# GPATCH4

> Gene · canonical: https://sugi.bio/atlas/gene/GPATCH4/
> Atlas v1.12.2 · generated 2026-10-13T13:32:47+00:00

## Summary

**GPATCH4** (G-patch domain containing 4 (gene/pseudogene), HGNC:25982) is a protein-coding gene on chromosome 1q22-q23.1, encoding **G patch domain-containing protein 4** (Q5T3I0).

Enables RNA binding activity. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be active in nucleolus.

*Source: [NCBI Gene 54865](https://www.ncbi.nlm.nih.gov/gene/54865) — automated summary from GO annotations (Alliance of Genome Resources).*

**At a glance**

- **Clinical variants (ClinVar):** 68 total — 1 pathogenic
- **Regional missense constraint (gnomAD):** 1 of 3 regions constrained (≈5% of expected missense variation)
- **GTEx eGene:** eQTL in 35 tissues, sQTL in 18 (q < 0.05)
- **Constraint (gnomAD):** pLI 0.00 (LoF-tolerant), LOEUF 1.67 (unconstrained)
- **Notable:** 68 clinical variants but no curated precision-oncology (CIViC) evidence yet




## Identifiers

### Gene identifiers

| Field | Value |
| --- | --- |
| HGNC ID | HGNC:25982 |
| Approved symbol | GPATCH4 |
| Name | G-patch domain containing 4 (gene/pseudogene) |
| Location | 1q22-q23.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ20249, DKFZP434F1735 |
| Ensembl gene | ENSG00000160818 |
| Ensembl biotype | protein_coding |
| Entrez | 54865 |

## Gene structure

### Transcript identifiers

**Ensembl transcripts: 15** — 7 retained_intron, 3 protein_coding_LoF, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

**Transcript support level (Ensembl TSL; 1 = fully mRNA-supported):** TSL 1: 1, TSL 2: 5, TSL 3: 5, TSL 4: 1, TSL 5: 3

`ENST00000368232`, `ENST00000415314`, `ENST00000438976`, `ENST00000463513`, `ENST00000473910`, `ENST00000474904`, `ENST00000494414`, `ENST00000497287`, `ENST00000498641`, `ENST00000498756`, `ENST00000506832`, `ENST00000525375`, `ENST00000527691`, `ENST00000531129`, `ENST00000531900`

**RefSeq mRNA: 2**
`NM_015590`, `NM_182679`

#### Canonical transcript exons

`ENST00000368232` — 8 exons

| Exon | Start | End |
| --- | --- | --- |
| ENSE00001861395 | 156601409 | 156601479 |
| ENSE00001956829 | 156594301 | 156595849 |
| ENSE00003545923 | 156596081 | 156596131 |
| ENSE00003574142 | 156596387 | 156596478 |
| ENSE00003594841 | 156598968 | 156599104 |
| ENSE00003609278 | 156598227 | 156598319 |
| ENSE00003610106 | 156598035 | 156598121 |
| ENSE00003665803 | 156598421 | 156598494 |

### Expression profiles

**Bgee:** expression breadth **ubiquitous**, 250 present calls, max score 95.09.

**FANTOM5 (CAGE):** breadth **ubiquitous**, TPM avg 18.9495 / max 602.8518, expressed in 1785 samples.

**Highest expression (Bgee):** gastrocnemius, muscle of leg, sural nerve, tibialis anterior, C1 segment of cervical spinal cord.

#### Genetic regulation across tissues (GTEx eQTL / sQTL)

GPATCH4 is an **eGene** in GTEx v10 — its expression is genetically regulated (eQTL) in **35** tissues and its splicing (sQTL) in **18** (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant's alternative allele.

showing 20 of 53 significant tissue × QTL associations:

| Tissue | QTL | q-value | Slope | Lead variant |
| --- | --- | --- | --- | --- |
| Muscle Skeletal | eqtl | 3.5e-25 | -0.39 | 1:156596604:G:C |
| Brain Frontal Cortex BA9 | eqtl | 2.3e-17 | -0.68 | 1:156593649:G:A |
| Brain Cortex | eqtl | 1.6e-11 | -0.60 | 1:156583439:GC:G |
| Brain Hypothalamus | eqtl | 2.0e-11 | -0.59 | 1:156516817:C:T |
| Esophagus Muscularis | eqtl | 3.9e-10 | -0.31 | 1:156594785:A:G |
| Nerve Tibial | sqtl | 5.6e-10 | +1.05 | 1:156593649:G:A |
| Brain Putamen basal ganglia | eqtl | 6.3e-10 | -0.80 | 1:156583439:GC:G |
| Brain Nucleus accumbens basal ganglia | eqtl | 6.6e-10 | -0.56 | 1:156593649:G:A |
| Cells Cultured fibroblasts | eqtl | 3.9e-09 | +0.16 | 1:156590769:T:C |
| Muscle Skeletal | sqtl | 6.9e-09 | +0.79 | 1:156525847:C:T |
| Brain Anterior cingulate cortex BA24 | eqtl | 7.2e-09 | -0.67 | 1:156626617:C:T |
| Esophagus Mucosa | eqtl | 1.5e-07 | -0.27 | 1:156594785:A:G |
| Brain Cerebellar Hemisphere | eqtl | 2.8e-07 | -0.53 | 1:156593649:G:A |
| Cells EBV-transformed lymphocytes | sqtl | 7.8e-07 | +1.10 | 1:156593649:G:A |
| Skin Sun Exposed Lower leg | eqtl | 2.0e-06 | +0.15 | 1:156590832:C:T |
| Brain Caudate basal ganglia | eqtl | 2.7e-06 | +0.43 | 1:156625974:C:CAGG |
| Testis | eqtl | 4.2e-06 | -0.62 | 1:156594785:A:G |
| Brain Frontal Cortex BA9 | sqtl | 4.4e-06 | +1.02 | 1:156583439:GC:G |
| Artery Tibial | eqtl | 8.0e-06 | -0.29 | 1:156594785:A:G |
| Brain Cerebellum | eqtl | 2.1e-05 | -0.49 | 1:156593649:G:A |

#### FANTOM5 promoters

3 alternative TSS:

| Promoter ID | TPM avg | Samples expressed |
| --- | --- | --- |
| 15156 | 15.5124 | 1774 |
| 15154 | 3.0961 | 1148 |
| 15155 | 0.3410 | 161 |

#### Top tissues by expression

showing 100 of 255 tissues by Bgee expression score (0-100, higher = more expressed):

| Tissue | Anatomy ID | Expression score | Quality |
| --- | --- | --- | --- |
| gastrocnemius | UBERON:0001388 | 95.09 | gold quality |
| muscle of leg | UBERON:0001383 | 94.21 | gold quality |
| sural nerve | UBERON:0015488 | 94.19 | gold quality |
| tibialis anterior | UBERON:0001385 | 93.56 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 93.36 | gold quality |
| islet of Langerhans | UBERON:0000006 | 93.07 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 92.99 | gold quality |
| prefrontal cortex | UBERON:0000451 | 92.38 | gold quality |
| right frontal lobe | UBERON:0002810 | 92.38 | gold quality |
| putamen | UBERON:0001874 | 91.82 | gold quality |
| amygdala | UBERON:0001876 | 91.80 | gold quality |
| spinal cord | UBERON:0002240 | 91.60 | gold quality |
| tendon of biceps brachii | UBERON:0008188 | 91.57 | gold quality |
| nucleus accumbens | UBERON:0001882 | 91.52 | gold quality |
| hypothalamus | UBERON:0001898 | 91.47 | gold quality |
| deltoid | UBERON:0001476 | 91.35 | gold quality |
| hindlimb stylopod muscle | UBERON:0004252 | 91.22 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 91.09 | gold quality |
| substantia nigra | UBERON:0002038 | 91.07 | gold quality |
| secondary oocyte | CL:0000655 | 90.94 | gold quality |
| left uterine tube | UBERON:0001303 | 90.73 | gold quality |
| neocortex | UBERON:0001950 | 90.60 | gold quality |
| frontal cortex | UBERON:0001870 | 90.48 | gold quality |
| caudate nucleus | UBERON:0001873 | 90.39 | gold quality |
| heart left ventricle | UBERON:0002084 | 90.30 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 90.20 | gold quality |
| vermiform appendix | UBERON:0001154 | 90.17 | gold quality |
| cardiac ventricle | UBERON:0002082 | 90.01 | gold quality |
| oocyte | CL:0000023 | 89.89 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 89.86 | gold quality |
| lower esophagus | UBERON:0013473 | 89.84 | gold quality |
| midbrain | UBERON:0001891 | 89.76 | gold quality |
| pancreas | UBERON:0001264 | 89.52 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 89.33 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 89.11 | gold quality |
| cerebral cortex | UBERON:0000956 | 89.08 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 88.98 | gold quality |
| cerebellar cortex | UBERON:0002129 | 88.92 | gold quality |
| esophagus | UBERON:0001043 | 88.86 | gold quality |
| skeletal muscle tissue | UBERON:0001134 | 88.85 | gold quality |
| forebrain | UBERON:0001890 | 88.81 | gold quality |
| apex of heart | UBERON:0002098 | 88.75 | gold quality |
| cortical plate | UBERON:0005343 | 88.74 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 88.65 | gold quality |
| brain | UBERON:0000955 | 88.55 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 88.54 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 88.53 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 88.50 | gold quality |
| left adrenal gland | UBERON:0001234 | 88.40 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 88.39 | gold quality |
| body of pancreas | UBERON:0001150 | 88.31 | gold quality |
| heart | UBERON:0000948 | 88.25 | gold quality |
| body of stomach | UBERON:0001161 | 88.23 | gold quality |
| caecum | UBERON:0001153 | 88.22 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 88.22 | gold quality |
| esophagus mucosa | UBERON:0002469 | 88.18 | gold quality |
| peritoneum | UBERON:0002358 | 88.09 | gold quality |
| omental fat pad | UBERON:0010414 | 88.08 | gold quality |
| body of uterus | UBERON:0009853 | 88.04 | gold quality |
| right atrium auricular region | UBERON:0006631 | 87.97 | gold quality |
| adrenal cortex | UBERON:0001235 | 87.95 | gold quality |
| Ammon's horn | UBERON:0001954 | 87.94 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 87.90 | gold quality |
| kidney epithelium | UBERON:0004819 | 87.87 | silver quality |
| right adrenal gland | UBERON:0001233 | 87.86 | gold quality |
| muscle tissue | UBERON:0002385 | 87.86 | gold quality |
| cerebellum | UBERON:0002037 | 87.83 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 87.82 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 87.74 | gold quality |
| tibial artery | UBERON:0007610 | 87.70 | gold quality |
| popliteal artery | UBERON:0002250 | 87.69 | gold quality |
| colonic epithelium | UBERON:0000397 | 87.59 | gold quality |
| tibial nerve | UBERON:0001323 | 87.51 | gold quality |
| pericardium | UBERON:0002407 | 87.50 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 87.49 | gold quality |
| lymph node | UBERON:0000029 | 87.47 | gold quality |
| left coronary artery | UBERON:0001626 | 87.47 | gold quality |
| adrenal gland | UBERON:0002369 | 87.46 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 87.41 | silver quality |
| adipose tissue of abdominal region | UBERON:0007808 | 87.39 | gold quality |
| prostate gland | UBERON:0002367 | 87.28 | gold quality |
| coronary artery | UBERON:0001621 | 87.27 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 87.23 | gold quality |
| cardiac atrium | UBERON:0002081 | 87.22 | gold quality |
| temporal lobe | UBERON:0001871 | 87.10 | gold quality |
| rectum | UBERON:0001052 | 87.02 | gold quality |
| metanephros cortex | UBERON:0010533 | 87.02 | gold quality |
| stomach | UBERON:0000945 | 86.94 | gold quality |
| aorta | UBERON:0000947 | 86.78 | gold quality |
| transverse colon | UBERON:0001157 | 86.78 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 86.61 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 86.61 | gold quality |
| ectocervix | UBERON:0012249 | 86.55 | gold quality |
| quadriceps femoris | UBERON:0001377 | 86.50 | gold quality |
| right ovary | UBERON:0002118 | 86.47 | gold quality |
| left ovary | UBERON:0002119 | 86.42 | gold quality |
| colon | UBERON:0001155 | 86.39 | gold quality |
| anatomical system | UBERON:0000467 | 86.33 | gold quality |
| minor salivary gland | UBERON:0001830 | 86.32 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 86.30 | gold quality |

#### Single-cell (SCXA)

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

| Experiment | Marker? | Max mean expression |
| --- | --- | --- |
| [E-ANND-3](https://www.ebi.ac.uk/gxa/sc/experiments/E-ANND-3) | yes | 5.92 |
| [E-MTAB-7606](https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-7606) | no | 616.96 |

#### HPA expression

RNA tissue specificity: **Tissue enhanced**

showing 60 of 80 HPA tissues / cells by nTPM:

| Tissue / cell | Axis | nTPM | Protein (IHC) |
| --- | --- | --- | --- |
| Skeletal muscle | tissue | 30.3 | medium |
| Tongue | tissue | 26.1 |  |
| Postcentral gyrus | tissue | 24.8 |  |
| Caudate putamen | tissue | 20.2 |  |
| Urinary bladder | tissue | 17.8 | medium |
| Frontal cortex | tissue | 17.5 |  |
| Tonsil | tissue | 17.5 | low |
| Appendix | tissue | 15.5 | medium |
| Adipose tissue | tissue | 15.2 | not detected |
| Lymph node | tissue | 14.9 | not detected |
| Parathyroid gland | tissue | 14.3 | high |
| Smooth muscle | tissue | 12.9 | medium |
| Vagina | tissue | 12.8 | low |
| Liver | tissue | 12.8 | medium |
| Hippocampus | tissue | 12.6 | medium |
| Breast | tissue | 12.4 | low |
| Locus coeruleus | tissue | 12.3 |  |
| Nucleus accumbens | tissue | 12.2 |  |
| Rectum | tissue | 12.1 | high |
| Pancreas | tissue | 11.4 | medium |
| Adrenal gland | tissue | 11.1 | medium |
| Colon | tissue | 10.8 | medium |
| Prefrontal cortex | tissue | 10.6 |  |
| Cerebral cortex | tissue | 10.6 | medium |
| Thymus | tissue | 10.4 |  |
| Motor cortex | tissue | 10.3 |  |
| Putamen | tissue | 10.0 |  |
| Prostate | tissue | 10.0 | low |
| Esophagus | tissue | 9.9 | medium |
| Stomach 1 | tissue | 9.8 | medium |
| Seminal vesicle | tissue | 9.7 | high |
| Skin 1 | tissue | 9.6 | low |
| Salivary gland | tissue | 9.6 | not detected |
| Spleen | tissue | 9.6 | not detected |
| Kidney | tissue | 9.6 | medium |
| Bone marrow | tissue | 9.4 | low |
| Occipital cortex | tissue | 9.1 |  |
| Endometrium 1 | tissue | 9.0 | low |
| Fallopian tube | tissue | 9.0 | medium |
| Somatosensory cortex | tissue | 8.9 |  |
| Temporal cortex | tissue | 8.8 |  |
| Placenta | tissue | 8.7 | medium |
| Thyroid gland | tissue | 8.6 | high |
| Hippocampal formation | tissue | 8.6 |  |
| Entorhinal cortex | tissue | 8.6 |  |
| Epididymis | tissue | 8.5 | medium |
| Basal ganglia | tissue | 8.4 | low |
| Retrosplenial and cingulate cortex | tissue | 8.4 |  |
| Insular cortex | tissue | 8.4 |  |
| Retrosplenial cortex | tissue | 8.3 |  |
| Duodenum | tissue | 8.1 | medium |
| Ventral forebrain | tissue | 8.1 |  |
| Testis | tissue | 8.0 | medium |
| Small intestine | tissue | 8.0 | medium |
| Pituitary gland | tissue | 7.8 |  |
| Amygdala | tissue | 7.8 |  |
| Heart muscle | tissue | 7.7 | low |
| Pons | tissue | 7.7 |  |
| Septum | tissue | 7.7 |  |
| Ovary | tissue | 7.5 | low |

**Brain sub-regions (HPA Brain Atlas):** detected in 192; highest nTPM — Somatomor cortex, precentral gyrus (white matter) (20.1), Paracentral lobule, anterior (19.8), Somatosensory cortex, postcentral gyrus, ventral (white matter) (19.3), Orbitofrontal gyrus, anterior (18.9), Median raphe nucleus (18.2).

### Regulation

**Is transcription factor: no**

### Functional genomics

**gnomAD constraint:** pLI 2.21e-08, LOEUF 1.67, missense Z 1.17 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). [gnomAD](https://gnomad.broadinstitute.org/)

#### Regional missense constraint (gnomAD)

`ENST00000368232` splits into 3 regions with different missense tolerance; **1 is missense-constrained** (≈5% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. [gnomAD](https://gnomad.broadinstitute.org/)

| Region (GRCh38) | Missense obs / exp | o/e | Constrained |
| --- | --- | --- | --- |
| 1:156,595,216–156,598,106 | 307 / 337.1 | 0.91 | no |
| 1:156,598,107–156,598,260 | 4 / 20.2 | 0.20 | yes (p 3.2e-04) |
| 1:156,598,261–156,599,046 | 68 / 85.6 | 0.79 | no |

### Literature-anchored findings (GeneRIF, showing 3)

- G-patch domain-containing protein 4 localizes to both the nucleoli and Cajal bodies and regulates cell growth and nucleolar structure. (PMID:33933995)
- GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners. (PMID:38113271)
- GPATCH4 contributes to nucleolus morphology and its dysfunction impairs cell viability. (PMID:38113722)

### Cross-species orthologs

**4 orthologs**

| Organism | Symbol | Gene ID |
| --- | --- | --- |
| danio_rerio | gpatch4 | ENSDARG00000091931 |
| mus_musculus | Gpatch4 | ENSMUSG00000028069 |
| rattus_norvegicus | Gpatch4 | ENSRNOG00000018969 |
| drosophila_melanogaster | CG15561 | FBGN0039829 |

**Paralogs (1):** PINX1 (ENSG00000254093)

#### Mouse-model phenotypes

Observed phenotypes of the mouse ortholog ([MGI:1913864](https://www.informatics.jax.org/marker/MGI:1913864)) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 13 distinct phenotype terms.

| Mouse phenotype (MP) | Records |
| --- | --- |
| abnormal spleen morphology | 1 |
| small spleen | 1 |
| small seminal vesicle | 1 |
| decreased locomotor activity | 1 |
| abnormal seminal vesicle morphology | 1 |
| abnormal coat/hair pigmentation | 1 |
| decreased mean corpuscular volume | 1 |
| decreased lean body mass | 1 |
| immune system phenotype | 1 |
| decreased mean corpuscular hemoglobin | 1 |
| decreased CD8-positive, alpha-beta T cell number | 1 |
| increased fasting circulating glucose level | 1 |
| increased freezing behavior | 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 |
| --- | --- | --- | --- |
| Xenopus tropicalis | [Q6P859](https://www.uniprot.org/uniprotkb/Q6P859/entry) | 85.2% | Diamond |
| Xenopus laevis | [Q4V842](https://www.uniprot.org/uniprotkb/Q4V842/entry) | 84.9% | Diamond |
| Bos taurus | [Q2KJE1](https://www.uniprot.org/uniprotkb/Q2KJE1/entry) | 78.1% | 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 |
| --- | --- | --- |
| [NES](/atlas/gene/NES/) | protein-coding | 10763 |
| [BCAN-AS2](/atlas/gene/BCAN-AS2/) | ncRNA | 126568844 |
| [NAXE](/atlas/gene/NAXE/) | protein-coding | 128240 |
| [HAPLN2](/atlas/gene/HAPLN2/) | protein-coding | 60484 |
| [BCAN](/atlas/gene/BCAN/) | protein-coding | 63827 |
| [CRABP2](/atlas/gene/CRABP2/) | protein-coding | 1382 |
| [IQGAP3](/atlas/gene/IQGAP3/) | protein-coding | 128239 |
| [TTC24](/atlas/gene/TTC24/) | protein-coding | 164118 |
| [MEF2D](/atlas/gene/MEF2D/) | protein-coding | 4209 |

<a id="protein-Q5T3I0"></a>

## Protein

### Protein identifiers

**G patch domain-containing protein 4** — `Q5T3I0` (reviewed: Q5T3I0)

**All UniProt accessions (6):** `A0A0A0MRK1`, `A0AA34QVU8`, `E9PAV9`, `E9PPY4`, `F2Z3C6`, `F8W895`

#### UniProt curated annotations — [full annotation on UniProt →](https://www.uniprot.org/uniprotkb/Q5T3I0/entry)

**Polymorphism.** This gene contains polymorphic substitutions in the last exon causing a frameshift variant C-terminal sequence compared to the official human genome. However, this variant sequence is in agreement with ortholog sequences.

#### Isoforms (3)

| UniProt ID | Names | Canonical? |
| --- | --- | --- |
| Q5T3I0-1 | 1 | yes |
| Q5T3I0-2 | 2 |  |
| Q5T3I0-3 | 3 |  |

**RefSeq proteins (2):** `NP_056405`, `NP_872620`  (*=MANE)

#### Domains & families (InterPro)

| ID | Name | Type |
| --- | --- | --- |
| IPR000467 | G_patch_dom | Domain |
| IPR050656 | PINX1 | Family |

**Pfam:** `PF01585`

**UniProt features (24 total):** compositionally biased region 8, modified residue 6, splice variant 4, region of interest 2, chain 1, domain 1, cross-link 1, coiled-coil region 1

### Structure

#### Predicted structure (AlphaFold)

| Model | pLDDT | Fraction very-high |
| --- | --- | --- |
| AF-Q5T3I0-F1 | 57.52 | 0.12 |

### Human Protein Atlas

**Protein class:** Predicted intracellular proteins

**Protein evidence:** Evidence at protein level

**Subcellular location (HPA, imaging):** nucleoli; nucleoplasm

**Antibody reliability (HPA):** IH approved · IF enhanced

### 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)

| Type | Positions |
| --- | --- |
| N-acetylmethionine | 1 |
| Phosphothreonine | 4, 116 |
| Phosphoserine | 128, 130, 139 |
| Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2) | 46 |

## 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: 151** (showing top):
`CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1`, `WANG_LMO4_TARGETS_DN`, `MILI_PSEUDOPODIA_HAPTOTAXIS_UP`, `YY1_02`, `GARY_CD5_TARGETS_DN`, `FISCHER_DREAM_TARGETS`, `IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR`, `NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP`, `NUYTTEN_EZH2_TARGETS_DN`, `GOCC_NUCLEOLUS`, `STAT5A_01`, `MATSUDA_NATURAL_KILLER_DIFFERENTIATION`, `ATGAAGG_MIR205`, `KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN`, `KOYAMA_SEMA3B_TARGETS_DN`

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

**GO Cellular Component (1):**
nucleolus (GO:0005730)

#### GO top-level categories

4 GO namespaces:

| Category | Terms |
| --- | --- |
| nucleic acid binding | 1 |
| binding | 1 |
| nuclear lumen | 1 |
| intracellular membraneless organelle | 1 |

#### Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 3 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

| GO term | NS | Evidence |
| --- | --- | --- |
| [RNA binding](https://amigo.geneontology.org/amigo/term/GO:0003723) | MF | high-throughput assay |

### Protein interactions and networks

#### STRING

showing 15 of 1,388 interactions by confidence (×1000):

| Protein A | Protein B | Partner UniProt | Score |
| --- | --- | --- | --- |
| GPATCH4 | TMEM52 | Q8NDY8 | 567 |
| GPATCH4 | SINHCAF | Q9NP50 | 453 |
| GPATCH4 | RP1L1 | Q8IWN7 | 438 |
| GPATCH4 | NXPH4 | O95158 | 424 |
| GPATCH4 | MYBBP1A | Q9BQG0 | 413 |
| GPATCH4 | RPL36 | Q9Y3U8 | 410 |
| GPATCH4 | TBCB | Q99426 | 399 |
| GPATCH4 | SAXO5 | Q8NA69 | 395 |
| GPATCH4 | CFAP45 | Q9UL16 | 387 |
| GPATCH4 | MAGIX | Q9H6Y5 | 384 |
| GPATCH4 | NUFIP2 | Q7Z417 | 378 |
| GPATCH4 | ZNF250 | P15622 | 378 |
| GPATCH4 | PEAR1 | Q5VY43 | 370 |
| GPATCH4 | STEAP2 | Q8NFT2 | 362 |
| GPATCH4 | PELI2 | Q9HAT8 | 357 |

#### IntAct

Human interaction partners of GPATCH4 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

| Partner | Interaction type | MIscore | Records |
| --- | --- | --- | --- |
| CEP70 | physical association | 0.720 | 6 |
| KASH5 | physical association | 0.720 | 6 |

## Disease & clinical

### Genetic variants

**Variant evidence for GPATCH4:** [68 ClinVar records](#clinvar) (1 pathogenic / likely pathogenic). Per-variant detail is on [Sugi Variant](https://sugi.bio/variant/gene/GPATCH4).

#### ClinVar

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

| Classification | Count (floor) |
| --- | --- |
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 54 |
| Likely benign | 3 |
| Benign | 0 |

#### Top pathogenic / likely-pathogenic (1)

Showing all 1 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 |
| --- | --- | --- | --- | --- |
| 2427315 | NC_000001.10:g.(?_156554669)_(156568838_?)del | Pathogenic | criteria provided, single submitter | 1 |

#### Per-variant reference — Sugi Variant

Explore GPATCH4'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/GPATCH4).

#### SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 36 predictions of 663):

| Position(s) | Effect | Δscore | Sites |
| --- | --- | --- | --- |
| 1:156598225–156598226 | donor_loss | 1.0000 | 5 |
| 1:156598320–156598321 | acceptor_loss | 1.0000 | 6 |
| 1:156598324 | acceptor_gain | 1.0000 |  |
| 1:156601407–156601408 | donor_loss | 1.0000 | 4 |
| 1:156595850–156595851 | acceptor_loss | 0.9900 | 6 |
| 1:156596388 | donor_gain | 0.9900 |  |
| 1:156598122–156598123 | acceptor_loss | 0.9900 | 5 |
| 1:156598229 | donor_gain | 0.9900 |  |
| 1:156598325 | acceptor_gain | 0.9900 |  |
| 1:156598419–156598420 | donor_loss | 0.9900 | 6 |

### HPA cancer prognostics

**RNA cancer specificity:** Low cancer specificity

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

2 prognostic cancer types:

| Cancer | Prognostic | p-value |
| --- | --- | --- |
| Kidney Chromophobe (TCGA) | unfavorable | 2.39e-05 |
| Liver Hepatocellular Carcinoma (TCGA) | unfavorable | 3.73e-05 |

### Disease associations

**OMIM:** gene `` | disease phenotypes: 

## Drugs & pharmacology

### Drug and pharmacology data

**Is drug target: no**

**PharmGKB:** 1 entry (CPIC guideline: no)

#### CTD chemical–gene interactions

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

| Chemical | Actions (top 5) | PubMed papers |
| --- | --- | --- |
| Valproic Acid | increases expression, affects expression, decreases expression, increases methylation, affects cotreatment | 6 |
| trichostatin A | affects cotreatment, increases expression | 3 |
| sodium arsenite | decreases expression, affects cotreatment, increases abundance, increases expression | 3 |
| Estradiol | affects expression, increases expression | 3 |
| (+)-JQ1 compound | affects expression, decreases expression | 2 |
| Arsenic | affects cotreatment, increases abundance, increases expression | 2 |
| Nickel | increases expression | 2 |
| Tretinoin | decreases expression | 2 |
| GSK-J4 | decreases expression | 1 |
| afuresertib | decreases expression | 1 |
| FR900359 | affects phosphorylation | 1 |
| TAK-243 | increases sumoylation | 1 |
| TL8-506 | affects cotreatment, increases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| bisphenol A | decreases expression | 1 |
| beta-lapachone | increases expression | 1 |
| arsenite | increases methylation | 1 |
| manganese chloride | increases expression, affects cotreatment, increases abundance | 1 |
| potassium chromate(VI) | affects cotreatment, increases expression | 1 |
| coumarin | affects phosphorylation | 1 |
| epigallocatechin gallate | affects cotreatment, increases expression | 1 |
| cylindrospermopsin | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| abrine | increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| 3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol | decreases expression | 1 |
| Irinotecan | decreases expression | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Atrazine | decreases expression | 1 |

#### Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

| Cellosaurus | Name | Category | Sex |
| --- | --- | --- | --- |
| CVCL_B2Y3 | Abcam HEK293T GPATCH4 KO | Transformed cell line | Female |

#### Clinical trials (associated diseases)

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

## Related Atlas pages

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