GPATCH1

Summary

GPATCH1 (G-patch domain containing 1, HGNC:24658) is a protein-coding gene on chromosome 19q13.11, encoding G patch domain-containing protein 1 (Q9BRR8). It is a selective cancer dependency (DepMap: 19.7% of cell lines).

Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Part of catalytic step 2 spliceosome.

Source: NCBI Gene 55094 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 171 total
• Cancer dependency (DepMap): dependent in 19.7% of screened cell lines
• MANE Select transcript: NM_018025

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24658
Approved symbol	GPATCH1
Name	G-patch domain containing 1
Location	19q13.11
Locus type	gene with protein product
Status	Approved
Aliases	ECGP, FLJ10206, FLJ38686
Ensembl gene	ENSG00000076650
Ensembl biotype	protein_coding
Entrez	55094

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000170564, ENST00000590062, ENST00000592165, ENST00000592262, ENST00000880979, ENST00000880980, ENST00000939189

RefSeq mRNA: 1 — MANE Select: NM_018025 NM_018025

CCDS: CCDS12428

Canonical transcript exons

ENST00000170564 — 20 exons

Exon	Start	End
ENSE00000821681	33088134	33088268
ENSE00000821683	33090780	33090865
ENSE00000821684	33093359	33093519
ENSE00000821686	33094172	33094269
ENSE00000821700	33109717	33110016
ENSE00000821703	33112486	33112613
ENSE00000821705	33113767	33113903
ENSE00001012829	33081181	33081266
ENSE00002823779	33130130	33130542
ENSE00003464652	33126588	33126733
ENSE00003465147	33125105	33125202
ENSE00003466522	33097755	33097902
ENSE00003536344	33106695	33106899
ENSE00003554875	33114253	33114419
ENSE00003566778	33119010	33119117
ENSE00003571053	33096207	33096446
ENSE00003594449	33111724	33111902
ENSE00003663287	33101495	33101574
ENSE00003671307	33095762	33095820
ENSE00003687165	33117825	33118041

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 86.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.3695 / max 100.4753, expressed in 1656 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175072	5.9804	1647
175073	0.2192	80
175074	0.1699	64

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	86.02	gold quality
hair follicle	UBERON:0002073	83.80	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.85	gold quality
skin of leg	UBERON:0001511	82.07	gold quality
skin of abdomen	UBERON:0001416	81.66	gold quality
right ovary	UBERON:0002118	81.33	gold quality
cerebellar hemisphere	UBERON:0002245	81.16	gold quality
cerebellar cortex	UBERON:0002129	81.07	gold quality
sural nerve	UBERON:0015488	80.97	gold quality
tendon	UBERON:0000043	80.74	gold quality
zone of skin	UBERON:0000014	80.73	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.59	gold quality
popliteal artery	UBERON:0002250	80.58	gold quality
tibial artery	UBERON:0007610	80.58	gold quality
cerebellum	UBERON:0002037	80.41	gold quality
left ovary	UBERON:0002119	80.41	gold quality
tibial nerve	UBERON:0001323	80.11	gold quality
right lobe of liver	UBERON:0001114	79.88	gold quality
body of uterus	UBERON:0009853	79.79	gold quality
mucosa of stomach	UBERON:0001199	79.78	gold quality
ectocervix	UBERON:0012249	79.72	gold quality
endocervix	UBERON:0000458	79.52	gold quality
lower esophagus mucosa	UBERON:0035834	79.50	gold quality
muscle layer of sigmoid colon	UBERON:0035805	79.48	gold quality
aorta	UBERON:0000947	79.46	gold quality
granulocyte	CL:0000094	79.41	gold quality
mucosa of transverse colon	UBERON:0004991	79.31	gold quality
Brodmann (1909) area 23	UBERON:0013554	79.23	gold quality
ventricular zone	UBERON:0003053	79.16	gold quality
cerebellar vermis	UBERON:0004720	79.15	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting GPATCH1, 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-548C-3P	99.99	74.01	7587
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-622	98.99	66.48	1050
HSA-MIR-1843	98.97	66.07	838
HSA-MIR-4802-5P	98.97	66.26	833
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-513B-3P	98.76	68.12	1577
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-4782-5P	98.35	69.33	1474
HSA-MIR-5706	98.35	69.33	1463
HSA-MIR-2681-3P	98.18	65.28	577
HSA-MIR-4637	97.69	68.14	632
HSA-MIR-7154-3P	97.65	65.02	985
HSA-MIR-490-5P	96.75	65.81	661
HSA-MIR-6839-5P	96.74	68.29	1088
HSA-MIR-4436B-5P	96.71	68.37	1346

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 19.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• In vitro, OmpA+ Escherichia coli infection selectively upregulates Ecgp96 and TLR2 in human brain microvascular endothelial cells (HBMEC), whereas OmpA- E. coli upregulates TLR4 in these cells. (PMID:22963587)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	gpatch1	ENSDARG00000033418
mus_musculus	Gpatch1	ENSMUSG00000063808
rattus_norvegicus	Gpatch1	ENSRNOG00000011584
drosophila_melanogaster	CG8833	FBGN0036386
caenorhabditis_elegans		WBGENE00011109

Protein

Protein identifiers

G patch domain-containing protein 1 — Q9BRR8 (reviewed: Q9BRR8)

Alternative names: Evolutionarily conserved G-patch domain-containing protein

All UniProt accessions (2): Q9BRR8, K7EQ19

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GPATCH1 family.

RefSeq proteins (1): NP_060495* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000467	G_patch_dom	Domain
IPR011666	DUF1604	Domain

Pfam: PF01585, PF07713, PF26093

UniProt features (32 total): compositionally biased region 8, modified residue 6, sequence variant 6, region of interest 5, sequence conflict 3, initiator methionine 1, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRR8-F1	59.51	0.01

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 (7): 2, 6, 8, 357, 477, 715, 312

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway

MSigDB gene sets: 79 (showing top): IVANOVA_HEMATOPOIESIS_MATURE_CELL, CATTTCA_MIR203, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING, REACTOME_METABOLISM_OF_RNA, GAL_LEUKEMIC_STEM_CELL_UP, GOCC_CATALYTIC_STEP_2_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, MODULE_49, GOBP_MRNA_PROCESSING, LIU_IL13_PRIMING_MODEL, EGFR_UP.V1_DN, EBNA1BP2_TARGET_GENES

GO Biological Process (2): mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397)

GO Molecular Function (2): RNA binding (GO:0003723), nucleic acid binding (GO:0003676)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), catalytic step 2 spliceosome (GO:0071013)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
mRNA Splicing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
RNA processing	1
mRNA metabolic process	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
Prp19 complex	1
spliceosomal complex	1
U5 snRNP	1
catalytic complex	1

Protein interactions and networks

STRING

1046 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPATCH1	CCDC170	Q8IYT3	568
GPATCH1	TMEM135	Q86UB9	542
GPATCH1	SUGP1	Q8IWZ8	509
GPATCH1	MRM1	Q6IN84	491
GPATCH1	SNRNP27	Q8WVK2	487
GPATCH1	MPHOSPH6	Q99547	483
GPATCH1	LEKR1	Q6ZMV7	419
GPATCH1	GLG1	Q92896	418
GPATCH1	NRDE2	Q9H7Z3	416
GPATCH1	CDC5L	Q99459	415
GPATCH1	U2SURP	O15042	401
GPATCH1	A0A0A6YYL1	A0A0A6YYL1	394
GPATCH1	ASCL4	Q6XD76	394
GPATCH1	SRRM1	Q8IYB3	392
GPATCH1	CCDC138	Q96M89	386

IntAct

121 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
CEP290	CCP110	psi-mi:“MI:2364”(proximity)	0.890
PPIE	AQR	psi-mi:“MI:0914”(association)	0.810
PRPF19	AQR	psi-mi:“MI:0914”(association)	0.790
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
ISY1	AQR	psi-mi:“MI:0914”(association)	0.740
SYF2	AQR	psi-mi:“MI:0914”(association)	0.730
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SNW1	AQR	psi-mi:“MI:0914”(association)	0.650
EFTUD2	SART1	psi-mi:“MI:0914”(association)	0.610
CEP104	CCDC66	psi-mi:“MI:2364”(proximity)	0.540
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
PRPF19	STRN	psi-mi:“MI:0914”(association)	0.530
KIAA1143	AQR	psi-mi:“MI:0914”(association)	0.530
EAPP	SNRNP200	psi-mi:“MI:0914”(association)	0.530
SNRPE	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
SNRPF	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
WDR83	SH2B2	psi-mi:“MI:0914”(association)	0.530
EFTUD2	AQR	psi-mi:“MI:0914”(association)	0.530
PLRG1	AQR	psi-mi:“MI:0914”(association)	0.530

BioGRID (137): GPATCH1 (Affinity Capture-MS), GPATCH1 (Affinity Capture-MS), GPATCH1 (Affinity Capture-MS), GPATCH1 (Affinity Capture-MS), GPATCH1 (Affinity Capture-MS), GPATCH1 (Affinity Capture-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS), GPATCH1 (Proximity Label-MS)

ESM2 similar proteins: A1A5P2, A6QNR1, A8WY26, D3ZND0, O15213, O59678, P27672, P78316, Q0V8M0, Q15050, Q24K12, Q28IV8, Q2KIH4, Q2KII6, Q3T0Q8, Q3T0Z5, Q3UFY0, Q4KLC4, Q5M985, Q5RAS1, Q5RJT2, Q5TAP6, Q5TJE7, Q5ZKM1, Q640M1, Q6EJB6, Q6P0I6, Q6PFJ1, Q8BK35, Q8IY81, Q8N9T8, Q8NEJ9, Q8R3N1, Q8VDQ9, Q96BZ8, Q96EU6, Q9BRP8, Q9BRR8, Q9BVJ6, Q9C086

Diamond homologs: B8B2G4, Q21827, Q24K12, Q67VW6, Q8GXN9, Q9BRR8, Q9DBM1, Q9HE07, Q9VUA0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 111 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
Metabolism of non-coding RNA	6	49.4×	3e-08
mRNA Splicing - Minor Pathway	10	29.1×	3e-11
mRNA Splicing	19	27.1×	2e-20
Anchoring of the basal body to the plasma membrane	18	26.4×	2e-19
RNA Polymerase II Transcription Termination	9	25.7×	1e-09
Loss of Nlp from mitotic centrosomes	12	24.7×	2e-12
Loss of proteins required for interphase microtubule organization from the centrosome	12	24.7×	2e-12
AURKA Activation by TPX2	12	23.7×	2e-12

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	9	52.3×	2e-11
centriole replication	6	44.0×	4e-07
regulation of mitotic spindle organization	5	42.1×	6e-06
RNA splicing, via transesterification reactions	5	31.2×	2e-05
U2-type prespliceosome assembly	5	31.2×	2e-05
non-motile cilium assembly	8	23.2×	2e-07
mRNA splicing, via spliceosome	25	22.9×	1e-24
positive regulation of G1/S transition of mitotic cell cycle	5	20.1×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	139
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3276 predictions. Top by Δscore:

Variant	Effect	Δscore
19:33087152:G:GT	donor_gain	1.0000
19:33088129:TTTAG:T	acceptor_loss	1.0000
19:33088131:TAG:T	acceptor_loss	1.0000
19:33088132:A:AG	acceptor_gain	1.0000
19:33088132:AG:A	acceptor_gain	1.0000
19:33088132:AGGT:A	acceptor_gain	1.0000
19:33088133:G:GA	acceptor_gain	1.0000
19:33088133:GG:G	acceptor_gain	1.0000
19:33088133:GGT:G	acceptor_gain	1.0000
19:33088133:GGTG:G	acceptor_gain	1.0000
19:33088133:GGTGA:G	acceptor_gain	1.0000
19:33088191:G:GT	donor_gain	1.0000
19:33088192:A:T	donor_gain	1.0000
19:33088265:GAAG:G	donor_gain	1.0000
19:33088265:GAAGG:G	donor_loss	1.0000
19:33088266:A:T	donor_gain	1.0000
19:33088267:AGGTA:A	donor_loss	1.0000
19:33088268:GGTAT:G	donor_loss	1.0000
19:33090775:TTCA:T	acceptor_loss	1.0000
19:33090776:TCAGG:T	acceptor_loss	1.0000
19:33090778:A:AG	acceptor_gain	1.0000
19:33090778:AG:A	acceptor_gain	1.0000
19:33090778:AGG:A	acceptor_loss	1.0000
19:33090778:AGGAT:A	acceptor_gain	1.0000
19:33090779:G:GA	acceptor_gain	1.0000
19:33090779:GG:G	acceptor_gain	1.0000
19:33090779:GGAT:G	acceptor_gain	1.0000
19:33090779:GGATG:G	acceptor_gain	1.0000
19:33090863:GAG:G	donor_gain	1.0000
19:33090863:GAGGT:G	donor_loss	1.0000

AlphaMissense

6090 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:33112558:T:A	W613R	1.000
19:33112558:T:C	W613R	1.000
19:33088206:T:C	F49S	0.999
19:33088217:T:C	F53L	0.999
19:33088219:T:A	F53L	0.999
19:33088219:T:G	F53L	0.999
19:33088229:T:C	F57L	0.999
19:33088231:C:A	F57L	0.999
19:33088231:C:G	F57L	0.999
19:33094209:T:A	W165R	0.999
19:33094209:T:C	W165R	0.999
19:33112560:G:C	W613C	0.999
19:33112560:G:T	W613C	0.999
19:33112595:T:A	V625D	0.999
19:33088236:C:A	A59D	0.998
19:33088239:G:A	G60E	0.998
19:33090782:T:A	W71R	0.998
19:33090782:T:C	W71R	0.998
19:33094211:G:C	W165C	0.998
19:33094211:G:T	W165C	0.998
19:33097758:T:C	F286L	0.998
19:33097760:T:A	F286L	0.998
19:33097760:T:G	F286L	0.998
19:33111843:T:C	F569L	0.998
19:33111845:C:A	F569L	0.998
19:33111845:C:G	F569L	0.998
19:33112544:G:C	R608P	0.998
19:33112559:G:C	W613S	0.998
19:33088176:T:A	V39D	0.997
19:33088208:C:G	H50D	0.997

dbSNP variants (sampled 300 via entrez): RS1000066832 (19:33125535 C>T), RS1000087756 (19:33112115 G>A), RS1000249059 (19:33118753 C>T), RS1000320774 (19:33080078 C>A,T), RS1000386355 (19:33129100 A>C,T), RS1000436175 (19:33124889 T>C), RS1000442579 (19:33086346 G>C), RS1000600790 (19:33093941 C>T), RS1000731997 (19:33130528 G>A,C,T), RS1000735339 (19:33122565 T>C), RS1000741761 (19:33130746 A>C), RS1000808683 (19:33125179 G>A,C), RS1000809096 (19:33094020 A>G), RS1000861556 (19:33097166 A>C,T), RS1001022771 (19:33107127 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST001482_11	Lumbar spine bone mineral density	7.000000e-11
GCST002333_7	Bone properties (heel)	4.000000e-12
GCST002335_8	Bone properties (heel)	2.000000e-13
GCST002411_4	Colorectal cancer	7.000000e-08
GCST004168_1	Colorectal cancer	4.000000e-08
GCST004350_18	Bone ultrasound measurement (velocity of sound)	4.000000e-07
GCST004350_7	Bone ultrasound measurement (velocity of sound)	3.000000e-07
GCST004351_10	Bone ultrasound measurement (broadband ultrasound attenuation)	8.000000e-08
GCST006433_1548	Heel bone mineral density	3.000000e-153
GCST006979_678	Heel bone mineral density	2.000000e-41
GCST007856_50	Colorectal cancer or advanced adenoma	4.000000e-23
GCST010703_314	Brain morphology (MOSTest)	4.000000e-23

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005654	velocity of sound measurement
EFO:0004514	bone quantitative ultrasound measurement
EFO:0009270	heel bone mineral density
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	increases phosphorylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression, increases abundance	1
cobaltous chloride	increases expression	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	increases expression	1
Arsenic	increases expression, increases abundance	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Caffeine	affects phosphorylation	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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