GPATCH2

Summary

GPATCH2 (G-patch domain containing 2, HGNC:25499) is a protein-coding gene on chromosome 1q41, encoding G patch domain-containing protein 2 (Q9NW75). Enhances the ATPase activity of DHX15 in vitro.

The gene encodes a nuclear factor that may play a role in spermatogenesis and in tumor growth during breast cancer. The encoded protein contains a G-patch domain with an RNA binding motif. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 55105 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 79 total — 2 pathogenic
• Expression (HPA): Low tissue specificity — highest in white matter, corpus callosum, periaqueductal gray
• GTEx eGene: eQTL in 14 tissues, sQTL in 5 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.23 (unconstrained)
• MANE Select transcript: NM_018040
• Notable: 79 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25499
Approved symbol	GPATCH2
Name	G-patch domain containing 2
Location	1q41
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10252, CT110, PPP1R30, Pfa1
Ensembl gene	ENSG00000092978
Ensembl biotype	protein_coding
OMIM	616836
Entrez	55105

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

MANE Select: ENST00000366935

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 2, TSL 5: 1

ENST00000366935, ENST00000366934, ENST00000470014, ENST00000485274, ENST00000489246, ENST00000885578, ENST00000885579, ENST00000911526, ENST00000911527, ENST00000911528, ENST00000985309, ENST00000985310, ENST00001107841, ENST00001107842, ENST00001144667

RefSeq mRNA: 2 — MANE Select: NM_018040 NM_001297754, NM_018040

CCDS: CCDS1518, CCDS73031

Canonical transcript exons

ENST00000366935 — 10 exons

Exon	Start	End
ENSE00000792402	217619783	217620499
ENSE00000959524	217614141	217614202
ENSE00000959525	217610889	217611071
ENSE00001205102	217449249	217449337
ENSE00001205104	217491680	217491750
ENSE00001443042	217426992	217431365
ENSE00003546089	217498356	217498395
ENSE00003642465	217610321	217610400
ENSE00003683435	217514822	217514889
ENSE00003850311	217630916	217631090

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 98.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.7147 / max 344.4867, expressed in 1750 samples.

Highest expression (Bgee): buccal mucosa cell, sperm, male germ cell, calcaneal tendon, endothelial cell.

Genetic regulation across tissues (GTEx eQTL / sQTL)

GPATCH2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 14 tissues and its splicing (sQTL) in 5 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

19 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	sqtl	2.7e-30	-1.15	1:217440722:C:T
Testis	eqtl	1.1e-05	-0.15	1:217548936:G:T
Pituitary	eqtl	8.9e-05	-0.30	1:217674911:G:A
Pituitary	sqtl	1.5e-03	-0.65	1:217410764:A:T
Nerve Tibial	sqtl	2.0e-03	-0.39	1:217538443:A:T
Artery Aorta	eqtl	2.7e-03	-0.18	1:217498429:C:G
Thyroid	eqtl	5.8e-03	-0.11	1:217498429:C:G
Brain Cerebellar Hemisphere	eqtl	6.7e-03	+0.19	1:217622246:CA:C
Brain Caudate basal ganglia	eqtl	6.8e-03	-0.43	1:217472251:G:A
Brain Cerebellum	eqtl	1.1e-02	-0.32	1:217618380:C:G
Nerve Tibial	eqtl	1.2e-02	-0.13	1:217734374:G:T
Cells Cultured fibroblasts	sqtl	1.2e-02	+0.41	1:216975165:C:T
Brain Nucleus accumbens basal ganglia	eqtl	1.9e-02	-0.23	1:217620596:T:TTAA
Pancreas	sqtl	1.9e-02	+1.84	1:217981505:C:T
Brain Cortex	eqtl	2.3e-02	-0.36	1:217770082:T:C
Colon Transverse	eqtl	2.7e-02	+0.54	1:217654368:G:GCCTGCC
Esophagus Muscularis	eqtl	2.9e-02	-0.27	1:217663168:G:A
Skin Sun Exposed Lower leg	eqtl	3.2e-02	-0.12	1:217674911:G:A
Cells Cultured fibroblasts	eqtl	4.6e-02	+0.43	1:217447832:A:C

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
17500	20.3711	1750
17499	0.3436	163

Top tissues by expression

showing 100 of 277 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	98.60	gold quality
sperm	CL:0000019	95.88	gold quality
male germ cell	CL:0000015	91.89	gold quality
calcaneal tendon	UBERON:0003701	90.37	gold quality
endothelial cell	CL:0000115	89.58	gold quality
tendon	UBERON:0000043	86.63	gold quality
adrenal tissue	UBERON:0018303	86.14	gold quality
secondary oocyte	CL:0000655	85.77	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.19	gold quality
visceral pleura	UBERON:0002401	84.22	gold quality
ventricular zone	UBERON:0003053	83.95	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.27	gold quality
left testis	UBERON:0004533	82.34	gold quality
gall bladder	UBERON:0002110	82.31	gold quality
testis	UBERON:0000473	82.05	gold quality
right testis	UBERON:0004534	82.00	gold quality
sural nerve	UBERON:0015488	80.82	gold quality
colonic epithelium	UBERON:0000397	80.62	gold quality
cortical plate	UBERON:0005343	80.50	gold quality
tendon of biceps brachii	UBERON:0008188	80.46	gold quality
rectum	UBERON:0001052	80.42	gold quality
pleura	UBERON:0000977	80.35	gold quality
ganglionic eminence	UBERON:0004023	80.26	gold quality
left lobe of thyroid gland	UBERON:0001120	79.96	gold quality
thyroid gland	UBERON:0002046	79.77	gold quality
right uterine tube	UBERON:0001302	79.70	gold quality
bronchial epithelial cell	CL:0002328	79.51	gold quality
tibia	UBERON:0000979	79.36	gold quality
tibial nerve	UBERON:0001323	79.36	gold quality
mucosa of stomach	UBERON:0001199	79.09	gold quality
adenohypophysis	UBERON:0002196	78.95	gold quality
metanephros cortex	UBERON:0010533	78.90	gold quality
parietal pleura	UBERON:0002400	78.83	gold quality
right lobe of thyroid gland	UBERON:0001119	78.60	gold quality
prostate gland	UBERON:0002367	78.59	gold quality
stromal cell of endometrium	CL:0002255	78.34	gold quality
popliteal artery	UBERON:0002250	78.33	gold quality
tibial artery	UBERON:0007610	78.32	gold quality
monocyte	CL:0000576	77.99	gold quality
endometrium	UBERON:0001295	77.99	gold quality
tonsil	UBERON:0002372	77.79	gold quality
mononuclear cell	CL:0000842	77.74	gold quality
leukocyte	CL:0000738	77.70	gold quality
left coronary artery	UBERON:0001626	77.66	gold quality
body of pancreas	UBERON:0001150	77.58	gold quality
aorta	UBERON:0000947	77.56	gold quality
cerebellar vermis	UBERON:0004720	77.51	gold quality
corpus callosum	UBERON:0002336	77.38	gold quality
epithelium of nasopharynx	UBERON:0001951	77.35	gold quality
islet of Langerhans	UBERON:0000006	77.14	gold quality
body of uterus	UBERON:0009853	77.12	gold quality
vagina	UBERON:0000996	77.09	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.00	gold quality
pituitary gland	UBERON:0000007	76.98	gold quality
lower esophagus	UBERON:0013473	76.98	gold quality
descending thoracic aorta	UBERON:0002345	76.90	gold quality
pancreas	UBERON:0001264	76.87	gold quality
right coronary artery	UBERON:0001625	76.86	gold quality
lymph node	UBERON:0000029	76.77	gold quality
thoracic aorta	UBERON:0001515	76.76	gold quality
ascending aorta	UBERON:0001496	76.75	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.74	gold quality
coronary artery	UBERON:0001621	76.66	gold quality
germinal epithelium of ovary	UBERON:0001304	76.63	gold quality
muscle layer of sigmoid colon	UBERON:0035805	76.63	gold quality
minor salivary gland	UBERON:0001830	76.57	gold quality
esophagus	UBERON:0001043	76.51	gold quality
subcutaneous adipose tissue	UBERON:0002190	76.51	gold quality
hair follicle	UBERON:0002073	76.40	gold quality
skin of abdomen	UBERON:0001416	76.30	gold quality
omental fat pad	UBERON:0010414	76.20	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	76.19	gold quality
peritoneum	UBERON:0002358	76.15	gold quality
endocervix	UBERON:0000458	76.08	gold quality
esophagus mucosa	UBERON:0002469	75.92	gold quality
adipose tissue of abdominal region	UBERON:0007808	75.92	gold quality
right adrenal gland cortex	UBERON:0035827	75.92	gold quality
granulocyte	CL:0000094	75.86	gold quality
adrenal gland	UBERON:0002369	75.86	gold quality
Brodmann (1909) area 23	UBERON:0013554	75.76	gold quality
left adrenal gland cortex	UBERON:0035825	75.76	gold quality
skin of leg	UBERON:0001511	75.70	gold quality
ectocervix	UBERON:0012249	75.68	gold quality
upper lobe of left lung	UBERON:0008952	75.65	gold quality
smooth muscle tissue	UBERON:0001135	75.64	gold quality
left adrenal gland	UBERON:0001234	75.56	gold quality
right atrium auricular region	UBERON:0006631	75.56	gold quality
ovary	UBERON:0000992	75.55	gold quality
mucosa of paranasal sinus	UBERON:0005030	75.44	silver quality
right adrenal gland	UBERON:0001233	75.32	gold quality
left uterine tube	UBERON:0001303	75.23	gold quality
stomach	UBERON:0000945	75.22	gold quality
right ovary	UBERON:0002118	75.13	gold quality
female reproductive system	UBERON:0000474	75.05	gold quality
prefrontal cortex	UBERON:0000451	75.02	gold quality
mouth mucosa	UBERON:0003729	74.98	gold quality
adipose tissue	UBERON:0001013	74.92	gold quality
pigmented layer of retina	UBERON:0001782	74.90	gold quality
connective tissue	UBERON:0002384	74.87	gold quality
small intestine Peyer’s patch	UBERON:0003454	74.86	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	397.41
E-ANND-3	yes	6.33
E-GEOD-75367	no	183.82

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Corpus callosum	tissue	20.7
Periaqueductal gray	tissue	18.6
Choroid plexus	tissue	18.0
Hypothalamus	tissue	17.0
Hippocampal formation	tissue	17.0
Medulla oblongata	tissue	16.6
Septum	tissue	16.6
Midbrain	tissue	16.0
Prefrontal cortex	tissue	15.8
Cerebral cortex	tissue	15.8	high
Thalamus	tissue	15.7
Putamen	tissue	15.5
Insular cortex	tissue	15.5
Spinal cord	tissue	15.4
Retrosplenial and cingulate cortex	tissue	15.4
Temporal cortex	tissue	15.4
Amygdala	tissue	15.3
Entorhinal cortex	tissue	15.3
Pons	tissue	15.1
Basal ganglia	tissue	15.1	high
Substantia nigra	tissue	15.1
Motor cortex	tissue	15.0
Occipital cortex	tissue	14.9
Somatosensory cortex	tissue	14.8
Ventral forebrain	tissue	14.7
Cerebellum	tissue	14.6	high
Retrosplenial cortex	tissue	14.6
Superior colliculi	tissue	14.2
Postcentral gyrus	tissue	13.4
Olfactory bulb	tissue	13.4
Nucleus accumbens	tissue	12.2
Hippocampus	tissue	11.8	high
Locus coeruleus	tissue	11.5
Breast	tissue	6.7	high
Parathyroid gland	tissue	6.5	high
Prostate	tissue	6.5	high
Skeletal muscle	tissue	6.2	medium
Thyroid gland	tissue	6.2	high
Endometrium 1	tissue	6.1	high
Placenta	tissue	5.9	high
Caudate putamen	tissue	5.9
Testis	tissue	5.8	high
Gallbladder	tissue	5.8	high
Thymus	tissue	5.8
Urinary bladder	tissue	5.7	high
Frontal cortex	tissue	5.7
Cervix	tissue	5.5	high
Epididymis	tissue	5.5	high
Retina	tissue	5.3
Esophagus	tissue	5.2	high
Tonsil	tissue	5.2	medium
Seminal vesicle	tissue	5.0	medium
Kidney	tissue	4.9	high
Lymph node	tissue	4.8	medium
Smooth muscle	tissue	4.7	medium
Fallopian tube	tissue	4.7	high
Stomach 1	tissue	4.6	high
Ovary	tissue	4.6	low
Small intestine	tissue	4.6	high
Duodenum	tissue	4.6	high

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — White matter (20.7), Dorsal hippocampus (17.0), Ventral hippocampus (16.0), Subiculum (15.5), Arcuate nucleus (15.4).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting GPATCH2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 250 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-223-3P	99.99	70.14	1140
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-607	99.97	73.62	5593
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-570-3P	99.96	72.41	4910

Functional genomics

gnomAD constraint: pLI 5.17e-08, LOEUF 1.23, missense Z 0.53 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000366935 — one region, missense o/e 0.96.

Literature-anchored findings (GeneRIF, showing 2)

• Involvement of GPATCH2 overexpression in breast carcinogensis is reported. (PMID:19432882)
• GPATC2 may be involved in inhibiting G1-S phase transition in 293T cells. (PMID:25376275)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	gpatch2	ENSDARG00000101260
mus_musculus	Gpatch2	ENSMUSG00000039210
rattus_norvegicus	Gpatch2	ENSRNOG00000002512

Paralogs (1): GPATCH2L (ENSG00000089916)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1915019) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 1 distinct phenotype terms.

Mouse phenotype (MP)	Records
decreased B cell number	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Saccharomyces cerevisiae YJM789	A6ZRL6	99.9%	Diamond
Saccharomyces cerevisiae S288C	P53866	99.9%	Diamond
Bos taurus	Q1RMU5	99.1%	Diamond
Xenopus laevis	A0JMV4	89.1%	Diamond
Xenopus tropicalis	A4IGK4	88.9%	Diamond
Arabidopsis thaliana	F4JCU0	66.7%	Diamond
Vanderwaltozyma polyspora DSM 70294	A7TQN2	53.6%	Diamond
Yarrowia lipolytica CLIB122	Q6C233	53.3%	Diamond
Nakaseomyces glabratus CBS 138	Q6FP19	51.9%	Diamond
Debaryomyces hansenii CBS767	Q6BYP9	51.8%	Diamond
Kluyveromyces lactis NRRL Y-1140	Q6CQ59	51.1%	Diamond
Eremothecium gossypii ATCC 10895	Q75E62	50.0%	Diamond
Candida albicans SC5314	Q59UG4	48.4%	Diamond
Lodderomyces elongisporus NRRL YB-4239	A5DSB5	47.8%	Diamond

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).

Symbol	Type	Entrez
LINC00210	ncRNA	100885798
SPATA17	protein-coding	128153
ESRRG	protein-coding	2104
SPATA17-AS1	ncRNA	103752555
LINC01653	ncRNA	101929631

Protein

Protein identifiers

G patch domain-containing protein 2 — Q9NW75 (reviewed: Q9NW75)

All UniProt accessions (1): Q9NW75

UniProt curated annotations — full annotation on UniProt →

Function. Enhances the ATPase activity of DHX15 in vitro.

Subunit / interactions. Interacts with DHX15.

Subcellular location. Nucleus speckle. Nucleus. Nucleolus.

Tissue specificity. Testis.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NW75-1	1	yes
Q9NW75-2	2

RefSeq proteins (2): NP_001284683, NP_060510* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000467	G_patch_dom	Domain
IPR051189	SQS1_GPATCH2	Family

Pfam: PF01585

UniProt features (17 total): modified residue 4, compositionally biased region 4, region of interest 3, splice variant 2, sequence conflict 2, chain 1, domain 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NW75-F1	55.60	0.06

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nuclear speckles

Antibody reliability (HPA): IH uncertain · IF supported

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 (4)

Type	Positions
Phosphoserine	117, 146, 195, 115

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 189 (showing top): ELVIDGE_HYPOXIA_DN, GOZGIT_ESR1_TARGETS_DN, WANG_LMO4_TARGETS_DN, MODULE_206, HP1SITEFACTOR_Q6, DODD_NASOPHARYNGEAL_CARCINOMA_UP, AACTTT_UNKNOWN, AML1_01, BERNARD_PPAPDC1B_TARGETS_UP, WALLACE_PROSTATE_CANCER_RACE_DN, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, LIU_SOX4_TARGETS_DN, GOCC_RIBONUCLEOPROTEIN_GRANULE, CHEN_HOXA5_TARGETS_9HR_UP

GO Molecular Function (2): nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleolus (GO:0005730), nuclear speck (GO:0016607)

GO top-level categories

5 GO namespaces:

Category	Terms
binding	2
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular membraneless organelle	1
nuclear ribonucleoprotein granule	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 5 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
nuclear speck	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 546 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPATCH2	DHX15	O43143	731
GPATCH2	SPATA17	Q96L03	610
GPATCH2	TFIP11	Q9UBB9	606
GPATCH2	LTV1	Q96GA3	600
GPATCH2	RRP15	Q9Y3B9	575
GPATCH2	NOB1	Q9ULX3	539
GPATCH2	KCTD3	Q9Y597	503
GPATCH2	OR13C3	Q8NGS6	448
GPATCH2	DHX8	Q14562	436
GPATCH2	RIOK2	Q9BVS4	435
GPATCH2	FYTTD1	Q96QD9	432
GPATCH2	GPX4	P36969	430
GPATCH2	TTC33	Q6PID6	399
GPATCH2	SSC4D	Q8WTU2	395
GPATCH2	MRPL42	Q9Y6G3	393

IntAct

Human interaction partners of GPATCH2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

Partner	Interaction type	MIscore	Records
PPP1CA	direct interaction	0.440	1
SMC3	physical association	0.400	1

BioGRID (51 interactions; top human partners by supporting records): CSNK2A2 (Affinity Capture-MS; 7 records), CSNK2A1 (Two-hybrid; 5 records), PICK1 (Affinity Capture-MS; 3 records), CSNK2B (Affinity Capture-MS; 2 records), BCR (Affinity Capture-MS), BRPF3 (Affinity Capture-MS), CDK11A (Affinity Capture-MS), CDK11B (Affinity Capture-MS), COMMD4 (Affinity Capture-MS), COPA (Affinity Capture-MS), COPE (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), DPY30 (Two-hybrid), EGFR (Affinity Capture-MS), EGLN3 (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for GPATCH2: 79 ClinVar records (2 pathogenic / likely pathogenic); 10 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	63
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (2)

Showing all 2 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
60082	GRCh38/hg38 1q41(chr1:217452423-218818361)x1	Pathogenic	criteria provided, single submitter	1
443565	GRCh37/hg19 1q41(chr1:217699328-218689648)x1	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore GPATCH2’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; 28 predictions of 1,582):

Position(s)	Effect	Δscore	Sites
1:217491678–217491679	donor_loss	1.0000	4
1:217491760	acceptor_gain	1.0000
1:217491776	acceptor_gain	1.0000
1:217514820–217514821	donor_loss	1.0000	5
1:217514890–217514891	acceptor_loss	1.0000	3
1:217514902	acceptor_gain	1.0000
1:217610401–217610402	acceptor_loss	1.0000	6
1:217610939	donor_gain	1.0000
1:217614139–217614140	donor_loss	1.0000	5
1:217614149	donor_gain	1.0000

AlphaMissense

879 missense substitutions predicted likely pathogenic (of 3,506 scored), across 207 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:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M25	9	0.910	0.991
M167	9	0.908	0.990
D31	8	0.993	0.998
D280	8	0.989	0.997
D281	8	0.988	0.996
D274	8	0.986	0.997
D285	8	0.971	0.991
D116	8	0.945	0.979
D118	8	0.923	0.978
S284	8	0.914	0.999
D267	8	0.871	0.971
H30	8	0.780	0.982
W480	7	0.993	0.999
E282	7	0.987	0.995
E275	7	0.968	0.990
W286	7	0.967	0.996
R160	7	0.965	0.999
F271	7	0.963	0.990
E37	7	0.961	0.990
W305	7	0.940	0.988

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

1 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Papillary Cell Carcinoma (TCGA)	unfavorable	0.000157

Disease associations

OMIM: gene MIM:616836 | disease phenotypes:

GWAS associations

10 associations:

Study	Trait	p-value
GCST003992_27	Photic sneeze reflex	1e-72
GCST003818_10	Resting heart rate	1e-11
GCST004280_37	Diastolic blood pressure	2e-10
GCST007094_56	Diastolic blood pressure	2e-8
GCST010396_226	Gut microbiota (bacterial taxa, hurdle binary method)	3e-6
GCST001066_7	Dialysis-related mortality	4e-6
GCST006086_12	Familial lung cancer	4e-6
GCST011741_42	LDL cholesterol levels in HIV infection	4e-6
GCST001523_29	Visceral adipose tissue adjusted for BMI	6e-6
GCST004524_9	Energy expenditure (24h)	8e-6

EFO canonical traits (from GWAS)

6 canonical traits:

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007887	autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0006336	diastolic blood pressure
EFO:0006953	family history of lung cancer
EFO:0007874	gut microbiome measurement
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases expression	4
trichostatin A	affects cotreatment, decreases expression, increases expression	3
entinostat	increases expression, affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, affects expression	2
FR900359	increases phosphorylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
sodium arsenite	increases expression	1
benzo(e)pyrene	increases methylation	1
resorcinol	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, affects expression	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, decreases expression, affects expression	1
PCI 5002	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Vorinostat	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Caffeine	decreases phosphorylation	1
Demecolcine	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SQ32	HAP1 GPATCH2 (-) 1	Cancer cell line	Male
CVCL_SQ33	HAP1 GPATCH2 (-) 2	Cancer cell line	Male
CVCL_SQ34	HAP1 GPATCH2 (-) 3	Cancer cell line	Male
CVCL_SQ35	HAP1 GPATCH2 (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

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

showing 60 of 68 trials:

NCT	Phase	Status	Title
NCT02513940	Phase 4	COMPLETED	Influence of Testosterone Administration on Drug-Induced QT Interval Prolongation and Torsades de Pointes
NCT03834883	Phase 4	COMPLETED	Reducing the Risk of Drug-Induced QT Interval Lengthening in Women
NCT04169100	Phase 4	UNKNOWN	Novel Form of Acquired Long QT Syndrome
NCT04675788	Phase 4	COMPLETED	Novel Approaches for Minimizing Drug-Induced QT Interval Lengthening
NCT01648205	Phase 2	COMPLETED	Long-term Efficacy Study of Sodium Channel Blocker in LQT3 Patients
NCT02412709	Phase 2	UNKNOWN	Long QT Syndrome Screening in Newborns
NCT04581408	Phase 2	COMPLETED	Mutation-specific Therapy for the Long QT Syndrome
NCT00316459	Phase 1	COMPLETED	Study Evaluating the Effects of Multiple Oral Doses of ERB-041 on Cardiac Repolarization in Healthy Subjects
NCT01849003	Phase 1	COMPLETED	Study of the Effect of GS-6615 in Subjects With LQT-3
NCT02365532	Phase 1	COMPLETED	Effect of Oral GS-6615 on Dofetilide-Induced QT Prolongation, Safety, and Tolerability in Healthy Adults
NCT02412098	Phase 1	COMPLETED	Pharmacokinetics of Eleclazine in Adults With Normal and Impaired Hepatic Function
NCT02441829	Phase 1	COMPLETED	Pharmacokinetics of Eleclazine in Adults With Normal and Impaired Renal Function
NCT05759962	Phase 1	COMPLETED	Phase 1 Study of LQT-1213 in Healthy Adults
NCT05906732	Phase 1/2	TERMINATED	Study of LQT-1213 on QTc-induced Prolongation in Healthy Adult Subjects (Part1) and on Congenital Long QT in Patients Diagnosed With Type 2 or 3 Long QT Syndrome (Part 2).
NCT00005176	Not specified	COMPLETED	Long QT Syndrome-Population Genetics and Cardiac Studies
NCT00005250	Not specified	COMPLETED	Linkage Study of Long QT Syndrome In An Amish Kindred
NCT00005367	Not specified	COMPLETED	Epidemiology of Long QTand Asian Sudden Death in Sleep
NCT00221832	Not specified	UNKNOWN	Molecular Genetic Screening and Identification of Congenital Arrhythmogenic Diseases
NCT00292032	Not specified	COMPLETED	Registry of Unexplained Cardiac Arrest
NCT00335036	Not specified	TERMINATED	Pediatric Lead Extractability and Survival Evaluation (PLEASE)
NCT00399412	Not specified	COMPLETED	ECG Signal Collection From Long QT Syndrome, Wide QRS Complexes, Heart Failure, and Cardiac Resynchronization Patients
NCT00488254	Not specified	COMPLETED	The Long QT Syndrome in Pregnancy
NCT00588965	Not specified	COMPLETED	Effect of Beta-blocker Therapy on QTc Response in Exercise and Recovery in Normal Subjects
NCT01705925	Not specified	COMPLETED	Multicenter Evaluation of Children and Young Adults With Genotype Positive Long QT Syndrome
NCT01903564	Not specified	COMPLETED	Fetal and Neonatal Magnetophysiology
NCT02082431	Not specified	COMPLETED	Determine the Incidence of Long QT Amongst a Large Cohort of Subjects Diagnosed With Unilateral or Bilateral Sensorineural Hearing Loss.
NCT02413450	Not specified	ENROLLING_BY_INVITATION	Derivation of Human Induced Pluripotent Stem (iPS) Cells to Heritable Cardiac Arrhythmias
NCT02425189	Not specified	COMPLETED	The Canadian National Long QT Syndrome Registry
NCT02439645	Not specified	TERMINATED	A Registry to Determine the Clinical and Genetic Risk Factors for Torsade De Pointes
NCT02439658	Not specified	UNKNOWN	Genetics of QT Prolongation With Antiarrhythmics
NCT02549664	Not specified	COMPLETED	Exercise in Genetic Cardiovascular Conditions
NCT02581241	Not specified	COMPLETED	Abnormal QT-Response to the Sudden Tachycardia Provoked by Standing in Individuals With Drug-induced Long QT Syndrome
NCT02680080	Not specified	COMPLETED	Effect of Grapefruit on QT Interval in Healthy Volunteers and Patients With Congenital Long QT Syndrome
NCT02775513	Not specified	UNKNOWN	Metabolism of Patients With Genetically Caused Cardiac Arrhythmia
NCT02814981	Not specified	UNKNOWN	Hydroxyzine and Risk of Prolongation of QT Interval
NCT02876380	Not specified	COMPLETED	Prospective Identification of Long QT Syndrome in Fetal Life
NCT02931695	Not specified	COMPLETED	Ventricular Repolarization During the Pregnancy-to-Postpartum Transition (QuTe)
NCT03182777	Not specified	COMPLETED	Safety of Local Dental Anesthesia in Patients With Cardiac Channelopathies
NCT03544918	Not specified	COMPLETED	Prevalence of Congenital Long QT Syndrome and Acquired QT Prolongation in a Hospital Cohort
NCT03642405	Not specified	UNKNOWN	Drug-induced Repolarization ECG Changes
NCT03678311	Not specified	COMPLETED	Long QT Syndrome and Sleep Apnea
NCT03775954	Not specified	RECRUITING	Fetal Electrophysiologic Abnormalities in High-Risk Pregnancies Associated With Fetal Demise
NCT03783975	Not specified	TERMINATED	KCNQ1 Cascade Screening
NCT03868657	Not specified	COMPLETED	The Physiological Effects of Human Ether-a-go-go-Related Gene (hERG)Blockade on Metabolism
NCT04074122	Not specified	UNKNOWN	Electromechanical Profiling of the Long-QT Syndrome (LQTS)
NCT04124237	Not specified	COMPLETED	Long Term Monitoring for Risk of Sudden Death
NCT04189822	Not specified	ENROLLING_BY_INVITATION	Hearts in Rhythm Organization (HiRO)National Registry and Bio Bank
NCT04328376	Not specified	COMPLETED	Measurement of the Electromechanical Window to Improve the Diagnosis of Congenital Long QT Syndrome
NCT04336644	Not specified	RECRUITING	Continuous Versus Intermittent cARdiac Electrical moNitorinG
NCT04441892	Not specified	TERMINATED	Low Cost QTc Meter for Long QT Syndrome Screening in Primary Care
NCT04650009	Not specified	COMPLETED	Physical Activity in Children With Inherited Cardiac Diseases
NCT04699097	Not specified	COMPLETED	The Effect of Azithromycin Use on Conduction System of Heart in COVID-19 Positive Children
NCT04706104	Not specified	COMPLETED	QT Measurement Techniques and Anesthesia Management
NCT04712136	Not specified	COMPLETED	Healthy-related Quality of Life and Physical Activity of Children With Cardiac Malformations
NCT04715256	Not specified	UNKNOWN	Evaluation of the Effects of KCNQ1 Mutation on Insulin Tolerance and Obsessive Compulsive Features in Long QT Romano-Ward Syndrome Patients.
NCT04728100	Not specified	COMPLETED	LQT and Smartphone/Smartwatch
NCT05274646	Not specified	COMPLETED	Impact on Risk Stratification of Overlap Syndrome Phenotype in Patients With E1784K Mutation in SCN5A
NCT05348564	Not specified	RECRUITING	Comparing Direct vs Indirect Methods for Cascade Screening
NCT05521451	Not specified	RECRUITING	Clinical Cohort Study - TRUST
NCT05903313	Not specified	UNKNOWN	A Study to Evaluate Accuracy and Validity of the Chang Gung ECG Abnormality Detection Software