GOLGA3

Summary

GOLGA3 (golgin A3, HGNC:4426) is a protein-coding gene on chromosome 12q24.33, encoding Golgin subfamily A member 3 (Q08378). Golgi auto-antigen; probably involved in maintaining Golgi structure.

The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. This gene encodes a member of the golgin family of proteins which are localized to the Golgi. Its encoded protein has been postulated to play a role in nuclear transport and Golgi apparatus localization. Several alternatively spliced transcript variants that encode different protein isoforms have been described for this gene.

Source: NCBI Gene 2802 — RefSeq curated summary.

At a glance

• Gene–disease (curated): primary ciliary dyskinesia (Limited, GenCC)
• GWAS associations: 6
• Clinical variants (ClinVar): 327 total
• Druggable target: yes
• MANE Select transcript: NM_001389683

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4426
Approved symbol	GOLGA3
Name	golgin A3
Location	12q24.33
Locus type	gene with protein product
Status	Approved
Aliases	golgin-160, GCP170, MEA-2
Ensembl gene	ENSG00000090615
Ensembl biotype	protein_coding
OMIM	602581
Entrez	2802

Gene structure

Transcript identifiers

Ensembl transcripts: 43 — 28 protein_coding, 11 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000204726, ENST00000450791, ENST00000456883, ENST00000534967, ENST00000537317, ENST00000545875, ENST00000652603, ENST00000685120, ENST00000685195, ENST00000685283, ENST00000685450, ENST00000685580, ENST00000686425, ENST00000686751, ENST00000687165, ENST00000687190, ENST00000687479, ENST00000687502, ENST00000688068, ENST00000688114, ENST00000688251, ENST00000688772, ENST00000689441, ENST00000689813, ENST00000690057, ENST00000690178, ENST00000690465, ENST00000690511, ENST00000690573, ENST00000690709, ENST00000690897, ENST00000691636, ENST00000691696, ENST00000692253, ENST00000692289, ENST00000692384, ENST00000692831, ENST00000692951, ENST00000693112, ENST00000693437, ENST00000693666, ENST00000867277, ENST00000920473

RefSeq mRNA: 9 — MANE Select: NM_001389683 NM_001172557, NM_001389683, NM_001389684, NM_001389685, NM_001389686, NM_001389687, NM_001389688, NM_001389689, NM_005895

CCDS: CCDS53846, CCDS91785, CCDS9281

Canonical transcript exons

ENST00000450791 — 24 exons

Exon	Start	End
ENSE00000757615	132784164	132784307
ENSE00000757616	132782296	132782493
ENSE00000757617	132780798	132780914
ENSE00000757618	132777666	132777805
ENSE00000757619	132776958	132777090
ENSE00000757620	132776634	132776756
ENSE00000874404	132821996	132822311
ENSE00000896261	132775141	132775305
ENSE00003551605	132774157	132774320
ENSE00003801386	132786693	132786787
ENSE00003802150	132816540	132816812
ENSE00003803151	132795852	132796220
ENSE00003803780	132789027	132789290
ENSE00003803892	132791216	132791293
ENSE00003804068	132807177	132807288
ENSE00003807603	132796539	132796700
ENSE00003807639	132786339	132786555
ENSE00003808247	132798340	132798477
ENSE00003810173	132807891	132808549
ENSE00003810716	132801767	132801969
ENSE00003810834	132804716	132805022
ENSE00003811284	132813307	132813419
ENSE00003842772	132768914	132773294
ENSE00003924495	132828803	132828869

Expression profiles

Bgee: expression breadth ubiquitous, 296 present calls, max score 98.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.5189 / max 118.3078, expressed in 1812 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134241	19.6668	1810
134243	1.3411	1031
134240	0.8177	584
134242	0.5765	367
134239	0.1167	55

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	98.01	gold quality
tibia	UBERON:0000979	96.81	gold quality
thymus	UBERON:0002370	95.25	gold quality
medial globus pallidus	UBERON:0002477	94.29	gold quality
cardia of stomach	UBERON:0001162	94.15	gold quality
stromal cell of endometrium	CL:0002255	93.77	gold quality
saphenous vein	UBERON:0007318	93.56	gold quality
oocyte	CL:0000023	93.52	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	93.50	gold quality
pylorus	UBERON:0001166	93.32	gold quality
sural nerve	UBERON:0015488	93.11	gold quality
trachea	UBERON:0003126	93.00	gold quality
globus pallidus	UBERON:0001875	92.93	gold quality
endometrium epithelium	UBERON:0004811	92.89	gold quality
type B pancreatic cell	CL:0000169	92.88	silver quality
vein	UBERON:0001638	92.65	gold quality
middle temporal gyrus	UBERON:0002771	92.26	gold quality
tongue squamous epithelium	UBERON:0006919	92.25	silver quality
tendon	UBERON:0000043	92.13	gold quality
Brodmann (1909) area 23	UBERON:0013554	91.81	gold quality
mammalian vulva	UBERON:0000997	91.45	gold quality
epithelium of nasopharynx	UBERON:0001951	91.32	gold quality
nasopharynx	UBERON:0001728	91.30	gold quality
bone marrow cell	CL:0002092	91.11	gold quality
layer of synovial tissue	UBERON:0007616	91.06	gold quality
pericardium	UBERON:0002407	91.01	gold quality
middle frontal gyrus	UBERON:0002702	91.00	gold quality
olfactory bulb	UBERON:0002264	90.82	silver quality
Brodmann (1909) area 10	UBERON:0013541	90.81	gold quality
nipple	UBERON:0002030	90.80	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	3977.16
E-MTAB-9543	yes	21.79
E-ANND-3	yes	16.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

151 targeting GOLGA3, 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-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502

Literature-anchored findings (GeneRIF, showing 12)

• NH2 terminal domain of Golgin 160 has a role in nuclear transport and Golgi apparatus localization (PMID:12130652)
• results indicate that GCP16 is the acylated membrane protein, associated with GCP170, and possibly involved in vesicular transport from the Golgi to the cell surface (PMID:14522980)
• Caspase-resistant GOLGA3 disrupts apoptosis induced by secretory pathway stress and ligation of death receptors. (PMID:15829563)
• golgin-160 assosiates in an isoform-specific manner with the Golgi-associated protein PIST (PMID:15951434)
• GCP60 interacts preferentially with one of the golgin-160 caspase cleavage fragments (residues 140-311). This strong interaction prevented the golgin-160 fragment from accumulating in the nucleus when this fragment and GCP60 were overexpressed. (PMID:16870622)
• golgin-160 may promote efficient surface delivery of a subset of cargo molecules (PMID:17118120)
• nuclear translocation of golgin-160-(140-311) is a highly coordinated event regulated not only by cleavage of the golgin-160 head but also by the oxidation state of GCP60 (PMID:17711851)
• A common epitope of proteins golgin-160, voltage-gated potassium channel and disulfide isomerase was identified by screening with autoantibodies of a type 1 diabetic patient (PMID:20170975)
• Golgi protein golgin160 recruits dynein to Golgi membranes. (PMID:22814606)
• The golgin-160 binds directly to the third intracellular loop of beta1AR and that this binding depends on three basic residues in this loop. (PMID:24566136)
• Golgin-160 disperses from Golgi membranes in cells subjected to cold temperature. Activated ARF1 can prevent cold-induced dispersal of golgin-160. (PMID:29467256)
• An exome-first approach to aid in the diagnosis of primary ciliary dyskinesia. (PMID:32367404)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	golga3	ENSDARG00000062511
mus_musculus	Golga3	ENSMUSG00000029502
rattus_norvegicus	Golga3	ENSRNOG00000037437
drosophila_melanogaster	GCC185	FBGN0037979

Paralogs (3): CEP164 (ENSG00000110274), GCC2 (ENSG00000135968), NUMA1 (ENSG00000137497)

Protein

Protein identifiers

Golgin subfamily A member 3 — Q08378 (reviewed: Q08378)

Alternative names: Golgi complex-associated protein of 170 kDa, Golgin-160

All UniProt accessions (23): Q08378, A0A494C129, A0A8I5KPC9, A0A8I5KQ98, A0A8I5KQH9, A0A8I5KQL7, A0A8I5KQN2, A0A8I5KSF0, A0A8I5KSV3, A0A8I5KSX1, A0A8I5KTE5, A0A8I5KU25, A0A8I5KU69, A0A8I5KU99, A0A8I5KUK6, A0A8I5KVX9, A0A8I5KW20, A0A8I5KWY9, A0A8I5KXF8, A0A8I5KYV8, A0A8I5QJ69, A0A8I5QKK4, A0A8I5QKX6

UniProt curated annotations — full annotation on UniProt →

Function. Golgi auto-antigen; probably involved in maintaining Golgi structure.

Subunit / interactions. Homodimer. Interacts with GOLGA7. Isoform 1 interacts with GOPC while isoform 3 does not.

Subcellular location. Cytoplasm. Golgi apparatus. Golgi stack membrane.

Tissue specificity. Expressed in all tissues tested. Expressed in liver, testis, lung, heart, salivary gland and kidney.

Post-translational modifications. Cleaved by caspases in apoptotic cells.

Domain organisation. Extended rod-like protein with coiled-coil domains.

Miscellaneous. May be due to an intron retention.

Isoforms (3)

UniProt ID	Names	Canonical?
Q08378-1	1, Golgin-160B	yes
Q08378-2	2
Q08378-4	3

RefSeq proteins (9): NP_001166028, NP_001376612, NP_001376613, NP_001376614, NP_001376615, NP_001376616, NP_001376617, NP_001376618, NP_005886 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051841	MT-Golgi_org_protein	Family

UniProt features (53 total): region of interest 9, modified residue 9, sequence conflict 9, compositionally biased region 8, mutagenesis site 6, splice variant 4, site 3, sequence variant 3, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q08378-F1	68.76	0.07

Functional residue map

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

Catalytic / active sites (3): 59–60 (cleavage; by caspase-2); 139–140 (cleavage; by caspase-3); 311–312 (cleavage; by caspase-7)

Post-translational modifications (9): 1, 18, 57, 272, 385, 389, 465, 983, 1392

Mutagenesis-validated functional residues (6):

Position	Phenotype
59	abolishes cleavage by caspase-2.
121	loss of interaction with gopc; when associated with a-128 and a-135.
128	loss of interaction with gopc; when associated with a-121 and a-135.
135	loss of interaction with gopc; when associated with a-121 and a-128.
139	abolishes cleavage by caspase-3.
311	abolishes cleavage by caspase-7.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9696270	RND2 GTPase cycle

MSigDB gene sets: 179 (showing top): MORF_ATRX, FOSTER_TOLERANT_MACROPHAGE_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, FUJIWARA_PARK2_IN_LIVER_CANCER_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, DOUGLAS_BMI1_TARGETS_DN, SANSOM_APC_TARGETS_UP, CUI_TCF21_TARGETS_2_DN, SENESE_HDAC3_TARGETS_DN, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, GOCC_GOLGI_CISTERNA_MEMBRANE, SCGGAAGY_ELK1_02, GOCC_ORGANELLE_SUBCOMPARTMENT, NUYTTEN_NIPP1_TARGETS_DN

GO Biological Process (0):

GO Molecular Function (2): cadherin binding (GO:0045296), protein binding (GO:0005515)

GO Cellular Component (8): Golgi membrane (GO:0000139), nucleoplasm (GO:0005654), nucleolus (GO:0005730), Golgi apparatus (GO:0005794), cytosol (GO:0005829), membrane (GO:0016020), Golgi cisterna membrane (GO:0032580), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
nuclear lumen	2
cytoplasm	2
cell adhesion molecule binding	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
intracellular membraneless organelle	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
Golgi cisterna	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA3	GOLGA7	Q7Z5G4	917
GOLGA3	GOLGA2	Q08379	915
GOLGA3	MEA1	Q16626	887
GOLGA3	GOPC	Q9HD26	849
GOLGA3	SPATA16	Q9BXB7	847
GOLGA3	GORASP1	Q9BQQ3	841
GOLGA3	ZDHHC9	Q9Y397	804
GOLGA3	ACBD3	Q9H3P7	791
GOLGA3	GOLGB1	Q14789	776
GOLGA3	GOLGA1	Q92805	742
GOLGA3	USO1	O60763	708
GOLGA3	TSNAX	Q99598	704
GOLGA3	TRIP11	Q15643	703
GOLGA3	COPB1	P53618	670
GOLGA3	GOLGA8B	A8MQT2	666

IntAct

91 interactions, top by confidence:

A	B	Type	Score
TRAF2	HTRA2	psi-mi:“MI:0914”(association)	0.750
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
rep	TBKBP1	psi-mi:“MI:0914”(association)	0.530
KXD1	HIP1	psi-mi:“MI:0914”(association)	0.530
DEUP1	HIP1	psi-mi:“MI:0914”(association)	0.530
KXD1	TRAK2	psi-mi:“MI:0914”(association)	0.530
GOLGA3	ACBD3	psi-mi:“MI:0915”(physical association)	0.400
RPS3	GOLGA3	psi-mi:“MI:0915”(physical association)	0.400
Cntrl	SNAP29	psi-mi:“MI:0915”(physical association)	0.400
GOLGA3	FXR1	psi-mi:“MI:0915”(physical association)	0.370
GOLGA3	ATXN7	psi-mi:“MI:0915”(physical association)	0.370
Itsn2	EIF3F	psi-mi:“MI:0914”(association)	0.350
RETREG2	SLC27A2	psi-mi:“MI:0914”(association)	0.350
TSNAX		psi-mi:“MI:0914”(association)	0.350
Prkacb	TBC1D31	psi-mi:“MI:0914”(association)	0.350
Prkar2a	TBC1D31	psi-mi:“MI:0914”(association)	0.350
Uso1	SLC30A6	psi-mi:“MI:0914”(association)	0.350
Cul3		psi-mi:“MI:0914”(association)	0.350
SYNCRIP	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
SORT1	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
CENPU	CENPX	psi-mi:“MI:0914”(association)	0.350
CNTROB	CENPX	psi-mi:“MI:0914”(association)	0.350
PDHA1		psi-mi:“MI:0914”(association)	0.350
RNF31	HNRNPCL2	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (306): GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Proximity Label-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS)

ESM2 similar proteins: A0JNH6, A0JNT9, A1A5D9, A7YH32, A7YWC8, A9QT41, A9X1A5, B0KWC9, B1MTG4, B3EX63, E1U8D0, O75145, O75335, P55937, P58660, P59242, P60469, Q08378, Q2KJ21, Q2TAC2, Q3LUD3, Q3TMW1, Q3UHU5, Q3UMT1, Q4QRL3, Q5TZA2, Q60952, Q6DFL0, Q6NZW0, Q6PGZ0, Q6PHN1, Q6QZQ4, Q6ZP65, Q8BP01, Q8C7U1, Q8CHW5, Q8CJ40, Q8K2I2, Q8N137, Q8TF21

Diamond homologs: P55937, Q08378

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
GOLGA3	“up-regulates activity”	GOPC	binding
MAP3K11	“up-regulates activity”	GOLGA3	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 119 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
protein transport	11	4.7×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	243
Likely benign	27
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

5170 predictions. Top by Δscore:

Variant	Effect	Δscore
12:132774152:CGTA:C	donor_loss	1.0000
12:132774153:GTA:G	donor_loss	1.0000
12:132774154:TACTT:T	donor_loss	1.0000
12:132774155:A:AC	donor_gain	1.0000
12:132774155:A:C	donor_loss	1.0000
12:132774156:C:CT	donor_gain	1.0000
12:132774319:CT:C	acceptor_gain	1.0000
12:132774321:C:CC	acceptor_gain	1.0000
12:132775065:CACGT:C	donor_gain	1.0000
12:132775079:T:TA	donor_gain	1.0000
12:132775140:CCGT:C	donor_gain	1.0000
12:132775302:CGTT:C	acceptor_gain	1.0000
12:132775303:GTT:G	acceptor_gain	1.0000
12:132775304:TT:T	acceptor_gain	1.0000
12:132775304:TTC:T	acceptor_loss	1.0000
12:132775306:C:CC	acceptor_gain	1.0000
12:132775306:CTGT:C	acceptor_loss	1.0000
12:132775308:G:C	acceptor_gain	1.0000
12:132776666:T:TA	donor_gain	1.0000
12:132776754:CATCT:C	acceptor_loss	1.0000
12:132776755:ATCT:A	acceptor_loss	1.0000
12:132776756:TC:T	acceptor_loss	1.0000
12:132776757:C:CC	acceptor_gain	1.0000
12:132776758:T:G	acceptor_loss	1.0000
12:132776959:T:TA	donor_gain	1.0000
12:132777659:CACT:C	donor_loss	1.0000
12:132777661:CTCA:C	donor_gain	1.0000
12:132777662:TCA:T	donor_loss	1.0000
12:132777663:CACTG:C	donor_loss	1.0000
12:132777664:A:AC	donor_gain	1.0000

AlphaMissense

9832 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:132774160:A:G	L1435P	0.998
12:132798353:A:G	L642P	0.998
12:132786433:A:G	L1010P	0.997
12:132798440:A:G	L613P	0.997
12:132804853:A:G	L487P	0.997
12:132782315:A:G	L1149P	0.996
12:132782340:C:G	A1141P	0.996
12:132798407:A:G	L624P	0.996
12:132801822:A:G	L582P	0.996
12:132805000:A:G	L438P	0.996
12:132774169:A:G	L1432P	0.995
12:132782322:C:G	A1147P	0.995
12:132784237:A:G	L1065P	0.995
12:132801805:C:G	A588P	0.995
12:132804769:A:G	L515P	0.995
12:132801792:A:G	L592P	0.994
12:132801855:A:G	L571P	0.994
12:132804791:C:G	A508P	0.994
12:132804866:C:G	A483P	0.994
12:132804874:A:G	L480P	0.994
12:132804895:A:G	L473P	0.994
12:132773277:A:G	L1442P	0.993
12:132774160:A:T	L1435H	0.993
12:132774181:A:G	L1428P	0.993
12:132796630:A:G	L670P	0.993
12:132782348:A:G	L1138P	0.992
12:132786425:C:G	A1013P	0.992
12:132786445:A:G	L1006P	0.992
12:132789232:A:G	L869P	0.992
12:132796655:C:G	A662P	0.992

dbSNP variants (sampled 300 via entrez): RS1000052334 (12:132823240 A>G), RS1000119749 (12:132820347 GTAA>G), RS1000138974 (12:132802178 G>A), RS1000144524 (12:132789532 T>C), RS1000227337 (12:132772584 A>C,G), RS1000231201 (12:132780573 C>A,T), RS1000241002 (12:132780399 C>T), RS1000287420 (12:132777249 G>A), RS1000303751 (12:132814353 G>A), RS1000312072 (12:132795241 G>A,C,T), RS1000343571 (12:132800369 C>T), RS1000451523 (12:132781052 T>A,C), RS1000487545 (12:132823076 T>C), RS1000493698 (12:132819858 C>G,T), RS1000513811 (12:132814149 T>C)

Disease associations

OMIM: gene MIM:602581 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
primary ciliary dyskinesia	Limited	Autosomal recessive

Mondo (1): primary ciliary dyskinesia (MONDO:0016575)

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001491_3	Immune response to smallpox vaccine (IL-6)	3.000000e-07
GCST008158_99	Body mass index	2.000000e-06
GCST009106_3	Basal metabolic rate variance	2.000000e-09
GCST009129_3	Basal metabolic rate	2.000000e-12
GCST010002_179	Refractive error	1.000000e-12
GCST011703_13	Smoking initiation	1.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004645	response to vaccine
EFO:0004340	body mass index
EFO:0007777	base metabolic rate measurement
EFO:0005670	smoking initiation

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D002925	Ciliary Motility Disorders	C08.200; C09.150; C16.131.077.245.500; C16.320.184.500
D007619	Kartagener Syndrome	C08.127.384.500; C08.200.531; C08.695.501; C09.150.531; C14.240.400.280.500; C14.280.400.280.500; C16.131.077.245.500.531; C16.131.240.400.280.500; C16.131.740.501; C16.131.810.250.500; C16.320.184.500.531; C16.320.480

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067099 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.22	Kd	59.52	nM	CHEMBL5653589
7.22	ED50	59.52	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148448: Binding affinity to human GOLGA3 incubated for 45 mins by Kinobead based pull down assay	kd	0.0595	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, increases methylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation, decreases methylation	1
arsenite	decreases reaction, affects binding	1
methylparaben	increases expression	1
sodium arsenite	increases expression	1
perfluorooctanoic acid	decreases expression	1
benzo(e)pyrene	decreases methylation	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
K 7174	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
bisphenol AF	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Caffeine	decreases phosphorylation	1
Cisplatin	decreases expression	1
Clozapine	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Gallic Acid	increases expression	1
Ivermectin	decreases expression	1
Ketoconazole	decreases expression	1
Methapyrilene	decreases methylation	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651490	Binding	Binding affinity to human GOLGA3 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02871778	PHASE2	COMPLETED	Clearing Lungs With ENaC Inhibition in Primary Ciliary Dyskinesia
NCT07318974	PHASE2	ACTIVE_NOT_RECRUITING	Melatonin Therapy for Improving ICSI Outcomes in Women With Diminished Ovarian Reserve
NCT05737485	PHASE1	COMPLETED	Study Evaluating the Safety and Tolerability of RCT1100 in Healthy and PCD Subjects
NCT06600425	PHASE1	COMPLETED	A Study to Assess the Safety, Tolerability, Ciliary Rescue, and Pharmacodynamics of RCT1100 in Adults With PCD
NCT06633757	PHASE1	COMPLETED	Study of Inhaled RCT1100 in Adults With PCD Caused by Pathogenic Mutations in the DNAI1 Gene to Measure Mucociliary Clearance
NCT04901715	EARLY_PHASE1	COMPLETED	Functional Studies of Novel Genes Mutated in Primary Ciliary Dyskinesia II: Genotype to Phenotype
NCT00005650	Not specified	COMPLETED	Genetic Study of Patients With Primary Ciliary Dyskinesia
NCT00323167	Not specified	COMPLETED	Rare Genetic Disorders of the Breathing Airways
NCT00368446	Not specified	COMPLETED	Genetic Disorders of Mucociliary Clearance in Nontuberculous Mycobacterial Lung Disease
NCT00450918	Not specified	COMPLETED	Evaluating Progression of and Diagnostic Tools for Primary Ciliary Dyskinesia in Children and Adolescents
NCT00608556	Not specified	COMPLETED	Dyskinesia, Heterotaxy and Congenital Heart Disease
NCT00686309	Not specified	UNKNOWN	Comparison of On-line and Off-line Measurements of Exhaled Nitric Oxide (NO)
NCT00722878	Not specified	COMPLETED	Long-term Lung Function and Disease Progression in Children With Early Onset Primary Ciliary Dyskinesia Lung Disease
NCT00739817	Not specified	UNKNOWN	Screening for Primary Ciliary Dyskinesia Using Nasal Nitric Oxide
NCT00783887	Not specified	COMPLETED	Diagnosis of Primary Ciliary Dyskinesia
NCT00807482	Not specified	RECRUITING	Pathogenesis of Primary Ciliary Dyskinesia (PCD) Lung Disease
NCT01070914	Not specified	UNKNOWN	Early Detection and Characterization of Primary Ciliary Dyskinesia
NCT01155115	Not specified	COMPLETED	Inflammatory and Microbiologic Markers in Sputum: Comparing Cystic Fibrosis With Primary Ciliary Dyskinesia
NCT01246258	Not specified	COMPLETED	Otolith Function in Patients With Primary Ciliary Dyskinesia
NCT01929356	Not specified	RECRUITING	Chest Physiotherapy and Lung Function in Primary Ciliary Dyskinesia
NCT02389049	Not specified	COMPLETED	Genetics of Primary Ciliary Dyskinesia
NCT02419365	Not specified	RECRUITING	International Primary Ciliary Dyskinesia (PCD) Registry
NCT02699177	Not specified	UNKNOWN	In Vivo Measurements of Nasal Ciliary Beat Frequency by Using Interferometry
NCT02704455	Not specified	NOT_YET_RECRUITING	Registry Study on Primary Ciliary Dyskinesia in Chinese Children
NCT03271840	Not specified	COMPLETED	Registry for Primary Ciliary Dyskinesia
NCT03279965	Not specified	UNKNOWN	MRI in Cystic Fibrosis and Primary Ciliary Dyskinesia
NCT03320382	Not specified	UNKNOWN	Multiple Breath Washout, a Clinimetric Dataset
NCT03370029	Not specified	COMPLETED	Respiratory Muscle Strength, Exercise Capacity and Physical Activity Levels in Children Primary Ciliary Dyskinesia
NCT03494894	Not specified	COMPLETED	Bacteriological Link Between Upper and Lower Airways in Cystic Fibrosis and Primary Ciliary Dyskinesia
NCT03517865	Not specified	ACTIVE_NOT_RECRUITING	International Primary Ciliary Dyskinesia Cohort
NCT03606200	Not specified	RECRUITING	Swiss Primary Ciliary Dyskinesia Registry
NCT03704207	Not specified	RECRUITING	Utility of PCD Diagnostics to Improve Clinical Care
NCT03704896	Not specified	UNKNOWN	PRospective Observational Multicentre Study on VAriability of Lung Function in Stable PCD Patients
NCT03801395	Not specified	COMPLETED	PCD New Gene Discovery
NCT03809091	Not specified	UNKNOWN	WGS of Korean Idiopathic Bronchiectasis
NCT03832491	Not specified	COMPLETED	Effect of Game Based Approach on Oxygenation, Functional Capacity and Quality of Life in Primary Ciliary Dyskinesia
NCT04161313	Not specified	COMPLETED	Respiratory Function, Exercise Capacity and Peripheral Muscle Strength Among Patients With CF, PCD and Healthy Children
NCT04476433	Not specified	COMPLETED	Intervention in Chronic Pediatric Patients and Their Families.
NCT04489472	Not specified	UNKNOWN	The Effect of a Dietary Supplement Rich in Nitric Oxide in Patients Diagnosed With Primary Ciliary Dyskinesia.
NCT04602481	Not specified	RECRUITING	Living With Primary Ciliary Dyskinesia (Living With PCD)