COPZ1

Summary

COPZ1 (coat protein complex I subunit zeta 1, HGNC:2243) is a protein-coding gene on chromosome 12q13.13, encoding Coatomer subunit zeta-1 (P61923). The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. It is a common-essential gene (DepMap: required in 98.6% of cancer cell lines).

This gene encodes a subunit of the cytoplasmic coatamer protein complex, which is involved in autophagy and intracellular protein trafficking. The coatomer protein complex is comprised of seven subunits and functions as the coat protein of coat protein complex (COP)I-vesicles. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 22818 — RefSeq curated summary.

At a glance

• GWAS associations: 20
• Clinical variants (ClinVar): 39 total — 2 pathogenic
• Phenotypes (HPO): 51
• Cancer dependency (DepMap): dependent in 98.6% of screened cell lines (common-essential)
• MANE Select transcript: NM_016057

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2243
Approved symbol	COPZ1
Name	coat protein complex I subunit zeta 1
Location	12q13.13
Locus type	gene with protein product
Status	Approved
Aliases	CGI-120
Ensembl gene	ENSG00000111481
Ensembl biotype	protein_coding
OMIM	615472
Entrez	22818

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 14 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000262061, ENST00000455864, ENST00000548076, ENST00000548281, ENST00000548753, ENST00000549043, ENST00000549116, ENST00000550027, ENST00000550171, ENST00000550713, ENST00000551412, ENST00000551779, ENST00000551962, ENST00000552218, ENST00000552362, ENST00000552848, ENST00000553009, ENST00000553231, ENST00000912206, ENST00000945182, ENST00000945183

RefSeq mRNA: 4 — MANE Select: NM_016057 NM_001271734, NM_001271735, NM_001271736, NM_016057

CCDS: CCDS61137, CCDS61138, CCDS61139, CCDS8877

Canonical transcript exons

ENST00000262061 — 9 exons

Exon	Start	End
ENSE00001254040	54350476	54351846
ENSE00002354810	54325131	54325181
ENSE00003498386	54348000	54348051
ENSE00003522930	54343225	54343316
ENSE00003553393	54345460	54345515
ENSE00003558310	54340547	54340615
ENSE00003568074	54342206	54342287
ENSE00003598325	54349620	54349658
ENSE00003636474	54347767	54347844

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 99.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 157.6318 / max 3058.0518, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125895	157.5308	1823
125894	0.1010	47

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	99.12	gold quality
body of pancreas	UBERON:0001150	98.64	gold quality
ventricular zone	UBERON:0003053	98.27	gold quality
stromal cell of endometrium	CL:0002255	98.19	gold quality
ganglionic eminence	UBERON:0004023	98.16	gold quality
rectum	UBERON:0001052	98.14	gold quality
cortical plate	UBERON:0005343	98.09	gold quality
pancreas	UBERON:0001264	97.99	gold quality
monocyte	CL:0000576	97.90	gold quality
mononuclear cell	CL:0000842	97.83	gold quality
leukocyte	CL:0000738	97.79	gold quality
right adrenal gland	UBERON:0001233	97.73	gold quality
smooth muscle tissue	UBERON:0001135	97.65	gold quality
gall bladder	UBERON:0002110	97.65	gold quality
right adrenal gland cortex	UBERON:0035827	97.57	gold quality
right lobe of thyroid gland	UBERON:0001119	97.47	gold quality
adenohypophysis	UBERON:0002196	97.45	gold quality
left lobe of thyroid gland	UBERON:0001120	97.34	gold quality
left adrenal gland	UBERON:0001234	97.29	gold quality
pituitary gland	UBERON:0000007	97.24	gold quality
saliva-secreting gland	UBERON:0001044	97.10	gold quality
minor salivary gland	UBERON:0001830	97.08	gold quality
thyroid gland	UBERON:0002046	97.07	gold quality
mucosa of transverse colon	UBERON:0004991	97.07	gold quality
left adrenal gland cortex	UBERON:0035825	97.03	gold quality
right atrium auricular region	UBERON:0006631	97.01	gold quality
body of stomach	UBERON:0001161	96.97	gold quality
esophagus mucosa	UBERON:0002469	96.93	gold quality
adrenal gland	UBERON:0002369	96.90	gold quality
heart left ventricle	UBERON:0002084	96.86	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7606	no	2169.06
E-MTAB-6524	no	139.68
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting COPZ1, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-548AU-3P	99.70	68.22	1373
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-2276-3P	98.76	67.75	1384
HSA-MIR-4725-5P	98.67	65.42	628
HSA-MIR-504-5P	98.67	65.40	631
HSA-MIR-3135B	98.61	65.33	1470

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 4)

• The knockdown of COPZ1, but not of COPZ2 encoding isoform coatomer protein complex zeta2, caused Golgi apparatus collapse, blocked autophagy, and induced apoptosis in both proliferating and nondividing tumor cells. (PMID:21746916)
• siRNA-mediated COPZ1 depletion causes abortive autophagy, endoplasmic reticulum stress, unfolded protein response and apoptosis in thyroid tumor cells. (PMID:28951131)
• Loss of COPZ1 induces NCOA4 mediated autophagy and ferroptosis in glioblastoma cell lines. (PMID:33420375)
• COPZ1 regulates ferroptosis through NCOA4-mediated ferritinophagy in lung adenocarcinoma. (PMID:39181476)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	copz1	ENSDARG00000017844
mus_musculus	Copz1	ENSMUSG00000060992
rattus_norvegicus	Copz1	ENSRNOG00000036835
drosophila_melanogaster	zetaCOP	FBGN0040512
caenorhabditis_elegans		WBGENE00010333

Paralogs (1): COPZ2 (ENSG00000005243)

Protein

Protein identifiers

Coatomer subunit zeta-1 — P61923 (reviewed: P61923)

Alternative names: Zeta-1-coat protein

All UniProt accessions (10): P61923, F8VUC5, F8VVA7, F8VXB1, F8VXR1, F8VYE0, F8VYK5, F8VYZ4, F8W156, F8W651

UniProt curated annotations — full annotation on UniProt →

Function. The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. The zeta subunit may be involved in regulating the coat assembly and, hence, the rate of biosynthetic protein transport due to its association-dissociation properties with the coatomer complex.

Subunit / interactions. Oligomeric complex that consists of at least the alpha, beta, beta’, gamma, delta, epsilon and zeta subunits.

Subcellular location. Cytoplasm. Golgi apparatus membrane. Cytoplasmic vesicle. COPI-coated vesicle membrane.

Similarity. Belongs to the adaptor complexes small subunit family.

Isoforms (5)

UniProt ID	Names	Canonical?
P61923-1	1	yes
P61923-2	2
P61923-3	3
P61923-4	4
P61923-5	5

RefSeq proteins (4): NP_001258663, NP_001258664, NP_001258665, NP_057141* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000804	Clathrin_sm-chain_CS	Conserved_site
IPR011012	Longin-like_dom_sf	Homologous_superfamily
IPR022775	AP_mu_sigma_su	Domain
IPR039652	Coatomer_zeta	Family

Pfam: PF01217

UniProt features (21 total): strand 6, helix 5, splice variant 5, mutagenesis site 2, chain 1, modified residue 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
5MC7	X-RAY DIFFRACTION	1.6
2HF6	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P61923-F1	89.37	0.75

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 (1): 1

Mutagenesis-validated functional residues (2):

Position	Phenotype
58–59	reduced interaction with gamma subunit.
87–88	reduced interaction with gamma subunit.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6807878	COPI-mediated anterograde transport
R-HSA-6811434	COPI-dependent Golgi-to-ER retrograde traffic

MSigDB gene sets: 172 (showing top): GCM_GSPT1, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_INTRA_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOCC_COATED_VESICLE, USF_01, JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP, GOCC_GOLGI_ASSOCIATED_VESICLE, GOCC_VESICLE_COAT, HIF1_Q3, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, USF_02, PARENT_MTOR_SIGNALING_UP

GO Biological Process (5): intracellular protein transport (GO:0006886), retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), intra-Golgi vesicle-mediated transport (GO:0006891), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (0):

GO Cellular Component (11): Golgi membrane (GO:0000139), endoplasmic reticulum membrane (GO:0005789), cytosol (GO:0005829), COPI vesicle coat (GO:0030126), transport vesicle (GO:0030133), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), membrane (GO:0016020), membrane coat (GO:0030117), COPI-coated vesicle membrane (GO:0030663), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
ER to Golgi Anterograde Transport	1
Golgi-to-ER retrograde transport	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
cellular anatomical structure	3
intracellular protein localization	2
Golgi vesicle transport	2
transport	2
Golgi apparatus	2
endomembrane system	2
protein transport	1
intracellular transport	1
establishment of protein localization	1
cellular process	1
bounding membrane of organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
vesicle coat	1
COPI-coated vesicle membrane	1
cytoplasmic vesicle	1
intracellular anatomical structure	1
intracellular membrane-bounded organelle	1
coated membrane	1
membrane protein complex	1
COPI-coated vesicle	1
Golgi-associated vesicle membrane	1
coated vesicle membrane	1
intracellular vesicle	1

Protein interactions and networks

STRING

1670 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
COPZ1	COPB1	P53618	999
COPZ1	ARCN1	P48444	999
COPZ1	COPB2	P35606	999
COPZ1	COPA	P53621	998
COPZ1	COPE	O14579	996
COPZ1	COPG1	Q9Y678	898
COPZ1	ARF1	P10947	805
COPZ1	COPG2	Q9UBF2	787
COPZ1	ATOX1	O00244	622
COPZ1	COPRS	Q9NQ92	621
COPZ1	AP4E1	Q9UPM8	602
COPZ1	SEC13	P55735	535
COPZ1	SEC24B	O95487	517
COPZ1	ZNF134	P52741	507
COPZ1	ZNF160	Q9HCG1	479

IntAct

76 interactions, top by confidence:

A	B	Type	Score
COPG1	COPB1	psi-mi:“MI:0914”(association)	0.730
COPG1	COPB2	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SCYL1	SEC31A	psi-mi:“MI:0914”(association)	0.710
COPB1	COPZ1	psi-mi:“MI:0914”(association)	0.640
COPG1	COPE	psi-mi:“MI:0914”(association)	0.640
Copa	COPE	psi-mi:“MI:0915”(physical association)	0.560
COPZ1	COPE	psi-mi:“MI:0914”(association)	0.530
SGF29	MATN2	psi-mi:“MI:0914”(association)	0.530
	AP3D1	psi-mi:“MI:0914”(association)	0.460
	MYL12B	psi-mi:“MI:0914”(association)	0.460
FLT4	ILVBL	psi-mi:“MI:0914”(association)	0.420
lef	COPZ1	psi-mi:“MI:0915”(physical association)	0.400
Copa	BCAP29	psi-mi:“MI:0914”(association)	0.350
Sacm1l	COPE	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
KSR1	FBLL1	psi-mi:“MI:0914”(association)	0.350
DLD	NFKBIE	psi-mi:“MI:0914”(association)	0.350
DLST		psi-mi:“MI:0914”(association)	0.350
DLD	IRS4	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
EPHA8	NDUFA4	psi-mi:“MI:0914”(association)	0.350

BioGRID (209): COPA (Co-fractionation), COPB1 (Co-fractionation), COPG1 (Co-fractionation), COPG2 (Co-fractionation), COPZ1 (Co-fractionation), COPZ1 (Co-fractionation), COPZ1 (Co-fractionation), SF3B1 (Co-fractionation), COPZ1 (Synthetic Growth Defect), COPZ1 (Affinity Capture-Western), COPZ1 (Proximity Label-MS), COPZ1 (Affinity Capture-MS), COPZ1 (Affinity Capture-MS), COPZ1 (Affinity Capture-MS), COPZ1 (Affinity Capture-MS)

ESM2 similar proteins: B0G185, O02173, O17901, O23685, O43041, O50016, O82201, P35181, P35604, P47064, P53290, P53680, P56377, P61923, P61924, P61966, P61967, P62743, P62744, Q00381, Q09905, Q17QC5, Q1JQ98, Q28IG8, Q3ZBB6, Q3ZBS3, Q4ICG5, Q4WS49, Q54H39, Q54NZ4, Q54WW3, Q553S2, Q557G3, Q59QC5, Q5BFF8, Q5R5F2, Q5R940, Q5ZKP4, Q75F71, Q7SAQ1

Diamond homologs: O17901, O74891, P35604, P53600, P61923, P61924, Q54HD4, Q5NA06, Q5R5F2, Q6Z844, Q84LG4, Q8H1F4, Q940S5, Q9JHH9, Q9MAX5, Q9P299, Q54CA7, P47064, Q8VZ37

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 82 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
COPI-dependent Golgi-to-ER retrograde traffic	6	12.6×	1e-03
COPI-mediated anterograde transport	6	12.4×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
intra-Golgi vesicle-mediated transport	6	43.9×	3e-06
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	5	23.4×	4e-04
endoplasmic reticulum to Golgi vesicle-mediated transport	8	15.1×	2e-05
intracellular protein transport	9	8.1×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	19
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
4537445	COPZ1, GLN141TER	Pathogenic
4537446	COPZ1, GLY132ARG (rs1229660782)	Pathogenic

SpliceAI

1347 predictions. Top by Δscore:

Variant	Effect	Δscore
12:54340611:CCAAG:C	donor_loss	1.0000
12:54340612:CAAG:C	donor_loss	1.0000
12:54340614:AGGTG:A	donor_loss	1.0000
12:54340617:T:G	donor_loss	1.0000
12:54342199:T:TA	acceptor_gain	1.0000
12:54342203:CA:C	acceptor_loss	1.0000
12:54342204:A:AC	acceptor_loss	1.0000
12:54342204:A:AG	acceptor_gain	1.0000
12:54342205:G:GA	acceptor_gain	1.0000
12:54342205:GT:G	acceptor_gain	1.0000
12:54342205:GTA:G	acceptor_gain	1.0000
12:54342205:GTAC:G	acceptor_gain	1.0000
12:54342205:GTACT:G	acceptor_gain	1.0000
12:54342284:GACA:G	donor_gain	1.0000
12:54342285:ACA:A	donor_gain	1.0000
12:54342287:AG:A	donor_loss	1.0000
12:54342288:G:GG	donor_gain	1.0000
12:54342289:T:A	donor_loss	1.0000
12:54345456:ACAGC:A	acceptor_loss	1.0000
12:54345457:CA:C	acceptor_loss	1.0000
12:54345458:A:AC	acceptor_loss	1.0000
12:54345458:A:AG	acceptor_gain	1.0000
12:54345458:AGCT:A	acceptor_gain	1.0000
12:54345459:G:GG	acceptor_gain	1.0000
12:54345459:GC:G	acceptor_gain	1.0000
12:54345459:GCT:G	acceptor_gain	1.0000
12:54345459:GCTG:G	acceptor_gain	1.0000
12:54345513:GAG:G	donor_gain	1.0000
12:54345514:AGGTG:A	donor_loss	1.0000
12:54345515:GGTG:G	donor_loss	1.0000

AlphaMissense

1156 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:54350489:C:A	A167D	1.000
12:54340566:T:A	V13D	0.999
12:54340571:G:C	A15P	0.999
12:54340584:T:C	L19P	0.999
12:54342253:G:C	E45D	0.999
12:54342253:G:T	E45D	0.999
12:54343279:T:C	L75P	0.999
12:54343291:T:A	V79E	0.999
12:54343296:G:C	G81R	0.999
12:54343297:G:A	G81D	0.999
12:54343297:G:T	G81V	0.999
12:54343312:A:T	N86I	0.999
12:54343313:T:A	N86K	0.999
12:54343313:T:G	N86K	0.999
12:54345461:T:C	L88P	0.999
12:54345467:T:C	L90P	0.999
12:54345479:T:C	L94P	0.999
12:54345486:T:G	C96W	0.999
12:54345488:T:C	L97P	0.999
12:54347820:C:A	A124D	0.999
12:54347843:G:A	G132R	0.999
12:54347843:G:C	G132R	0.999
12:54347843:G:T	G132W	0.999
12:54347844:G:A	G132E	0.999
12:54347844:G:T	G132V	0.999
12:54350488:G:C	A167P	0.999
12:54350501:T:C	I171T	0.999
12:54340572:C:A	A15D	0.998
12:54340596:G:T	G23V	0.998
12:54343255:T:A	V67E	0.998

dbSNP variants (sampled 300 via entrez): RS1000062469 (12:54334627 G>C), RS1000088423 (12:54334377 C>G,T), RS1000222358 (12:54331173 CTTTTTTTTTTTTTTTT>C,CTTT,CTTTT,CTTTTT,CTTTTTT,CTTTTTTT,CTTTTTTTT,CTTTTTTTTT,CTTTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTTTTT,CTTTTTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT), RS1000310747 (12:54341038 C>T), RS1000695211 (12:54328690 T>A), RS1000853006 (12:54339436 C>G,T), RS1000940208 (12:54329802 A>C), RS1001173183 (12:54329227 T>C), RS1001333465 (12:54346377 C>G,T), RS1001424705 (12:54323658 TTC>T,TTCTC), RS1001467912 (12:54333398 T>G), RS1001544030 (12:54342527 C>T), RS1001690106 (12:54336082 A>G), RS1001810523 (12:54349216 C>G,T), RS1001987465 (12:54329040 G>A,C)

Disease associations

OMIM: gene MIM:615472 | disease phenotypes: MIM:621439

GenCC curated gene-disease

Mondo (1): neutropenia, severe congenital, 12, autosomal recessive (MONDO:0980936)

Orphanet (0):

HPO phenotypes

51 total (30 of 51 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000230	Gingivitis
HP:0000407	Sensorineural hearing impairment
HP:0000545	Myopia
HP:0000729	Autistic behavior
HP:0001047	Atopic dermatitis
HP:0001249	Intellectual disability
HP:0001287	Meningitis
HP:0001433	Hepatosplenomegaly
HP:0001762	Talipes equinovarus
HP:0001873	Thrombocytopenia
HP:0001875	Decreased total neutrophil count
HP:0001882	Decreased total leukocyte count
HP:0001888	Decreased total lymphocyte count
HP:0001890	Autoimmune hemolytic anemia
HP:0001903	Anemia
HP:0002090	Pneumonia
HP:0002650	Scoliosis
HP:0002719	Recurrent infections
HP:0002728	Chronic mucocutaneous candidiasis
HP:0002754	Osteomyelitis
HP:0002788	Recurrent upper respiratory tract infections
HP:0003212	Increased circulating IgE concentration
HP:0003237	Increased circulating IgG concentration
HP:0003261	Increased circulating IgA concentration
HP:0003496	Increased circulating IgM level
HP:0003593	Infantile onset
HP:0003623	Neonatal onset
HP:0004387	Enterocolitis
HP:0005403	Decreased total T cell count

GWAS associations

20 associations (top):

Study	Trait	p-value
GCST001335_22	Mean platelet volume	2.000000e-14
GCST001783_5	Platelet count	5.000000e-08
GCST002184_1	Mean platelet volume	2.000000e-09
GCST004599_190	Mean platelet volume	2.000000e-152
GCST004601_164	Red blood cell count	1.000000e-10
GCST004621_32	Red cell distribution width	9.000000e-43
GCST005962_20	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	7.000000e-13
GCST005991_29	Platelet count	3.000000e-13
GCST007576_171	Chronotype	5.000000e-11
GCST010002_217	Refractive error	6.000000e-174
GCST010143_26	Meat-related diet	2.000000e-09
GCST90002383_6	Hematocrit	1.000000e-15
GCST90002386_323	High light scatter reticulocyte percentage of red cells	9.000000e-13
GCST90002395_131	Mean platelet volume	3.000000e-57
GCST90002395_132	Mean platelet volume	3.000000e-18
GCST90002400_91	Plateletcrit	8.000000e-78
GCST90002401_242	Platelet distribution width	5.000000e-65
GCST90002402_132	Platelet count	5.000000e-74
GCST90002403_451	Red blood cell count	1.000000e-18
GCST90002404_137	Red cell distribution width	7.000000e-146

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0004309	platelet count
EFO:0004305	erythrocyte count
EFO:0009188	Red cell distribution width
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0008328	chronotype measurement
EFO:0008111	diet measurement
EFO:0004348	hematocrit
EFO:0007985	platelet crit
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	3
bisphenol F	affects cotreatment, increases expression	2
Air Pollutants	affects expression, affects cotreatment, increases abundance, increases oxidation	2
Ozone	increases abundance, affects expression, affects cotreatment, increases oxidation	2
Rotenone	increases expression	2
2,4,6-tribromophenol	decreases expression	1
alpha-pinene	increases abundance, affects cotreatment, increases oxidation	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
tetrabromobisphenol A	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
K 7174	decreases expression	1
ICG 001	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol AF	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Ketoconazole	decreases expression	1
T-2 Toxin	increases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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