4A5). Phosphatidylinositol-4-phosphate-binding protein that may antagonize the action of GOLPH3 which is required for the process of vesicle budding at the Golgi and anterograde transport to the plasma membrane.

The Golgi complex plays a key role in the sorting and modification of proteins exported from the endoplasmic reticulum. The protein encoded by this gene is localized at the Golgi stack and may have a regulatory role in Golgi trafficking.

Source: NCBI Gene 55204 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_018178

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24882
Approved symbol	GOLPH3L
Name	golgi phosphoprotein 3 like
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	GPP34R
Ensembl gene	ENSG00000143457
Ensembl biotype	protein_coding
OMIM	612208
Entrez	55204

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000271732, ENST00000427665, ENST00000479757, ENST00000854641, ENST00000854642, ENST00000854643, ENST00000854644, ENST00000943663, ENST00000943664

RefSeq mRNA: 1 — MANE Select: NM_018178 NM_018178

CCDS: CCDS966

Canonical transcript exons

ENST00000271732 — 5 exons

Exon	Start	End
ENSE00001044393	150661814	150661928
ENSE00001186225	150663632	150663763
ENSE00001186227	150646230	150648748
ENSE00001186230	150694656	150694850
ENSE00001864797	150696992	150697154

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 96.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.6415 / max 535.5347, expressed in 1764 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14340	21.7607	1752
14341	3.8420	1433
14339	2.0387	1015

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	96.42	gold quality
secondary oocyte	CL:0000655	96.00	gold quality
caput epididymis	UBERON:0004358	95.40	gold quality
ileal mucosa	UBERON:0000331	95.06	gold quality
colonic mucosa	UBERON:0000317	93.93	gold quality
rectum	UBERON:0001052	93.88	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.43	gold quality
epithelium of bronchus	UBERON:0002031	93.42	gold quality
bronchus	UBERON:0002185	93.17	gold quality
bronchial epithelial cell	CL:0002328	93.08	gold quality
esophagus squamous epithelium	UBERON:0006920	93.02	gold quality
islet of Langerhans	UBERON:0000006	92.97	gold quality
epithelium of esophagus	UBERON:0001976	92.87	gold quality
oocyte	CL:0000023	92.75	gold quality
nasal cavity epithelium	UBERON:0005384	92.49	gold quality
lower esophagus mucosa	UBERON:0035834	92.08	gold quality
palpebral conjunctiva	UBERON:0001812	92.07	gold quality
cauda epididymis	UBERON:0004360	91.79	gold quality
epithelium of nasopharynx	UBERON:0001951	91.40	gold quality
nasopharynx	UBERON:0001728	91.39	gold quality
choroid plexus epithelium	UBERON:0003911	91.38	gold quality
mucosa of transverse colon	UBERON:0004991	90.76	gold quality
buccal mucosa cell	CL:0002336	90.70	gold quality
amniotic fluid	UBERON:0000173	90.65	gold quality
parotid gland	UBERON:0001831	90.26	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.17	gold quality
eye	UBERON:0000970	90.13	gold quality
pancreas	UBERON:0001264	90.09	gold quality
mucosa of paranasal sinus	UBERON:0005030	89.93	gold quality
nasal cavity mucosa	UBERON:0001826	89.89	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.34
E-MTAB-7303	no	635.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting GOLPH3L, 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-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-150-5P	99.99	66.69	1976
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
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-96-5P	99.95	72.80	2140

Literature-anchored findings (GeneRIF, showing 3)

• GOLPH3L differs critically from GOLPH3 in that it is largely unable to bind to MYO18A; data demonstrate that despite their similarities, unexpectedly, GOLPH3L antagonizes GOLPH3/MYO18A at the Golgi (PMID:23345592)
• The miR-1185-2-3p-GOLPH3L pathway promotes glucose metabolism in breast cancer by stabilizing p53-induced SERPINE1. (PMID:33509226)
• GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles. (PMID:34473204)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	golph3l	ENSDARG00000036943
mus_musculus	Golph3l	ENSMUSG00000046519
rattus_norvegicus	Golph3l	ENSRNOG00000047620
drosophila_melanogaster	sau	FBGN0267378
caenorhabditis_elegans	Y47G6A.18	WBGENE00021644

Paralogs (1): GOLPH3 (ENSG00000113384)

Protein

Protein identifiers

Golgi phosphoprotein 3-like — Q9H4A5 (reviewed: Q9H4A5)

Alternative names: GPP34-related protein

All UniProt accessions (2): Q9H4A5, Q5T5I6

UniProt curated annotations — full annotation on UniProt →

Function. Phosphatidylinositol-4-phosphate-binding protein that may antagonize the action of GOLPH3 which is required for the process of vesicle budding at the Golgi and anterograde transport to the plasma membrane.

Subunit / interactions. Homooligomer. Does not interact MYO18; differs from GOLPH3 by its inability to interact with MYO18. May interact with ARF1.

Subcellular location. Golgi apparatus. Golgi stack membrane. trans-Golgi network membrane.

Similarity. Belongs to the GOLPH3/VPS74 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H4A5-1	1	yes
Q9H4A5-2	2

RefSeq proteins (1): NP_060648* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008628	GPP34-like	Family
IPR038261	GPP34-like_sf	Homologous_superfamily

Pfam: PF05719

UniProt features (12 total): binding site 4, region of interest 2, chain 1, mutagenesis site 1, sequence conflict 1, compositionally biased region 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H4A5-F1	84.75	0.71

Functional residue map

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

Ligand- & substrate-binding residues (4): 67; 76; 157; 160

Post-translational modifications (1): 112

Mutagenesis-validated functional residues (1):

Position	Phenotype
7–10	loss of binding to coatomer.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 237 (showing top): CCAWYNNGAAR_UNKNOWN, GOBP_VESICLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_PROTEIN_TARGETING, AP4_Q6, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, CAGCTG_AP4_Q5, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, EFC_Q6, MODULE_331, GOBP_REGULATION_OF_PROTEIN_SECRETION, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, WTGAAAT_UNKNOWN

GO Biological Process (6): retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), Golgi organization (GO:0007030), Golgi to plasma membrane protein transport (GO:0043001), Golgi vesicle budding (GO:0048194), positive regulation of protein secretion (GO:0050714), protein targeting to Golgi apparatus (GO:0140450)

GO Molecular Function (4): phosphatidylinositol-4-phosphate binding (GO:0070273), cargo adaptor activity (GO:0140312), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (8): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), cytosol (GO:0005829), Golgi cisterna (GO:0031985), Golgi cisterna membrane (GO:0032580), trans-Golgi network membrane (GO:0032588), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
Golgi vesicle transport	2
binding	2
cytoplasm	2
Golgi apparatus subcompartment	2
cellular anatomical structure	2
organelle membrane	2
organelle organization	1
endomembrane system organization	1
Golgi to plasma membrane transport	1
protein transport	1
establishment of protein localization to plasma membrane	1
protein localization to plasma membrane	1
Golgi membrane	1
vesicle budding from membrane	1
protein secretion	1
regulation of protein secretion	1
positive regulation of protein transport	1
positive regulation of secretion by cell	1
protein targeting	1
establishment of protein localization to organelle	1
anion binding	1
phosphatidylinositol phosphate binding	1
vesicle-mediated transport	1
protein-macromolecule adaptor activity	1
Golgi apparatus	1
bounding membrane of organelle	1
endomembrane system	1
intracellular membrane-bounded organelle	1
Golgi stack	1
Golgi cisterna	1
trans-Golgi network	1

Protein interactions and networks

STRING

1084 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLPH3L	MYO18A	Q92614	771
GOLPH3L	GALNT2	Q10471	554
GOLPH3L	PI4KB	P78405	548
GOLPH3L	HORMAD1	Q86X24	508
GOLPH3L	RAB1A	P11476	478
GOLPH3L	ST6GAL1	P15907	469
GOLPH3L	ARCN1	P48444	442
GOLPH3L	NAGPA	Q9UK23	441
GOLPH3L	DNAJB5	O75953	437
GOLPH3L	CHPF	Q8IZ52	433
GOLPH3L	VGLL4	Q14135	417
GOLPH3L	MAN2A1	Q16706	410
GOLPH3L	THOC5	Q13769	410
GOLPH3L	ZNF772	Q68DY9	410
GOLPH3L	POMT1	Q9Y6A1	406

IntAct

89 interactions, top by confidence:

A	B	Type	Score
HTT	GOLPH3L	psi-mi:“MI:0915”(physical association)	0.700
GOLPH3L	HTT	psi-mi:“MI:0915”(physical association)	0.700
STX12	SNAP23	psi-mi:“MI:0914”(association)	0.640
SLC39A5	FAM171A2	psi-mi:“MI:0914”(association)	0.640
LNX1	GOLPH3L	psi-mi:“MI:0915”(physical association)	0.560
GOLPH3L	LNX1	psi-mi:“MI:0915”(physical association)	0.560
GOLPH3L	DNM2	psi-mi:“MI:0915”(physical association)	0.560
GOLPH3L	TOR1A	psi-mi:“MI:0915”(physical association)	0.560
GOLPH3L		psi-mi:“MI:0915”(physical association)	0.560

BioGRID (132): LNX1 (Two-hybrid), GOLPH3L (Affinity Capture-RNA), GOLPH3L (Affinity Capture-RNA), GOLPH3L (Two-hybrid), GOLPH3L (Affinity Capture-Western), COP1 (Reconstituted Complex), SEC26 (Reconstituted Complex), SEC27 (Reconstituted Complex), SEC21 (Reconstituted Complex), RET2 (Reconstituted Complex), SEC28 (Reconstituted Complex), GOLPH3L (Affinity Capture-MS), GOLPH3L (Affinity Capture-MS), GOLPH3L (Affinity Capture-MS), GOLPH3L (Two-hybrid)

ESM2 similar proteins: A0JPI4, A6H7F6, A8WZU5, A8XEZ1, A8XYX3, D8WUA4, F4JIN3, F4JMJ3, O14205, O74737, P0C5E7, P46555, P62583, Q06385, Q0VCR7, Q14156, Q23541, Q3V3R1, Q4VBT2, Q54J20, Q5PPU5, Q5SPP5, Q5U4Q6, Q61T02, Q641A2, Q66H74, Q6C710, Q6FLD4, Q6FPH9, Q6ZQ18, Q75B51, Q8AVH4, Q8BG67, Q8GWG2, Q8IGJ0, Q8R088, Q8STE5, Q8VZM7, Q8WT44, Q96TA2

Diamond homologs: A0JPI4, A6H7F6, O14205, P62583, Q06385, Q5PPU5, Q5U4Q6, Q66H74, Q8R088, Q9CRA5, Q9ERE4, Q9H4A5, Q9H4A6, Q9VQ93

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TFEB	“up-regulates quantity by expression”	GOLPH3L	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1103 predictions. Top by Δscore:

Variant	Effect	Δscore
1:150648744:CTCAC:C	acceptor_gain	1.0000
1:150648746:CAC:C	acceptor_gain	1.0000
1:150648747:ACC:A	acceptor_loss	1.0000
1:150648748:CCT:C	acceptor_loss	1.0000
1:150648749:C:CC	acceptor_gain	1.0000
1:150648750:T:A	acceptor_loss	1.0000
1:150661807:ATCTT:A	donor_loss	1.0000
1:150661808:TCTTA:T	donor_loss	1.0000
1:150661809:CTTAC:C	donor_loss	1.0000
1:150661810:TTAC:T	donor_loss	1.0000
1:150661811:T:TG	donor_loss	1.0000
1:150661812:A:AC	donor_gain	1.0000
1:150661812:A:AG	donor_loss	1.0000
1:150661813:C:CC	donor_gain	1.0000
1:150661928:CCTT:C	acceptor_gain	1.0000
1:150661931:T:C	acceptor_gain	1.0000
1:150661931:T:TC	acceptor_gain	1.0000
1:150663628:GTAC:G	donor_loss	1.0000
1:150663629:TA:T	donor_loss	1.0000
1:150663630:ACCTT:A	donor_loss	1.0000
1:150663631:C:CT	donor_loss	1.0000
1:150663631:CCTTT:C	donor_gain	1.0000
1:150663759:TACCC:T	acceptor_gain	1.0000
1:150663760:ACCC:A	acceptor_gain	1.0000
1:150663761:CCC:C	acceptor_gain	1.0000
1:150663761:CCCC:C	acceptor_gain	1.0000
1:150663762:CC:C	acceptor_gain	1.0000
1:150663762:CCC:C	acceptor_gain	1.0000
1:150663763:CC:C	acceptor_gain	1.0000
1:150663764:C:CC	acceptor_gain	1.0000

AlphaMissense

1851 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:150648617:G:C	H188D	1.000
1:150648630:A:C	F183L	1.000
1:150648630:A:T	F183L	1.000
1:150648631:A:C	F183C	1.000
1:150648631:A:G	F183S	1.000
1:150648632:A:G	F183L	1.000
1:150648639:G:C	F180L	1.000
1:150648639:G:T	F180L	1.000
1:150648640:A:G	F180S	1.000
1:150648641:A:G	F180L	1.000
1:150648661:A:G	L173P	1.000
1:150648679:A:G	L167P	1.000
1:150648684:C:A	K165N	1.000
1:150648684:C:G	K165N	1.000
1:150648740:A:G	W147R	1.000
1:150648740:A:T	W147R	1.000
1:150648748:C:T	G144D	1.000
1:150661819:A:G	L142P	1.000
1:150661822:A:G	L141P	1.000
1:150661832:A:G	W138R	1.000
1:150661832:A:T	W138R	1.000
1:150663699:A:G	L83P	1.000
1:150663717:C:T	G77E	1.000
1:150663723:A:G	L75P	1.000
1:150663748:A:G	W67R	1.000
1:150663748:A:T	W67R	1.000
1:150663762:C:T	G62E	1.000
1:150663763:C:A	G62W	1.000
1:150663763:C:G	G62R	1.000
1:150663763:C:T	G62R	1.000

dbSNP variants (sampled 300 via entrez): RS1000028554 (1:150682095 C>A), RS1000048454 (1:150689981 C>A), RS1000151668 (1:150682528 C>G), RS1000156933 (1:150649712 T>C), RS1000206613 (1:150685978 A>T), RS1000210115 (1:150675372 A>G), RS1000248515 (1:150649235 A>C), RS1000285727 (1:150685705 A>G), RS1000390416 (1:150668977 A>G), RS1000492942 (1:150662284 G>A), RS1000566543 (1:150662728 A>T), RS1000622821 (1:150666769 ATTTT>A,AT,ATT), RS1000630421 (1:150652945 TAA>T), RS1000655326 (1:150666601 G>T), RS1000693721 (1:150655543 A>T)

Disease associations

OMIM: gene MIM:612208 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

15 associations (top):

Study	Trait	p-value
GCST001966_1	Rhegmatogenous retinal detachment	1.000000e-07
GCST002606_27	Prostate cancer	3.000000e-09
GCST002606_8	Prostate cancer	6.000000e-11
GCST004633_95	Neutrophil percentage of white cells	9.000000e-19
GCST005951_38	Body mass index	4.000000e-09
GCST007565_51	Morning person	6.000000e-15
GCST007576_309	Chronotype	3.000000e-10
GCST008870_9	Keratinocyte cancer (MTAG)	8.000000e-14
GCST008871_73	Basal cell carcinoma	1.000000e-14
GCST008971_131	Urate levels	1.000000e-14
GCST010002_366	Refractive error	3.000000e-15
GCST010244_169	Triglyceride levels	2.000000e-08
GCST011124_1	Caffeine consumption from tea	6.000000e-10
GCST011125_1	Caffeine consumption from coffee	5.000000e-09
GCST011126_7	Caffeine consumption from coffee or tea	1.000000e-26

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007990	neutrophil percentage of leukocytes
EFO:0004340	body mass index
EFO:0008328	chronotype measurement
EFO:0010176	keratinocyte carcinoma
EFO:0004531	urate measurement
EFO:0004530	triglyceride measurement
EFO:0010091	tea consumption measurement
EFO:0006781	coffee consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation	3
Cyclosporine	increases expression	3
sodium arsenite	increases expression, affects cotreatment	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
bisphenol F	affects cotreatment, increases expression	1
pirinixic acid	increases expression, affects binding, increases activity	1
perfluorooctanoic acid	increases expression	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
pentabromodiphenyl ether	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
ICG 001	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ketoconazole	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1
Silicon Dioxide	decreases expression	1
Tretinoin	increases expression, affects cotreatment	1
Tunicamycin	increases expression	1
Urethane	increases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1

Clinical trials (associated diseases)

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