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COG1

gene
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Also known as KIAA1381

Summary

COG1 (component of oligomeric golgi complex 1, HGNC:6545) is a protein-coding gene on chromosome 17q25.1, encoding Conserved oligomeric Golgi complex subunit 1 (Q8WTW3). Required for normal Golgi function. It is a selective cancer dependency (DepMap: 52.8% of cell lines).

The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. It is thought that this protein is required for steps in the normal medial and trans Golgi-associated processing of glycoconjugates and plays a role in the organization of the Golgi-localized complex.

Source: NCBI Gene 9382 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): COG1-congenital disorder of glycosylation (Definitive, GenCC)
  • Clinical variants (ClinVar): 519 total — 14 pathogenic, 7 likely-pathogenic (top 6% of genes corpus-wide)
  • GTEx eGene: eQTL in 19 tissues, sQTL in 18 (q < 0.05)
  • Phenotypes (HPO): 91
  • Cancer dependency (DepMap): dependent in 52.8% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.72 (unconstrained)
  • MANE Select transcript: NM_018714

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6545
Approved symbolCOG1
Namecomponent of oligomeric golgi complex 1
Location17q25.1
Locus typegene with protein product
StatusApproved
AliasesKIAA1381
Ensembl geneENSG00000166685
Ensembl biotypeprotein_coding
OMIM606973
Entrez9382

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 18 nonsense_mediated_decay, 13 protein_coding, 3 retained_intron

MANE Select: ENST00000299886

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 4, TSL 3: 3

ENST00000299886, ENST00000438720, ENST00000577238, ENST00000577844, ENST00000580271, ENST00000582512, ENST00000582587, ENST00000582672, ENST00000582973, ENST00000876963, ENST00000876964, ENST00000876965, ENST00000923183, ENST00000947884, ENST00000947885, ENST00000992734, ENST00000992735, ENST00000992736, ENST00001025276, ENST00001025277, ENST00001025280, ENST00001025281, ENST00001025282, ENST00001025284, ENST00001025285, ENST00001079998, ENST00001109060, ENST00001109061, ENST00001109062, ENST00001109063, ENST00001109064, ENST00001113514, ENST00001123559, ENST00001141917

RefSeq mRNA: 1 — MANE Select: NM_018714 NM_018714

CCDS: CCDS11692

Canonical transcript exons

ENST00000299886 — 14 exons

ExonStartEnd
ENSE000011056017320670873206817
ENSE000011056047319722673197396
ENSE000011056147319650773196751
ENSE000011056197320363273203793
ENSE000011056317320110973201900
ENSE000011056407320555373205680
ENSE000011056477320300073203146
ENSE000011056517319690073197081
ENSE000011368347320056673200776
ENSE000011368387319986573200021
ENSE000027196337319305573193384
ENSE000035013267320718173207256
ENSE000035258717320615473206262
ENSE000036019937320831473208507

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 95.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.9904 / max 128.3385, expressed in 1810 samples.

Highest expression (Bgee): hemisphere of cerebellum, cerebellar hemisphere, apex of heart, cerebellar cortex, frontal lobe.

Genetic regulation across tissues (GTEx eQTL / sQTL)

COG1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 19 tissues and its splicing (sQTL) in 18 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 37 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Testiseqtl4.2e-22+0.4917:73193924:C:T
Thyroideqtl4.0e-18+0.2817:73218354:T:C
Cells Cultured fibroblastseqtl3.0e-17+1.0817:73198466:G:T
Muscle Skeletaleqtl4.9e-17+0.2317:73256884:G:A
Whole Bloodeqtl7.7e-17-0.1617:73192144:C:T
Brain Frontal Cortex BA9sqtl1.8e-15-1.9117:73205817:G:A
Brain Nucleus accumbens basal gangliasqtl2.9e-13-2.0617:73198067:G:GC
Brain Caudate basal gangliasqtl3.2e-11-1.5917:73194333:C:T
Brain Cortexsqtl1.9e-10-1.5717:73198067:G:GC
Brain Anterior cingulate cortex BA24sqtl5.5e-09+1.9117:73181564:G:A
Esophagus Mucosaeqtl6.9e-09+0.2017:73179889:G:A
Brain Putamen basal gangliasqtl1.3e-08-1.8917:73223884:A:G
Brain Cerebellumsqtl1.7e-07-1.0217:73205817:G:A
Pancreaseqtl5.9e-07+0.2117:73256884:G:A
Brain Cerebellar Hemispheresqtl2.4e-06-0.6517:73205817:G:A
Heart Atrial Appendageeqtl2.1e-05-0.2017:73192144:C:T
Heart Left Ventricleeqtl2.2e-05-0.1317:73192144:C:T
Testissqtl2.2e-05-1.0117:73205817:G:A
Brain Frontal Cortex BA9eqtl3.4e-05+0.1817:73218611:G:A
Brain Cortexeqtl4.2e-05+0.1817:73218611:G:A

FANTOM5 promoters

1 alternative TSS:

Promoter IDTPM avgSamples expressed
16256322.99041810

Top tissues by expression

showing 100 of 260 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489095.76gold quality
cerebellar hemisphereUBERON:000224595.68gold quality
apex of heartUBERON:000209895.64gold quality
cerebellar cortexUBERON:000212995.59gold quality
right frontal lobeUBERON:000281095.05gold quality
cerebellumUBERON:000203795.00gold quality
adenohypophysisUBERON:000219694.91gold quality
Brodmann (1909) area 9UBERON:001354094.83gold quality
nucleus accumbensUBERON:000188294.69gold quality
pituitary glandUBERON:000000794.54gold quality
prefrontal cortexUBERON:000045194.34gold quality
anterior cingulate cortexUBERON:000983594.25gold quality
hindlimb stylopod muscleUBERON:000425294.00gold quality
caudate nucleusUBERON:000187393.83gold quality
body of pancreasUBERON:000115093.72gold quality
heart left ventricleUBERON:000208493.70gold quality
dorsolateral prefrontal cortexUBERON:000983493.61gold quality
gastrocnemiusUBERON:000138893.55gold quality
right uterine tubeUBERON:000130293.54gold quality
amygdalaUBERON:000187693.48gold quality
putamenUBERON:000187493.35gold quality
cardiac ventricleUBERON:000208293.30gold quality
frontal cortexUBERON:000187093.27gold quality
frontal lobeUBERON:001652593.27gold quality
muscle of legUBERON:000138393.08gold quality
endocervixUBERON:000045892.99gold quality
neocortexUBERON:000195092.95gold quality
right ovaryUBERON:000211892.90gold quality
left ovaryUBERON:000211992.69gold quality
muscle layer of sigmoid colonUBERON:003580592.48gold quality
transverse colonUBERON:000115792.40gold quality
forebrainUBERON:000189092.39gold quality
small intestine Peyer’s patchUBERON:000345492.31gold quality
brainUBERON:000095592.30gold quality
body of uterusUBERON:000985392.28gold quality
right atrium auricular regionUBERON:000663192.26gold quality
left adrenal gland cortexUBERON:003582592.25gold quality
left adrenal glandUBERON:000123492.20gold quality
hypothalamusUBERON:000189892.18gold quality
metanephros cortexUBERON:001053392.17gold quality
cerebral cortexUBERON:000095692.16gold quality
rectumUBERON:000105292.14gold quality
tibialis anteriorUBERON:000138592.14silver quality
right adrenal gland cortexUBERON:003582792.14gold quality
right adrenal glandUBERON:000123392.03gold quality
body of stomachUBERON:000116192.02gold quality
lower esophagus muscularis layerUBERON:003583392.00gold quality
lower esophagusUBERON:001347391.99gold quality
mucosa of transverse colonUBERON:000499191.95gold quality
heartUBERON:000094891.88gold quality
cardiac atriumUBERON:000208191.87gold quality
mucosa of stomachUBERON:000119991.86gold quality
right lobe of thyroid glandUBERON:000111991.78gold quality
tibial nerveUBERON:000132391.78gold quality
ectocervixUBERON:001224991.75gold quality
left lobe of thyroid glandUBERON:000112091.72gold quality
esophagogastric junction muscularis propriaUBERON:003584191.71gold quality
adrenal cortexUBERON:000123591.69gold quality
pancreasUBERON:000126491.67gold quality
popliteal arteryUBERON:000225091.64gold quality
tibial arteryUBERON:000761091.64gold quality
adrenal glandUBERON:000236991.43gold quality
kidney epitheliumUBERON:000481991.43silver quality
Ammon’s hornUBERON:000195491.39gold quality
skin of legUBERON:000151191.36gold quality
islet of LangerhansUBERON:000000691.32gold quality
left ventricle myocardiumUBERON:000656691.31silver quality
temporal lobeUBERON:000187191.29gold quality
stromal cell of endometriumCL:000225591.24gold quality
aortaUBERON:000094791.21gold quality
lower esophagus mucosaUBERON:003583491.21gold quality
smooth muscle tissueUBERON:000113591.16gold quality
thyroid glandUBERON:000204691.15gold quality
olfactory segment of nasal mucosaUBERON:000538690.92gold quality
minor salivary glandUBERON:000183090.88gold quality
right lungUBERON:000216790.87gold quality
right coronary arteryUBERON:000162590.86gold quality
ascending aortaUBERON:000149690.81gold quality
small intestineUBERON:000210890.80gold quality
thoracic aortaUBERON:000151590.78gold quality
left uterine tubeUBERON:000130390.74gold quality
colonUBERON:000115590.72gold quality
descending thoracic aortaUBERON:000234590.69gold quality
left coronary arteryUBERON:000162690.58gold quality
deltoidUBERON:000147690.57silver quality
spleenUBERON:000210690.57gold quality
large intestineUBERON:000005990.47gold quality
intestineUBERON:000016090.41gold quality
stomachUBERON:000094590.41gold quality
uterine cervixUBERON:000000290.34gold quality
skin of abdomenUBERON:000141690.29gold quality
granulocyteCL:000009490.28gold quality
fundus of stomachUBERON:000116090.25gold quality
right lobe of liverUBERON:000111490.24gold quality
subcutaneous adipose tissueUBERON:000219090.24gold quality
coronary arteryUBERON:000162190.13gold quality
ovaryUBERON:000099290.05gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.01gold quality
prostate glandUBERON:000236789.99gold quality
sural nerveUBERON:001548889.94gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.71
E-MTAB-10137no516.06

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Nucleus accumbenstissue49.9
Hippocampustissue46.5medium
Postcentral gyrustissue46.0
Skeletal muscletissue38.9medium
Locus coeruleustissue37.1
Cerebral cortextissue36.3medium
Somatosensory cortextissue36.3
Tonguetissue33.2
Pituitary glandtissue32.3
Thalamustissue32.2
Heart muscletissue31.2low
Occipital cortextissue30.6
Superior colliculitissue30.3
Motor cortextissue30.2
Hippocampal formationtissue30.2
Choroid plexustissue29.8
Cerebellumtissue28.9high
Midbraintissue28.8
Caudate putamentissue28.5
Prefrontal cortextissue28.3
Ponstissue28.2
Temporal cortextissue27.8
Medulla oblongatatissue27.7
Hypothalamustissue27.3
Entorhinal cortextissue27.2
Retrosplenial and cingulate cortextissue26.9
Substantia nigratissue26.5
Retrosplenial cortextissue26.4
Spinal cordtissue26.1
Insular cortextissue26.1
Corpus callosumtissue25.9
Basal gangliatissue25.3medium
Frontal cortextissue25.0
Putamentissue25.0
Periaqueductal graytissue25.0
Septumtissue25.0
Ventral forebraintissue24.9
Retinatissue23.5
Amygdalatissue23.5
Pancreastissue21.3medium
Olfactory bulbtissue21.3
Rectumtissue18.4medium
Ovarytissue18.0high
Cervixtissue17.8medium
Salivary glandtissue17.8high
Adrenal glandtissue17.8high
Smooth muscletissue17.6low
Vaginatissue16.7medium
Parathyroid glandtissue16.6low
Epididymistissue16.6medium
Seminal vesicletissue16.5high
Colontissue16.3high
Fallopian tubetissue16.2high
Endometrium 1tissue16.1high
Duodenumtissue15.3high
Prostatetissue15.2high
Bone marrowtissue15.1high
Testistissue14.9high
Skin 1tissue14.4medium
Stomach 1tissue14.2medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Perirhinal gyrus (67.3), Olfactory area (64.7), Olfactory tubercle (61.2), Nucleus of the diagonal band (60.1), Temporal pole (57.1).

Regulation

Is transcription factor: no

Functional genomics

gnomAD constraint: pLI 6.1e-11, LOEUF 0.718, missense Z 1.13 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000299886 — one region, missense o/e 0.94. ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 52.8% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): SNB75 (-1.372), 769-P (-1.297), KARPAS-422 (-1.246), SNU-16 (-1.237), OAW42 (-1.237), COV362 (-1.231), 786-O (-1.228), MPP 89 (-1.214), LOU-NH91 (-1.164), KMS-34 (-1.162), RT-112 (-1.153), SU-DHL-10 (-1.145), NCI-H2452 (-1.129), NCI-H2882 (-1.116), huH-1 (-1.077).

Literature-anchored findings (GeneRIF, showing 5)

  • Sec34 is implicated in traffic from the endoplasmic reticulum to the Golgi and exists in a complex with GTC-90 and ldlBp (PMID:11929878)
  • These findings support the proposal that COG is directly involved in controlling vesicular retrograde transport of Golgi resident proteins throughout the Golgi apparatus. (PMID:16857184)
  • A novel mutation in COG1 was found in two patients with a cerebrocostomandibular-like syndrome. (PMID:19008299)
  • This study reports a novel set of Dengue virus (DENV) NS1-interacting host cell proteins in the HepG2 cell line and proposes possible roles for human NEK2, TAO1, and COG1 in DENV infection. (PMID:27108190)
  • Chronic renal patients with more atherogenic lipoprotein LDL B phenotype are in advanced state of oxidative stress compared with control subjects. (PMID:27412679)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocog1ENSDARG00000105131
mus_musculusCog1ENSMUSG00000018661
rattus_norvegicusCog1ENSRNOG00000002795
drosophila_melanogasterCog1FBGN0037998
caenorhabditis_eleganscogc-1WBGENE00003258

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1333873) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 4 distinct phenotype terms.

Mouse phenotype (MP)Records
abnormal embryo implantation1
abnormal inner cell mass morphology1
embryonic lethality between implantation and somite formation, complete penetrance1
preweaning lethality, complete penetrance1

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
SDK2-AS1ncRNA101928251
CDC42EP4protein-coding23580
SDK2protein-coding54549
MTNAP1protein-coding55028
CPSF4Lprotein-coding642843
VCF1protein-coding84923
SSTR2protein-coding6752
SLC39A11protein-coding201266

Protein

Protein identifiers

Conserved oligomeric Golgi complex subunit 1 — Q8WTW3 (reviewed: Q8WTW3)

Alternative names: Component of oligomeric Golgi complex 1

All UniProt accessions (6): Q8WTW3, E9PBL8, J3KRP4, J3KSY3, J3QKY9, J3QLT5

UniProt curated annotations — full annotation on UniProt →

Function. Required for normal Golgi function.

Subunit / interactions. Component of the conserved oligomeric Golgi complex which is composed of eight different subunits and is required for normal Golgi morphology and localization.

Subcellular location. Golgi apparatus membrane.

Disease relevance. Congenital disorder of glycosylation 2G (CDG2G) [MIM:611209] A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. Clinical features of CDG2G include failure to thrive, generalized hypotonia, growth retardation and mild psychomotor retardation. CDG2G is biochemically characterized by a defect in O-glycosylation as well as N-glycosylation. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the COG1 family.

RefSeq proteins (1): NP_061184* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR033370COG1Family

Pfam: PF08700

UniProt features (7 total): sequence variant 3, modified residue 2, initiator methionine 1, chain 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WTW3-F177.820.40

Human Protein Atlas

Protein class: Predicted intracellular proteins, Disease related genes, Human disease related genes, Congenital disorders of metabolism, Congenital disorders of glycan/glycoprotein metabolism, Essential proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH approved

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)

TypePositions
N-acetylalanine2
Phosphoserine7

Function

Pathways and Gene Ontology

Reactome pathways

4 curated (TAS) of 12; 1 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

12 pathways:

IDPathwayEvidence
R-HSA-9918481Dengue Virus-Host Interactions ⚕curated
R-HSA-6807878COPI-mediated anterograde transportcurated
R-HSA-6811438Intra-Golgi trafficcurated
R-HSA-6811440Retrograde transport at the Trans-Golgi-Networkcurated
R-HSA-446203Asparagine N-linked glycosylation—
R-HSA-199977ER to Golgi Anterograde Transport—
R-HSA-6811442Intra-Golgi and retrograde Golgi-to-ER traffic—
R-HSA-199991Membrane Trafficking—
R-HSA-392499Metabolism of proteins—
R-HSA-597592Post-translational protein modification—
R-HSA-948021Transport to the Golgi and subsequent modification—
R-HSA-5653656Vesicle-mediated transport—

MSigDB gene sets: 289 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_INTRA_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOBP_GOLGI_ORGANIZATION, GOCC_GOLGI_TRANSPORT_COMPLEX, GOCC_TRANS_GOLGI_NETWORK_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT, GOBP_GOLGI_VESICLE_TRANSPORT, HATADA_METHYLATED_IN_LUNG_CANCER_UP, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION

GO Biological Process (4): retrograde transport, vesicle recycling within Golgi (GO:0000301), intra-Golgi vesicle-mediated transport (GO:0006891), Golgi organization (GO:0007030), protein transport (GO:0015031)

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

GO Cellular Component (4): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), COG complex (GO:0017119), trans-Golgi network membrane (GO:0032588)

Reactome top-level categories

9 top-level categories:

CategoryPathways
Intra-Golgi and retrograde Golgi-to-ER traffic2
Membrane Trafficking2
ER to Golgi Anterograde Transport1
Dengue Virus Infection1
Transport to the Golgi and subsequent modification1
Vesicle-mediated transport1
Post-translational protein modification1
Metabolism of proteins1
Asparagine N-linked glycosylation1

GO top-level categories

16 GO namespaces:

CategoryTerms
Golgi apparatus2
intra-Golgi vesicle-mediated transport1
Golgi vesicle transport1
organelle organization1
endomembrane system organization1
transport1
intracellular protein localization1
establishment of protein localization1
binding1
bounding membrane of organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
vesicle tethering complex1
trans-Golgi network1
organelle membrane1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 9 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO termNSEvidence
Golgi organizationBPmutant phenotype
retrograde transport, vesicle recycling within GolgiBPmutant phenotype
COG complexCCdirect assay
Golgi apparatusCCdirect assay

Protein interactions and networks

STRING

showing 15 of 998 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
COG1COG2Q14746991
COG1COG3Q96JB2984
COG1COG5Q9UP83984
COG1COG7P83436983
COG1COG8Q96MW5964
COG1COG4Q9H9E3945
COG1COG6Q9Y2V7933
COG1GOSR2O14653724
COG1VPS51Q9UID3688
COG1VPS53Q5VIR6666
COG1VPS54Q9P1Q0665
COG1COPB1P53618653
COG1STX16O14662633
COG1RINT1Q6NUQ1630
COG1STX5Q13190629

IntAct

Human interaction partners of COG1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

5 partners by confidence:

PartnerInteraction typeMIscoreRecords
COG4physical association0.5602
CDC42physical association0.3701
COG8association0.3501
DSCAMphysical association0.0001
MTNR1Aphysical association0.0001

BioGRID (150 interactions; top human partners by supporting records): COG3 (Affinity Capture-MS; 8 records), COG4 (Co-fractionation; 6 records), COG5 (Co-fractionation; 5 records), COG6 (Co-fractionation; 5 records), COG2 (Co-fractionation; 4 records), COG7 (Co-fractionation; 4 records), COG8 (Co-fractionation; 4 records), BSG (Affinity Capture-MS; 3 records), CD274 (Affinity Capture-MS; 3 records), PARP16 (Affinity Capture-MS; 3 records), SCN2B (Affinity Capture-MS; 3 records), COMMD8 (Affinity Capture-MS; 2 records), GOLGA2 (Proximity Label-MS; 2 records), OPRM1 (Affinity Capture-MS; 2 records), AKT1 (Affinity Capture-MS)

SIGNOR signaling

1 signaling interactions:

AEffectBMechanism
COG1“form complex”“COG tethering complex”binding

Protein complexes (CORUM) (4)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

4 complexes by size:

ComplexSubunitsMembers
COG complex8COG2, COG3, COG4, COG5, COG6, COG7, COG8, COG1
COG1-COG8-COG2-COG3-COG4 subcomplex5COG1, COG2, COG3, COG4, COG8
COG1-COG8-COG5-COG6-COG7 subcomplex5COG1, COG5, COG6, COG7, COG8
COG1-COG8 subcomplex2COG1, COG8

Disease & clinical

Genetic variants

Variant evidence for COG1: 519 ClinVar records (21 pathogenic / likely pathogenic). Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic14
Likely pathogenic7
Uncertain significance253
Likely benign157
Benign36

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 21 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
3655NM_018714.3(COG1):c.1070+5G>APathogeniccriteria provided, multiple submitters, no conflicts4
2195938NM_018714.3(COG1):c.1006C>T (p.Arg336Ter)Pathogeniccriteria provided, multiple submitters, no conflicts2
1480682NM_018714.3(COG1):c.1130del (p.Lys377fs)Pathogeniccriteria provided, single submitter1
2027635NM_018714.3(COG1):c.2686C>T (p.Gln896Ter)Pathogeniccriteria provided, single submitter1
2028309NM_018714.3(COG1):c.254dup (p.Tyr86fs)Pathogeniccriteria provided, single submitter1
2805911NM_018714.3(COG1):c.1091del (p.Asn364fs)Pathogeniccriteria provided, single submitter1
3684462NM_018714.3(COG1):c.1401dup (p.Glu468Ter)Pathogeniccriteria provided, single submitter1
3728028NM_018714.3(COG1):c.2665del (p.Arg889fs)Pathogeniccriteria provided, single submitter1
3728286NM_018714.3(COG1):c.2665_2666insCG (p.Arg889fs)Pathogeniccriteria provided, single submitter1
4710995NM_018714.3(COG1):c.415C>T (p.Gln139Ter)Pathogeniccriteria provided, single submitter1
4740975NM_018714.3(COG1):c.2626_2629dup (p.Gly877fs)Pathogeniccriteria provided, single submitter1
4764410NM_018714.3(COG1):c.1717C>T (p.Gln573Ter)Pathogeniccriteria provided, single submitter1
4780564NM_018714.3(COG1):c.1487del (p.Gly496fs)Pathogeniccriteria provided, single submitter1
450371NM_018714.3(COG1):c.2084_2085insCCTGGTAATAAAATGAC (p.His695_Gly696insLeuValIleLysTer)Likely pathogeniccriteria provided, single submitter1
452106NM_018714.3(COG1):c.1823del (p.Leu608fs)Likely pathogeniccriteria provided, single submitter1

Per-variant reference — Sugi Variant

Explore COG1’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 32 predictions of 1,198):

Position(s)EffectΔscoreSites
17:73193385–73193386donor_loss1.00005
17:73200564–73200565acceptor_loss1.00005
17:73200777–73200778donor_loss1.00004
17:73203794–73203795donor_loss1.00003
17:73206263–73206264donor_loss1.00002
17:73206674acceptor_gain1.0000
17:73196479acceptor_gain0.9900
17:73196752–73196753donor_loss0.99005
17:73197046donor_gain0.9900
17:73200022–73200023donor_loss0.99005

AlphaMissense

1,298 missense substitutions predicted likely pathogenic (of 6,395 scored), across 423 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M6990.9210.993
D85380.9770.991
F2280.9690.991
D85080.9690.993
F85280.9660.997
F91180.9520.996
D48280.9290.965
D81280.9240.976
D5880.9130.956
F27380.9060.973
F85780.8730.981
D6480.8510.936
D85580.7770.876
W47670.9730.997
W71670.9700.996
W35470.9410.996
W41470.9290.977
W48970.9220.981
W68570.9200.993
M5170.9170.970

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Liver Hepatocellular Carcinoma (TCGA)unfavorable5.96e-05
Head and Neck Squamous Cell Carcinoma (TCGA)unfavorable9.71e-05

Disease associations

OMIM: gene MIM:606973 | disease phenotypes: MIM:611209

GenCC curated gene-disease

1 curated gene-disease records:

DiseaseClassificationInheritanceRecords
COG1-congenital disorder of glycosylationDefinitiveAutosomal recessive3

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

1 validity classifications:

DiseaseClassificationInheritance
COG1-congenital disorder of glycosylationModerateAR

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (12 panels, 12 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

12 panels:

PanelRating
Congenital disorders of glycosylationgreen
DDG2Pgreen
Fetal anomaliesgreen
Hereditary ataxia and cerebellar anomalies, childhood onsetgreen
Hypotonic infantgreen
Intellectual disabilitygreen
Leukodystrophy, childhood onsetgreen
Likely inborn error of metabolismgreen
Paediatric disordersgreen
Skeletal dysplasiagreen
Undiagnosed metabolic disordersgreen
Unexplained death in infancy and sudden unexplained death in childhoodgreen

Mondo (2): COG1-congenital disorder of glycosylation (MONDO:0012637), nephrotic syndrome (MONDO:0005377)

Orphanet (1): COG1-CDG (Orphanet:263508)

HPO phenotypes

showing 60 of 91 phenotypes (HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000028Cryptorchidism
HP:0000047Hypospadias
HP:0000083Renal insufficiency
HP:0000126Hydronephrosis
HP:0000160Narrow mouth
HP:0000162Glossoptosis
HP:0000175Cleft palate
HP:0000201Pierre-Robin sequence
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000252Microcephaly
HP:0000253Progressive microcephaly
HP:0000274Small face
HP:0000316Hypertelorism
HP:0000319Smooth philtrum
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000358Posteriorly rotated ears
HP:0000369Low-set ears
HP:0000402Stenosis of the external auditory canal
HP:0000405Conductive hearing impairment
HP:0000431Wide nasal bridge
HP:0000463Anteverted nares
HP:0000470Short neck
HP:0000475Broad neck
HP:0000494Downslanted palpebral fissures
HP:0000520Proptosis
HP:0000582Upslanted palpebral fissure
HP:0000750Delayed speech and language development
HP:0000902Rib fusion
HP:0000938Osteopenia
HP:0000954Single transverse palmar crease
HP:0001103Abnormal macular morphology
HP:0001252Hypotonia
HP:0001256Mild intellectual disability
HP:0001263Global developmental delay
HP:0001272Cerebellar atrophy
HP:0001290Generalized hypotonia
HP:0001320Cerebellar vermis hypoplasia
HP:0001433Hepatosplenomegaly
HP:0001508Failure to thrive
HP:0001511Intrauterine growth retardation
HP:0001531Failure to thrive in infancy
HP:0001712Left ventricular hypertrophy
HP:0001762Talipes equinovarus
HP:0001773Short foot
HP:0001873Thrombocytopenia
HP:0001902Giant platelets
HP:0001903Anemia
HP:0001999Abnormal facial shape
HP:0002059Cerebral atrophy
HP:0002092Pulmonary arterial hypertension
HP:0002280Enlarged cisterna magna
HP:0002342Moderate intellectual disability
HP:0002673Coxa valga
HP:0002719Recurrent infections
HP:0002751Kyphoscoliosis
HP:0002943Thoracic scoliosis
HP:0003026Short long bone

MeSH disease descriptors

2 disease descriptors:

DescriptorNameTree numbers
D009404Nephrotic SyndromeC12.050.351.968.419.630.643; C12.200.777.419.630.643; C12.950.419.630.643
C535756Congenital disorder of glycosylation, type 2G *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105805 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (2 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
CHEMBL5653589KD1440 nM

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.41Kd3.9nMCHEMBL3752910
8.41ED503.9nMCHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 6 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.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148104: Binding affinity to human COG1 incubated for 45 mins by Kinobead based pull down assaykd0.0039uM

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases methylation3
aristolochic acid Iincreases expression1
FR900359decreases phosphorylation1
2,4,6-tribromophenoldecreases expression1
bisphenol Adecreases expression1
decabromobiphenyl etherdecreases expression1
sodium arseniteincreases expression1
tetrabromobisphenol Aincreases expression1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
abrineincreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
bisphenol Sincreases methylation1
Temozolomideincreases expression1
Sunitinibincreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Doxorubicindecreases expression1
Ethyl Methanesulfonateincreases expression1
Ivermectindecreases expression1
Smokedecreases expression1
Urethanedecreases expression1
Cyclosporineincreases expression1
Aflatoxin B1increases expression1
Asbestos, Crocidolitedecreases expression1
Thapsigarginincreases expression1
Copper Sulfatedecreases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4012601BindingBinding affinity to COG1 in human INA-6 cells after 3 hrs by nanoLC-MS/MS methodUgi Reaction-Derived α-Acyl Aminocarboxamides Bind to Phosphatidylinositol 3-Kinase-Related Kinases, Inhibit HSF1-Dependent Heat Shock Response, and Induce Apoptosis in Multiple Myeloma Cells. — *J Med Chem*

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A637KMS-18Cancer cell lineMale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 300 trials:

NCTPhaseStatusTitle
NCT00029224Phase 4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997Phase 4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609Phase 4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623Phase 4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392Phase 4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029Phase 4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485Phase 4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219Phase 4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271Phase 4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146Phase 4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554Phase 4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098Phase 4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696Phase 4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139Phase 4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765Phase 4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690Phase 4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708Phase 4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331Phase 4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213Phase 4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330Phase 4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966Phase 4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701Phase 4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027Phase 4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269Phase 4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277Phase 4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800Phase 4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199Phase 4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226Phase 4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563Phase 4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905Phase 4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672Phase 4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143Phase 4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742Phase 4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563Phase 4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874Phase 4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472Phase 4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416Phase 4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544Phase 4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749Phase 4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635Phase 4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer
NCT01673984Phase 4TERMINATEDGP Extended Action Triptorelin
NCT01753297Phase 4COMPLETEDA Study of Immediate 9 Months Adjuvant Hormone Therapy With Triptorelin 11.25 mg Versus Active Surveillance After Radical Prostatectomy in High Risk Prostate Cancer Patients.
NCT01794793Phase 4COMPLETEDStudy to Allow Access to Pasireotide for Patients Benefiting From Pasireotide Treatment in Novartis-sponsored Studies
NCT01950871Phase 4TERMINATEDProstate Guided Biopsy Study Evaluating the Diagnostic Performance of Prostate HistoScanning
NCT01995513Phase 4COMPLETEDSafety Study of Continued Enzalutamide Treatment In Prostate Cancer Patients
NCT02102646Phase 4COMPLETEDMRI Substudy; Metabolic Changes Due to Iatrogenic Hypogonadism
NCT02116582Phase 4COMPLETEDA Study to Evaluate Enzalutamide After Abiraterone in Metastatic Castration-Resistant Prostate Cancer
NCT02149628Phase 4COMPLETEDThe Effect of Propofol Based Total Intravenous Anesthesia on Oxidative Stress and Nitric Oxide
NCT02405858Phase 4COMPLETEDA Study of Abiraterone Acetate in Metastatic Castration-Resistant Prostate Cancer Participants Who Responded Poorly to the First-line Combined Androgen Blockade Therapy
NCT02441517Phase 4TERMINATEDA Study of Enzalutamide Re-treatment in Metastatic Castration-resistant Prostate Cancer After Docetaxel and/or Cabazitaxel Treatment
NCT02441894Phase 4COMPLETEDCombination of Cabazitaxel With Prednisolone With Primary Prophylaxis With PEG-G-CSF in Treatment of Patients With Prostate Cancer
NCT02475057Phase 4COMPLETEDEndothelial Function in Prostate Cancer Patients on Degarelix vs. Luteinizing Hormone-Releasing Hormone Agonists
NCT02511665Phase 4UNKNOWNMetformin And Longevity
NCT02651948Phase 4COMPLETEDTransperineal, MRI-guided, Prostate Biopsy
NCT02721433Phase 4COMPLETED4-weekly Versus 12-weekly Administration of Bone-targeted Agents in Patients With Bone Metastases
NCT02726009Phase 4COMPLETEDA Trial to Evaluate Safety of Firmagon® (Degarelix) in Indian Patients Diagnosed With Advanced Hormone-dependent Prostate Cancer
NCT02749825Phase 4TERMINATEDComparison of Trelstar Versus Lupron or Zoladex in Advanced Prostate Cancer
NCT02757365Phase 4UNKNOWNEfficiency Study of Aspirin to Prevent the Occurrence of Prostate Cancer
NCT02773251Phase 4COMPLETEDThe Effect of Guardix-solution for the Prevention of Postoperative Intestinal Adhesion and Intestinal Obstruction After Laparoscopic Pelvic Cavity Surgery
NCT02812186Phase 4COMPLETEDDeep Versus Moderate Neuromuscular Blockade During Laparoscopic Surgery

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for COG1 across ~30M SureChEMBL compounds — explore on Sugi Predict.