# GPATCH2 > Gene · canonical: https://sugi.bio/atlas/gene/GPATCH2/ > Atlas v1.13.0 · generated 2026-10-14T18:20:41+00:00 ## 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](https://www.ncbi.nlm.nih.gov/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](https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-100618) | yes | 397.41 | | [E-ANND-3](https://www.ebi.ac.uk/gxa/sc/experiments/E-ANND-3) | yes | 6.33 | | [E-GEOD-75367](https://www.ebi.ac.uk/gxa/sc/experiments/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](https://gnomad.broadinstitute.org/) **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](https://www.informatics.jax.org/marker/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](https://www.uniprot.org/uniprotkb/A6ZRL6/entry) | 99.9% | Diamond | | Saccharomyces cerevisiae S288C | [P53866](https://www.uniprot.org/uniprotkb/P53866/entry) | 99.9% | Diamond | | Bos taurus | [Q1RMU5](https://www.uniprot.org/uniprotkb/Q1RMU5/entry) | 99.1% | Diamond | | Xenopus laevis | [A0JMV4](https://www.uniprot.org/uniprotkb/A0JMV4/entry) | 89.1% | Diamond | | Xenopus tropicalis | [A4IGK4](https://www.uniprot.org/uniprotkb/A4IGK4/entry) | 88.9% | Diamond | | Arabidopsis thaliana | [F4JCU0](https://www.uniprot.org/uniprotkb/F4JCU0/entry) | 66.7% | Diamond | | Vanderwaltozyma polyspora DSM 70294 | [A7TQN2](https://www.uniprot.org/uniprotkb/A7TQN2/entry) | 53.6% | Diamond | | Yarrowia lipolytica CLIB122 | [Q6C233](https://www.uniprot.org/uniprotkb/Q6C233/entry) | 53.3% | Diamond | | Nakaseomyces glabratus CBS 138 | [Q6FP19](https://www.uniprot.org/uniprotkb/Q6FP19/entry) | 51.9% | Diamond | | Debaryomyces hansenii CBS767 | [Q6BYP9](https://www.uniprot.org/uniprotkb/Q6BYP9/entry) | 51.8% | Diamond | | Kluyveromyces lactis NRRL Y-1140 | [Q6CQ59](https://www.uniprot.org/uniprotkb/Q6CQ59/entry) | 51.1% | Diamond | | Eremothecium gossypii ATCC 10895 | [Q75E62](https://www.uniprot.org/uniprotkb/Q75E62/entry) | 50.0% | Diamond | | Candida albicans SC5314 | [Q59UG4](https://www.uniprot.org/uniprotkb/Q59UG4/entry) | 48.4% | Diamond | | Lodderomyces elongisporus NRRL YB-4239 | [A5DSB5](https://www.uniprot.org/uniprotkb/A5DSB5/entry) | 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](/atlas/gene/LINC00210/) | ncRNA | 100885798 | | [SPATA17](/atlas/gene/SPATA17/) | protein-coding | 128153 | | [ESRRG](/atlas/gene/ESRRG/) | protein-coding | 2104 | | [SPATA17-AS1](/atlas/gene/SPATA17-AS1/) | ncRNA | 103752555 | | [LINC01653](/atlas/gene/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 →](https://www.uniprot.org/uniprotkb/Q9NW75/entry) **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](https://amigo.geneontology.org/amigo/term/GO:0016607) | 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](#clinvar) (2 pathogenic / likely pathogenic); [10 GWAS associations](#gwas-assoc). Per-variant detail is on [Sugi Variant](https://sugi.bio/variant/gene/GPATCH2). #### 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](https://sugi.bio/variant/gene/GPATCH2). #### 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 | ## Related Atlas pages *No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.*