GPATCH8

gene
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Summary

GPATCH8 (G-patch domain containing 8, HGNC:29066) is a protein-coding gene on chromosome 17q21.31, encoding G patch domain-containing protein 8 (Q9UKJ3).

The protein encoded by this gene contains an RNA-processing domain, a zinc finger domain, a lysine-rich region and a serine-rich region. A mutation in the serine-rich region of the protein is thought to be associated with hyperuricemia (PMID: 21594610). Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 23131 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 202 total
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_001002909

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29066
Approved symbolGPATCH8
NameG-patch domain containing 8
Location17q21.31
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000186566
Ensembl biotypeprotein_coding
OMIM614396
Entrez23131

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 5 protein_coding, 4 retained_intron, 4 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000335500, ENST00000585614, ENST00000586037, ENST00000586265, ENST00000587228, ENST00000588554, ENST00000590041, ENST00000591680, ENST00000592154, ENST00000592746, ENST00000635257, ENST00000928548, ENST00000928549, ENST00000928550

RefSeq mRNA: 6 — MANE Select: NM_001002909 NM_001002909, NM_001304939, NM_001304940, NM_001304941, NM_001304942, NM_001304943

CCDS: CCDS32666

Canonical transcript exons

ENST00000591680 — 8 exons

ExonStartEnd
ENSE000034773764439528144401453
ENSE000035205594446447244464544
ENSE000035358294442434944424492
ENSE000035992474447482944474903
ENSE000036060394450332644503406
ENSE000036272034443647844436545
ENSE000036445284440592144406051
ENSE000036778774443506544435151

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 96.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.6575 / max 251.8593, expressed in 1808 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
16638211.65491771
1663856.01201583
1663841.7096811
1663830.2810115

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548896.18gold quality
secondary oocyteCL:000065595.45gold quality
right hemisphere of cerebellumUBERON:001489094.88gold quality
cerebellar hemisphereUBERON:000224594.80gold quality
cerebellar cortexUBERON:000212994.68gold quality
cerebellumUBERON:000203793.98gold quality
olfactory bulbUBERON:000226493.32gold quality
gastrocnemiusUBERON:000138893.16gold quality
calcaneal tendonUBERON:000370193.06gold quality
nippleUBERON:000203092.98gold quality
muscle of legUBERON:000138392.97gold quality
colonic epitheliumUBERON:000039792.89gold quality
lateral globus pallidusUBERON:000247692.51gold quality
pylorusUBERON:000116692.39gold quality
inferior olivary complexUBERON:000212792.36gold quality
cardia of stomachUBERON:000116291.89gold quality
tendon of biceps brachiiUBERON:000818891.83gold quality
tendonUBERON:000004391.56gold quality
Brodmann (1909) area 23UBERON:001355491.29gold quality
type B pancreatic cellCL:000016991.28gold quality
muscle organUBERON:000163091.19gold quality
inferior vagus X ganglionUBERON:000536390.99gold quality
ventricular zoneUBERON:000305390.90gold quality
visceral pleuraUBERON:000240190.68gold quality
hindlimb stylopod muscleUBERON:000425290.64gold quality
primary visual cortexUBERON:000243690.56gold quality
lateral nuclear group of thalamusUBERON:000273690.51gold quality
substantia nigra pars reticulataUBERON:000196690.45gold quality
corpus callosumUBERON:000233690.44gold quality
tibialis anteriorUBERON:000138590.40gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.83
E-CURD-135no695.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

200 targeting GPATCH8, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4476100.0068.182030
HSA-MIR-6130100.0066.692012
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6133100.0066.482064
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-126-5P100.0072.713180
HSA-MIR-9-5P100.0072.282361
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-607799.9968.042299
HSA-MIR-150-5P99.9966.691976
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-548P99.9872.253784
HSA-MIR-32-5P99.9875.211964
HSA-MIR-548AN99.9770.912817
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-448799.9664.581252
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-570-3P99.9672.414910

Literature-anchored findings (GeneRIF, showing 2)

  • Two missense single-nucleotide variants in ZPBP2 and GPATCH8 on chromosome 17 were identified that cosegregated with hyperuricemia in the Japanese family. (PMID:21594610)
  • GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies. (PMID:38688280)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriogpatch8ENSDARG00000059768
mus_musculusGpatch8ENSMUSG00000034621
rattus_norvegicusGpatch8ENSRNOG00000021044

Paralogs (2): ZNF804A (ENSG00000170396), ZNF804B (ENSG00000182348)

Protein

Protein identifiers

G patch domain-containing protein 8Q9UKJ3 (reviewed: Q9UKJ3)

All UniProt accessions (3): K7EKU0, K7EQK8, Q9UKJ3

UniProt curated annotations — full annotation on UniProt →

Isoforms (3)

UniProt IDNamesCanonical?
Q9UKJ3-11yes
Q9UKJ3-22
Q9UKJ3-33

RefSeq proteins (5): NP_001002909, NP_001291868, NP_001291869, NP_001291870, NP_001291871 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000467G_patch_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR052445ZNF804A-like/GPATCH8Family

Pfam: PF01585

UniProt features (60 total): compositionally biased region 21, modified residue 16, sequence variant 5, region of interest 4, sequence conflict 4, cross-link 3, splice variant 3, chain 1, domain 1, zinc finger region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UKJ3-F146.490.05

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 (19): 479, 491, 653, 738, 740, 758, 911, 914, 981, 1009, 1014, 1033, 1035, 1081, 1107, 1175, 311, 577, 1105

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 163 (showing top): MORF_FLT1, MORF_MSH3, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, TTTGTAG_MIR520D, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MORF_BRCA1, MORF_ATRX, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MORF_ESR1, TTGGGAG_MIR150, GTGCCTT_MIR506, DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN, GOBP_RNA_SPLICING, GGCAGTG_MIR3243P

GO Biological Process (2): mRNA splicing, via spliceosome (GO:0000398), hemopoiesis (GO:0030097)

GO Molecular Function (6): RNA binding (GO:0003723), mRNA binding (GO:0003729), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
cell development1
nucleic acid binding1
RNA binding1
transition metal ion binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

980 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GPATCH8DDA1Q9BW61475
GPATCH8PCDHB13Q9Y5F0390
GPATCH8WDR6Q9NNW5371
GPATCH8UBE4BO95155368
GPATCH8RUNDC1Q96C34354
GPATCH8PYM1Q9BRP8354
GPATCH8GPRIN1Q7Z2K8342
GPATCH8NT5C3BQ969T7341
GPATCH8GARRE1O15063326
GPATCH8ZNF778Q96MU6324
GPATCH8CCDC43Q96MW1322
GPATCH8ADPRHL1Q8NDY3321
GPATCH8SCNM1Q9BWG6320
GPATCH8TMEM101Q96IK0317
GPATCH8BLTP1Q2LD37315

IntAct

107 interactions, top by confidence:

ABTypeScore
SNRPFGEMIN2psi-mi:“MI:0914”(association)0.910
SNRPEGEMIN2psi-mi:“MI:0914”(association)0.770
CAMKVAP3B1psi-mi:“MI:0914”(association)0.640
SNRPA1U2SURPpsi-mi:“MI:0914”(association)0.640
SNRPBSART1psi-mi:“MI:0914”(association)0.640
PIP4K2AAP3B1psi-mi:“MI:0914”(association)0.530
EPB41L2AP3B1psi-mi:“MI:0914”(association)0.530
SNIP1CASC3psi-mi:“MI:0914”(association)0.530
LACC1DUSP14psi-mi:“MI:0914”(association)0.530
JPH4ZSWIM8psi-mi:“MI:0914”(association)0.530
EPB41L1AP3B1psi-mi:“MI:0914”(association)0.530
EPB41L3AP3B1psi-mi:“MI:0914”(association)0.530
LUC7L2CASC3psi-mi:“MI:0914”(association)0.530
SRPK2RRP9psi-mi:“MI:0914”(association)0.530
SNRPCSNRPGP15psi-mi:“MI:0914”(association)0.530
U2AF2U2SURPpsi-mi:“MI:0914”(association)0.480
H1-5GPATCH8psi-mi:“MI:0915”(physical association)0.400
GPATCH8H2BC9psi-mi:“MI:0915”(physical association)0.400
H2AXGPATCH8psi-mi:“MI:0915”(physical association)0.400
GPATCH8HIST2H2BFpsi-mi:“MI:0915”(physical association)0.400

BioGRID (147): GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Affinity Capture-MS), GPATCH8 (Two-hybrid), GPATCH8 (Proximity Label-MS), ABCA2 (Affinity Capture-MS), FDX1 (Affinity Capture-MS), PON2 (Affinity Capture-MS)

ESM2 similar proteins: A2A6A1, B0BN49, B0QZF7, D2H526, E1BB50, E9PYH6, E9Q4F7, E9Q6J5, F1Q8W0, O15047, O88453, P30414, P30415, Q01538, Q14AX6, Q17QQ9, Q27450, Q3KPW4, Q3UMU9, Q4V8I5, Q505I5, Q5BKY9, Q5SW79, Q5VZP5, Q62417, Q66648, Q66PJ3, Q6A065, Q6P9P0, Q6UB99, Q7TQC7, Q7Z4V5, Q80U49, Q86VM9, Q8BYK8, Q8C5W0, Q8CFC2, Q8NEY8, Q8R0F5, Q8R2M2

Diamond homologs: A2A6A1, A2AKY4, B2GV05, P52756, Q1RMU5, Q6DF57, Q6DGZ0, Q7Z570, Q91YE7, Q94C11, Q9UKJ3, A4D1E1, A0JMV4, A4IGK4, P70501, P87143, P98175, Q0IIX9, Q4PC17, Q66J74, Q6C233, Q6DDU9, Q7TN31, Q7TQC7, Q8CH09, Q8N302, Q99KG3, Q9NW75, A6ZRL6, A8XYX2, A8XYX3, C6Y4A5, P53866, Q17784, Q2KI19, Q3UFS4, Q875B6, Q8IX01, Q8N954, Q9NAA5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 106 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:

PathwayPartnersFoldFDR
Transport of Mature Transcript to Cytoplasm737.0×2e-08
RNA Polymerase II Transcription Termination1030.5×3e-11
mRNA Splicing1827.4×2e-19
mRNA 3’-end processing821.9×9e-08
mRNA Splicing - Minor Pathway721.8×8e-07
Processing of Capped Intron-Containing Pre-mRNA1921.7×9e-19
mRNA Polyadenylation1619.5×5e-15
mRNA Splicing - Major Pathway2418.2×7e-22

GO biological processes:

GO termPartnersFoldFDR
negative regulation of mRNA splicing, via spliceosome647.9×2e-07
spliceosomal snRNP assembly742.4×4e-08
U2-type prespliceosome assembly639.0×8e-07
RNA splicing, via transesterification reactions532.5×3e-05
spliceosomal complex assembly531.4×3e-05
regulation of alternative mRNA splicing, via spliceosome717.8×1e-05
RNA processing716.0×2e-05
RNA splicing1614.7×7e-12

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance186
Likely benign7
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2490 predictions. Top by Δscore:

VariantEffectΔscore
17:44401452:CA:Cacceptor_gain1.0000
17:44401454:C:CCacceptor_gain1.0000
17:44401466:T:Cacceptor_gain1.0000
17:44401466:T:TCacceptor_gain1.0000
17:44405915:CCTCA:Cdonor_loss1.0000
17:44405916:CTCA:Cdonor_loss1.0000
17:44405919:A:ACdonor_gain1.0000
17:44405919:A:ATdonor_loss1.0000
17:44405919:AC:Adonor_gain1.0000
17:44405920:C:CCdonor_gain1.0000
17:44405920:C:CTdonor_loss1.0000
17:44405920:CC:Cdonor_gain1.0000
17:44405920:CCATT:Cdonor_gain1.0000
17:44406047:AATCT:Aacceptor_gain1.0000
17:44406048:ATCT:Aacceptor_gain1.0000
17:44406050:CT:Cacceptor_gain1.0000
17:44406052:C:CCacceptor_gain1.0000
17:44406056:G:GCacceptor_gain1.0000
17:44406057:T:Cacceptor_gain1.0000
17:44406057:T:TCacceptor_gain1.0000
17:44424344:CTCA:Cdonor_loss1.0000
17:44424345:TCA:Tdonor_loss1.0000
17:44424346:CA:Cdonor_loss1.0000
17:44424347:A:Cdonor_loss1.0000
17:44424348:C:CAdonor_loss1.0000
17:44424348:CCTG:Cdonor_gain1.0000
17:44424488:TAATC:Tacceptor_gain1.0000
17:44424501:CCCA:Cacceptor_gain1.0000
17:44424503:C:CTacceptor_gain1.0000
17:44424504:A:ACacceptor_gain1.0000

AlphaMissense

9855 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:44398097:G:TA1327D1.000
17:44398098:C:GA1327P1.000
17:44398101:C:GA1326P1.000
17:44398109:A:GL1323P1.000
17:44398109:A:TL1323H1.000
17:44398118:T:CY1320C1.000
17:44398119:A:GY1320H1.000
17:44398141:G:CF1312L1.000
17:44398141:G:TF1312L1.000
17:44398142:A:CF1312C1.000
17:44398142:A:GF1312S1.000
17:44398143:A:GF1312L1.000
17:44400424:C:AW551C1.000
17:44400424:C:GW551C1.000
17:44400426:A:GW551R1.000
17:44400426:A:TW551R1.000
17:44400458:A:TV540D1.000
17:44405957:A:GL196P1.000
17:44406011:A:TV178D1.000
17:44406013:A:CN177K1.000
17:44406013:A:TN177K1.000
17:44406017:C:GR176P1.000
17:44406022:A:CF174L1.000
17:44406022:A:TF174L1.000
17:44406023:A:CF174C1.000
17:44406023:A:GF174S1.000
17:44406024:A:GF174L1.000
17:44406027:C:TE173K1.000
17:44406028:T:AR172S1.000
17:44406028:T:GR172S1.000

dbSNP variants (sampled 300 via entrez): RS1000007733 (17:44482108 G>A,C), RS1000046764 (17:44456492 A>G), RS1000055704 (17:44499226 G>A,C), RS1000069128 (17:44493505 T>C), RS1000070753 (17:44493721 C>T), RS1000107192 (17:44412652 G>A), RS1000132007 (17:44441726 C>A,T), RS1000159290 (17:44471629 G>A), RS1000160476 (17:44420169 C>G,T), RS1000211150 (17:44476379 T>C), RS1000214675 (17:44419872 A>C), RS1000240885 (17:44469543 T>C), RS1000276168 (17:44450104 G>C), RS1000306524 (17:44469298 C>T), RS1000353803 (17:44422316 C>T)

Disease associations

OMIM: gene MIM:614396 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST007269_163Pulse pressure6.000000e-13
GCST010703_292Brain morphology (MOSTest)1.000000e-14

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005763pulse pressure measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523489 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

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).

pChemblTypeValueUnitMolecule
8.00IC5010nMMOLIBRESIB
7.92Kd12nMMOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 8 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
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2178759: Inhibition of GPATCH8 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysisic500.0100uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression2
FR900359affects phosphorylation1
TAK-243decreases sumoylation1
dicrotophosincreases expression1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
beta-lapachonedecreases expression1
arseniteaffects binding, decreases reaction1
ferrous chloridedecreases expression1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
abrineincreases expression1
bisphenol Saffects cotreatment, increases expression1
Caffeineaffects phosphorylation1
Cisplatindecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Hydrogen Peroxideaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Ribonucleotidesaffects binding1
Dronabinolincreases expression1
Theophyllineaffects cotreatment, increases expression1
Thiramincreases expression1
Vitamin Edecreases expression1
1-Methyl-3-isobutylxanthineincreases expression, affects cotreatment1
Palmitic Aciddecreases phosphorylation1
Lactic Aciddecreases expression1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4341442BindingBinding affinity to GPATCH8 in human A549 cells lysates grown on SILAC media at 10 uM incubated for 1 hr by LC-MS/MS analysis relative to untreated controlProfiling withanolide A for therapeutic targets in neurodegenerative diseases. — Bioorg Med Chem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.