GPATCH4

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. Located in nucleolus and nucleoplasm.

Source: NCBI Gene 54865 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 68 total — 1 pathogenic

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: 16 — 8 retained_intron, 3 protein_coding_LoF, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000368232, ENST00000415314, ENST00000438976, ENST00000463513, ENST00000473910, ENST00000474904, ENST00000494414, ENST00000497287, ENST00000498641, ENST00000498756, ENST00000506832, ENST00000525375, ENST00000527691, ENST00000529520, ENST00000531129, ENST00000531900

RefSeq mRNA: 2 — MANE Select: None 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.

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

255 total, 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

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.92
E-MTAB-7606	no	616.96

Regulation

Is transcription factor: 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)

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 →

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

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

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

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): 1, 4, 116, 128, 130, 139, 46

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

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 Biological Process (1): hematopoietic progenitor cell differentiation (GO:0002244)

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

GO Cellular Component (2): nucleolus (GO:0005730), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
hemopoiesis	1
cell differentiation	1
nucleic acid binding	1
binding	1
intracellular membraneless organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1652 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPATCH4	TRIM58	Q8NG06	611
GPATCH4	TMEM52	Q8NDY8	595
GPATCH4	RP1L1	Q8IWN7	500
GPATCH4	NXPH4	O95158	484
GPATCH4	SINHCAF	Q9NP50	477
GPATCH4	AKAP3	O75969	463
GPATCH4	PEAR1	Q5VY43	455
GPATCH4	CADM2	Q8N3J6	424
GPATCH4	PELI2	Q9HAT8	421
GPATCH4	NUFIP2	Q7Z417	416
GPATCH4	FOXL2NB	Q6ZUU3	416
GPATCH4	SAXO5	Q8NA69	413
GPATCH4	RPL36	Q9Y3U8	413
GPATCH4	MYBBP1A	Q9BQG0	411
GPATCH4	ZNF221	Q9UK13	404

IntAct

76 interactions, top by confidence:

A	B	Type	Score
KASH5	GPATCH4	psi-mi:“MI:0915”(physical association)	0.720
CEP70	GPATCH4	psi-mi:“MI:0915”(physical association)	0.720
GPATCH4	KASH5	psi-mi:“MI:0915”(physical association)	0.720
GPATCH4	CEP70	psi-mi:“MI:0915”(physical association)	0.720
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
OAZ1	AZIN1	psi-mi:“MI:0914”(association)	0.640
BCOR	CBX4	psi-mi:“MI:0914”(association)	0.530
Snu13		psi-mi:“MI:0915”(physical association)	0.400
Mis12		psi-mi:“MI:0914”(association)	0.350
Vps4b	CNOT1	psi-mi:“MI:0914”(association)	0.350
NES	RPL10	psi-mi:“MI:0914”(association)	0.350
Emc6	AAR2	psi-mi:“MI:0914”(association)	0.350
PAPD5	UNC119B	psi-mi:“MI:0914”(association)	0.350
PCDHB15	HLA-A	psi-mi:“MI:0914”(association)	0.350
SAMHD1	SF1	psi-mi:“MI:0914”(association)	0.350
Rock1		psi-mi:“MI:0914”(association)	0.350
NEIL3	SF3B2	psi-mi:“MI:0914”(association)	0.350
Cdkn2aip	SF1	psi-mi:“MI:0914”(association)	0.350
NLRP3	PHRF1	psi-mi:“MI:0914”(association)	0.350
NP	HNRNPCL1	psi-mi:“MI:0914”(association)	0.350
KSR1	FAM168B	psi-mi:“MI:0914”(association)	0.350
RRP1B	ZNF785	psi-mi:“MI:0914”(association)	0.350
DLST		psi-mi:“MI:0914”(association)	0.350
MKI67	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A4L691, D3ZTQ1, O75151, O88271, P35689, Q07G43, Q08288, Q12872, Q14241, Q24K12, Q2KJE1, Q3KRF3, Q3TFK5, Q3USH5, Q4ADK4, Q4ADK7, Q4V842, Q566R3, Q5BJN8, Q5RET9, Q5T3I0, Q5U3K5, Q5ZJJ1, Q5ZK28, Q60FC2, Q63187, Q68FU8, Q6AYK5, Q6IQ49, Q6NRI5, Q6P859, Q6PFK1, Q75QI0, Q75UQ2, Q7T293, Q7TN31, Q7ZVC9, Q8CB77, Q8CIL4, Q8HXY9

Diamond homologs: A4L691, Q2KJE1, Q3TFK5, Q4V842, Q566R3, Q5T3I0, Q6P859, Q96BK5, Q9CZX5, A5E4P1, Q6BUE3, Q6C1L3, Q9URX9, Q03525

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

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)

Variant ID	HGVS	Classification
2427315	NC_000001.10:g.(?156554669)(156568838_?)del	Pathogenic

SpliceAI

1212 predictions. Top by Δscore:

Variant	Effect	Δscore
1:156595845:CAGCC:C	acceptor_gain	1.0000
1:156595848:CC:C	acceptor_gain	1.0000
1:156595849:CC:C	acceptor_gain	1.0000
1:156595850:C:CC	acceptor_gain	1.0000
1:156596132:C:CC	acceptor_gain	1.0000
1:156596385:A:AC	donor_gain	1.0000
1:156596386:C:CC	donor_gain	1.0000
1:156596386:CAT:C	donor_gain	1.0000
1:156596400:TGG:T	donor_gain	1.0000
1:156597560:T:TA	donor_gain	1.0000
1:156598021:ACAG:A	donor_gain	1.0000
1:156598022:CAGC:C	donor_gain	1.0000
1:156598222:CATAC:C	donor_loss	1.0000
1:156598223:ATAC:A	donor_loss	1.0000
1:156598226:C:CA	donor_loss	1.0000
1:156598316:CTAC:C	acceptor_gain	1.0000
1:156598318:ACC:A	acceptor_loss	1.0000
1:156598320:C:CA	acceptor_loss	1.0000
1:156598324:C:CT	acceptor_gain	1.0000
1:156598324:C:T	acceptor_gain	1.0000
1:156598419:ACC:A	donor_gain	1.0000
1:156598420:CCC:C	donor_gain	1.0000
1:156601406:TACC:T	donor_loss	1.0000
1:156601407:A:AC	donor_gain	1.0000
1:156601407:A:AT	donor_loss	1.0000
1:156601408:C:CC	donor_gain	1.0000
1:156601408:CCGT:C	donor_gain	1.0000
1:156595846:AGCC:A	acceptor_gain	0.9900
1:156595847:GCC:G	acceptor_gain	0.9900
1:156595848:CCC:C	acceptor_gain	0.9900

AlphaMissense

2470 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000300307 (1:156602292 A>G), RS1001226519 (1:156602909 C>T), RS1001311129 (1:156596201 T>G), RS1001552664 (1:156596255 A>T), RS1001805970 (1:156602890 G>A,T), RS1002316846 (1:156594642 A>G), RS1002632734 (1:156601327 G>A), RS1003228634 (1:156599583 C>T), RS1003669159 (1:156599996 G>A), RS1005043948 (1:156598573 T>C), RS1005234135 (1:156594799 T>C), RS1005274353 (1:156596852 T>C), RS1005896153 (1:156601345 C>T), RS1006645317 (1:156595812 C>T), RS1006683455 (1:156601820 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression, increases methylation	6
trichostatin A	affects cotreatment, increases expression	3
sodium arsenite	increases abundance, increases expression, decreases expression, affects cotreatment	3
Estradiol	affects expression, increases expression	3
(+)-JQ1 compound	decreases expression, affects expression	2
Arsenic	increases expression, affects cotreatment, increases abundance	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	affects cotreatment, increases abundance, increases expression	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)

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