GPATCH2L

Summary

GPATCH2L (G-patch domain containing 2 like, HGNC:20210) is a protein-coding gene on chromosome 14q24.3, encoding G patch domain-containing protein 2-like (Q9NWQ4).

Predicted to be active in nucleus.

Source: NCBI Gene 55668 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_017926

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20210
Approved symbol	GPATCH2L
Name	G-patch domain containing 2 like
Location	14q24.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20689, FLJ10033
Ensembl gene	ENSG00000089916
Ensembl biotype	protein_coding
Entrez	55668

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 11 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000261530, ENST00000312858, ENST00000553588, ENST00000554125, ENST00000554375, ENST00000554799, ENST00000556109, ENST00000556372, ENST00000556663, ENST00000556675, ENST00000557207, ENST00000557263, ENST00000557542, ENST00000621494, ENST00000930299, ENST00000954001

RefSeq mRNA: 9 — MANE Select: NM_017926 NM_001322026, NM_001322027, NM_001322028, NM_001322029, NM_001322030, NM_001322031, NM_001322032, NM_017926, NM_017972

CCDS: CCDS9848, CCDS9849

Canonical transcript exons

ENST00000261530 — 10 exons

Exon	Start	End
ENSE00002533901	76151922	76151991
ENSE00002603976	76201691	76214343
ENSE00003535064	76173546	76173625
ENSE00003564900	76195878	76195972
ENSE00003567699	76154354	76155025
ENSE00003617322	76171843	76172019
ENSE00003639267	76180764	76180849
ENSE00003641979	76177988	76178042
ENSE00003642677	76176623	76176690
ENSE00003686420	76166663	76166727

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 95.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.6731 / max 181.5289, expressed in 1803 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
140710	16.9923	1802
140715	0.4765	239
140711	0.1975	73
207306	0.0068	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	95.50	gold quality
colonic epithelium	UBERON:0000397	91.38	gold quality
adrenal tissue	UBERON:0018303	90.78	gold quality
monocyte	CL:0000576	88.98	gold quality
cauda epididymis	UBERON:0004360	88.65	gold quality
mononuclear cell	CL:0000842	88.63	gold quality
calcaneal tendon	UBERON:0003701	88.49	gold quality
leukocyte	CL:0000738	88.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.33	gold quality
stromal cell of endometrium	CL:0002255	87.01	gold quality
cortical plate	UBERON:0005343	86.59	gold quality
ganglionic eminence	UBERON:0004023	85.89	gold quality
right testis	UBERON:0004534	85.87	gold quality
corpus epididymis	UBERON:0004359	85.81	gold quality
caput epididymis	UBERON:0004358	85.72	gold quality
gall bladder	UBERON:0002110	85.66	gold quality
ventricular zone	UBERON:0003053	85.63	gold quality
left testis	UBERON:0004533	85.39	gold quality
sural nerve	UBERON:0015488	84.98	gold quality
corpus callosum	UBERON:0002336	84.96	gold quality
islet of Langerhans	UBERON:0000006	84.77	gold quality
rectum	UBERON:0001052	84.44	gold quality
testis	UBERON:0000473	84.43	gold quality
tendon	UBERON:0000043	84.22	gold quality
gastrocnemius	UBERON:0001388	84.08	gold quality
tonsil	UBERON:0002372	83.98	gold quality
muscle of leg	UBERON:0001383	83.97	gold quality
right atrium auricular region	UBERON:0006631	83.97	gold quality
bone marrow	UBERON:0002371	83.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

239 targeting GPATCH2L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-218-5P	99.93	72.22	2103

Literature-anchored findings (GeneRIF, showing 1)

• N6-methyladenosine hypomethylation of circGPATCH2L regulates DNA damage and apoptosis through TRIM28 in intervertebral disc degeneration. (PMID:37438603)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gpatch2l	ENSMUSG00000021254
rattus_norvegicus	Gpatch2l	ENSRNOG00000010227

Paralogs (1): GPATCH2 (ENSG00000092978)

Protein

Protein identifiers

G patch domain-containing protein 2-like — Q9NWQ4 (reviewed: Q9NWQ4)

All UniProt accessions (7): Q9NWQ4, G3V290, G3V3M4, G3V4I8, G3V4L1, G3V553, G3V5D0

UniProt curated annotations — full annotation on UniProt →

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NWQ4-3	1	yes
Q9NWQ4-1	2
Q9NWQ4-4	4

RefSeq proteins (9): NP_001308955, NP_001308956, NP_001308957, NP_001308958, NP_001308959, NP_001308960, NP_001308961, NP_060396, NP_060442 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051189	Splicing_assoc_domain	Family

UniProt features (21 total): modified residue 6, compositionally biased region 4, splice variant 3, sequence conflict 3, region of interest 2, chain 1, cross-link 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NWQ4-F1	51.19	0.02

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): 91, 447, 449, 196, 31, 86, 88

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 228 (showing top): PEREZ_TP63_TARGETS, TGACCTY_ERR1_Q2, CACCAGC_MIR138, chr14q24, PEREZ_TP53_AND_TP63_TARGETS, CHANDRAN_METASTASIS_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, STAT1_02, SCGGAAGY_ELK1_02, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, MORI_PLASMA_CELL_DN, STAT1_03, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN, GHANDHI_DIRECT_IRRADIATION_UP, ODONNELL_METASTASIS_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPATCH2L	BLTP3B	A0JNW5	614
GPATCH2L	ZNF543	Q08ER8	505
GPATCH2L	IFT43	Q96FT9	475
GPATCH2L	PTPRH	Q9HD43	458
GPATCH2L	SVOPL	Q8N434	447
GPATCH2L	VPS13C	Q709C8	373
GPATCH2L	TTLL5	Q6EMB2	371
GPATCH2L	DHRS7B	Q6IAN0	371
GPATCH2L	PPP1R3E	Q9H7J1	370
GPATCH2L	ZNF135	P52742	351
GPATCH2L	MACO1	Q8N5G2	348
GPATCH2L	RRP15	Q9Y3B9	348
GPATCH2L	DHX15	O43143	345
GPATCH2L	AGTPBP1	Q9UPW5	334
GPATCH2L	SACK1A	Q86UY5	330
GPATCH2L	TSEN2	Q8NCE0	330

IntAct

81 interactions, top by confidence:

A	B	Type	Score
GPATCH2L	ZNF398	psi-mi:“MI:0915”(physical association)	0.670
GPATCH2L	ZNF473	psi-mi:“MI:0915”(physical association)	0.670
ZNF398	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.670
CSNK2B	NMT2	psi-mi:“MI:0914”(association)	0.660
CSNK2A2	PES1	psi-mi:“MI:0914”(association)	0.640
MEOX2	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
GPATCH2L		psi-mi:“MI:0915”(physical association)	0.560
GPATCH2L	ZNF263	psi-mi:“MI:0915”(physical association)	0.560
ZBTB48	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
DIP2A	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
ZNF165	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
KRT40	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
GPATCH2L	CEP70	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
GPATCH2L	RBPMS	psi-mi:“MI:0915”(physical association)	0.560
ZBTB8A	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
GPATCH2L	MDFI	psi-mi:“MI:0915”(physical association)	0.560
KRTAP4-12	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
GPATCH2L	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
PRDM14	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
ZNF408	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
THAP1	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (101): GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), GPATCH2L (Two-hybrid), ZNF398 (Two-hybrid), PRDM14 (Two-hybrid), ZNF408 (Two-hybrid), CCDC33 (Two-hybrid), CEP70 (Two-hybrid), KRTAP4-12 (Two-hybrid)

ESM2 similar proteins: A0A087WXM9, A0A140LI88, A2AKY4, A4D1E1, A4IGL8, E5FYH0, E9Q3S4, F6ULY3, F7DF15, G3S077, G7H7V7, G7NY55, O13859, O35923, O54952, O88491, P38299, P38398, P46013, P48754, P51587, P97929, Q09MP3, Q28DZ0, Q4V7J0, Q56UN5, Q5DTW7, Q5F2C3, Q5VWN6, Q5VYV7, Q6J6I8, Q6J6J0, Q6NS59, Q77PU6, Q7TSY8, Q7Z570, Q864S8, Q86TB3, Q86XD8, Q8N7Z5

Diamond homologs: Q6PE65, Q7TQC7, Q9NW75, Q9NWQ4, A0JMV4, A4IGK4, A5DEF8, A5DSB5, A6ZRL6, A7TQN2, B2GV05, F4JCU0, O15226, P52756, P53866, P70501, P98175, Q1RMU5, Q59UG4, Q6BYP9, Q6C233, Q6CQ59, Q6DDU9, Q6FP19, Q75E62, Q7TN31, Q8BY02, Q8CH09, Q8IX01, Q8N302, Q91YE7, Q99KG3, Q9UTK6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1657 predictions. Top by Δscore:

Variant	Effect	Δscore
14:76166186:A:AG	donor_gain	1.0000
14:76166661:A:AG	acceptor_gain	1.0000
14:76166661:AGT:A	acceptor_gain	1.0000
14:76166662:G:GG	acceptor_gain	1.0000
14:76166662:GT:G	acceptor_gain	1.0000
14:76166662:GTG:G	acceptor_gain	1.0000
14:76166662:GTGAA:G	acceptor_gain	1.0000
14:76171840:TAG:T	acceptor_loss	1.0000
14:76171841:A:AG	acceptor_gain	1.0000
14:76171842:G:GG	acceptor_gain	1.0000
14:76171842:G:GT	acceptor_loss	1.0000
14:76172017:GAG:G	donor_gain	1.0000
14:76172019:GGTG:G	donor_loss	1.0000
14:76172020:GT:G	donor_loss	1.0000
14:76172021:T:G	donor_loss	1.0000
14:76176689:GA:G	donor_gain	1.0000
14:76176691:G:GG	donor_gain	1.0000
14:76180762:A:AG	acceptor_gain	1.0000
14:76180763:G:GG	acceptor_gain	1.0000
14:76180763:GTTCA:G	acceptor_gain	1.0000
14:76201590:GAT:G	donor_gain	1.0000
14:76166186:A:G	donor_gain	0.9900
14:76166191:T:G	donor_gain	0.9900
14:76166657:TTACA:T	acceptor_loss	0.9900
14:76166659:ACAGT:A	acceptor_gain	0.9900
14:76166660:C:G	acceptor_gain	0.9900
14:76166661:A:AC	acceptor_loss	0.9900
14:76166662:GTGA:G	acceptor_gain	0.9900
14:76166723:ACAAG:A	donor_loss	0.9900
14:76166724:CAAG:C	donor_loss	0.9900

AlphaMissense

3152 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:76154374:T:C	L4P	0.999
14:76154386:T:C	L8S	0.999
14:76154750:G:C	R129S	0.999
14:76154750:G:T	R129S	0.999
14:76171849:A:T	D245V	0.999
14:76171857:A:C	S248R	0.999
14:76171859:T:A	S248R	0.999
14:76171859:T:G	S248R	0.999
14:76171863:T:A	W250R	0.999
14:76171863:T:C	W250R	0.999
14:76154398:T:C	L12S	0.998
14:76154745:C:A	R128S	0.998
14:76154749:G:C	R129T	0.998
14:76154749:G:T	R129M	0.998
14:76154760:A:G	K133E	0.998
14:76154762:G:C	K133N	0.998
14:76154762:G:T	K133N	0.998
14:76166670:A:C	S224R	0.998
14:76166672:C:A	S224R	0.998
14:76166672:C:G	S224R	0.998
14:76166673:A:C	S225R	0.998
14:76166675:T:A	S225R	0.998
14:76166675:T:G	S225R	0.998
14:76171845:G:C	D244H	0.998
14:76171846:A:T	D244V	0.998
14:76171848:G:C	D245H	0.998
14:76171849:A:C	D245A	0.998
14:76154374:T:A	L4Q	0.997
14:76154754:A:G	K131E	0.997
14:76154756:G:C	K131N	0.997

dbSNP variants (sampled 300 via entrez): RS1000029146 (14:76204695 T>A), RS1000035171 (14:76182127 G>A), RS1000056319 (14:76216251 C>T), RS1000091942 (14:76166588 A>C), RS1000276509 (14:76207891 A>C,G), RS1000309202 (14:76207549 A>G), RS1000361363 (14:76172804 T>C), RS1000391296 (14:76169926 G>A), RS1000428108 (14:76197526 T>C), RS1000438533 (14:76169573 A>T), RS1000535006 (14:76188185 G>A), RS1000559102 (14:76210011 C>T), RS1000561102 (14:76183919 A>G), RS1000580302 (14:76195136 G>A), RS1000608756 (14:76231684 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST000094_8	Blood pressure	5.000000e-06
GCST001320_25	Acute lymphoblastic leukemia (childhood)	3.000000e-06
GCST001320_29	Acute lymphoblastic leukemia (childhood)	1.000000e-06
GCST001320_4	Acute lymphoblastic leukemia (childhood)	4.000000e-06
GCST009391_268	Metabolite levels	8.000000e-06
GCST010083_350	Hemoglobin levels	7.000000e-09
GCST012147_7	Declining hemoglobin trajectory in blood donors	3.000000e-06
GCST90002383_262	Hematocrit	2.000000e-12
GCST90002384_370	Hemoglobin	2.000000e-13
GCST90002403_516	Red blood cell count	1.000000e-09

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0010427	triacylglycerol 54:9 measurement
EFO:0004509	hemoglobin measurement
EFO:0600027	hemoglobin change measurement
EFO:0004348	hematocrit
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	3
trichostatin A	affects cotreatment, increases expression	2
sodium arsenite	increases abundance, increases expression	2
Air Pollutants	increases expression, affects cotreatment, increases abundance	2
Arsenic	increases abundance, increases expression, decreases methylation	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
urushiol	increases expression	1
methylmercuric chloride	decreases expression, increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
nickel sulfate	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects 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
(+)-JQ1 compound	increases expression	1
Bortezomib	increases expression	1
Irinotecan	decreases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Vehicle Emissions	decreases expression, increases abundance	1
Caffeine	affects phosphorylation	1
Coumestrol	decreases expression	1

Clinical trials (associated diseases)

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