GPANK1

Summary

GPANK1 (G-patch domain and ankyrin repeats 1, HGNC:13920) is a protein-coding gene on chromosome 6p21.33, encoding G patch domain and ankyrin repeat-containing protein 1 (O95872).

This gene is located in a cluster of HLA-B-associated transcripts, which is included in the human major histocompatability complex III region. This gene encodes a protein which is thought to play a role in immunity. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 7918 — RefSeq curated summary.

At a glance

• GWAS associations: 28
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_033177

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13920
Approved symbol	GPANK1
Name	G-patch domain and ankyrin repeats 1
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Aliases	G5, D6S54E, GPATCH10, ANKRD59
Ensembl gene	ENSG00000204438
Ensembl biotype	protein_coding
OMIM	142610
Entrez	7918

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 23 protein_coding

ENST00000375893, ENST00000375895, ENST00000375896, ENST00000375900, ENST00000375906, ENST00000445768, ENST00000456540, ENST00000458083, ENST00000908857, ENST00000908858, ENST00000908859, ENST00000908860, ENST00000908861, ENST00000921266, ENST00000921267, ENST00000921268, ENST00000921269, ENST00000921270, ENST00000921271, ENST00000921272, ENST00000921273, ENST00000921274, ENST00000948314

RefSeq mRNA: 5 — MANE Select: NM_033177 NM_001199237, NM_001199238, NM_001199239, NM_001199240, NM_033177

CCDS: CCDS4711

Canonical transcript exons

ENST00000211377 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 91.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.5670 / max 130.5510, expressed in 1782 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72775	5.8720	1684
72778	1.3777	863
72779	1.3146	682
72780	1.2303	742
72777	0.9374	442
72774	0.8193	565
72776	0.0158	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	91.09	gold quality
right testis	UBERON:0004534	90.60	gold quality
testis	UBERON:0000473	90.19	gold quality
apex of heart	UBERON:0002098	89.58	gold quality
blood	UBERON:0000178	88.94	gold quality
sural nerve	UBERON:0015488	88.90	gold quality
gastrocnemius	UBERON:0001388	88.46	gold quality
muscle of leg	UBERON:0001383	88.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.11	gold quality
calcaneal tendon	UBERON:0003701	88.03	gold quality
heart left ventricle	UBERON:0002084	87.57	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.34	gold quality
skeletal muscle tissue	UBERON:0001134	87.04	gold quality
ganglionic eminence	UBERON:0004023	86.79	gold quality
granulocyte	CL:0000094	86.67	gold quality
heart	UBERON:0000948	86.50	gold quality
right atrium auricular region	UBERON:0006631	86.17	gold quality
muscle tissue	UBERON:0002385	86.01	gold quality
ventricular zone	UBERON:0003053	85.81	gold quality
descending thoracic aorta	UBERON:0002345	85.67	gold quality
bone marrow cell	CL:0002092	85.62	gold quality
mucosa of stomach	UBERON:0001199	85.56	gold quality
leukocyte	CL:0000738	85.34	gold quality
monocyte	CL:0000576	85.18	gold quality
popliteal artery	UBERON:0002250	85.14	gold quality
tibial artery	UBERON:0007610	85.14	gold quality
duodenum	UBERON:0002114	85.12	gold quality
body of stomach	UBERON:0001161	84.94	gold quality
bone marrow	UBERON:0002371	84.87	gold quality
ovary	UBERON:0000992	84.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-9543	yes	14.18
E-ANND-3	yes	3.62

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F4

miRNA regulators (miRDB)

49 targeting GPANK1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-4528	99.18	69.77	1936
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	gpank1	ENSDARG00000053995
mus_musculus	Gpank1	ENSMUSG00000092417
rattus_norvegicus	Gpank1	ENSRNOG00000000848
drosophila_melanogaster	CG8152	FBGN0034008
caenorhabditis_elegans		WBGENE00014256

Protein

Protein identifiers

G patch domain and ankyrin repeat-containing protein 1 — O95872 (reviewed: O95872)

Alternative names: Ankyrin repeat domain-containing protein 59, G patch domain-containing protein 10, HLA-B-associated transcript 4, Protein G5

All UniProt accessions (5): O95872, A0A024RCU2, A0A0A0MSL4, A0A0A0MSL5, F6QYZ9

RefSeq proteins (5): NP_001186166, NP_001186167, NP_001186168, NP_001186169, NP_149417* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000467	G_patch_dom	Domain
IPR002110	Ankyrin_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR039146	GPANK1	Family

Pfam: PF01585, PF13637

UniProt features (14 total): sequence variant 5, compositionally biased region 3, repeat 2, chain 1, domain 1, region of interest 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95872-F1	71.48	0.22

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 (1): 290

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GGAMTNNNNNTCCY_UNKNOWN, GGAANCGGAANY_UNKNOWN, NRF2_01, CETS1P54_01, TGGAAA_NFAT_Q4_01, NUYTTEN_EZH2_TARGETS_DN, MARSON_BOUND_BY_E2F4_UNSTIMULATED, OSF2_Q6, SCGGAAGY_ELK1_02, GEORGES_TARGETS_OF_MIR192_AND_MIR215, MIKKELSEN_MCV6_LCP_WITH_H3K4ME3, VANOEVELEN_MYOGENESIS_SIN3A_TARGETS

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2

Protein interactions and networks

STRING

368 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPANK1	APOM	O95445	967
GPANK1	PRRC2A	P48634	715
GPANK1	C6orf47	O95873	663
GPANK1	ABHD16A	O95870	654
GPANK1	LY6G5B	Q8NDX9	591
GPANK1	LY6G5C	Q5SRR4	518
GPANK1	ALDH18A1	P54886	496
GPANK1	ZNF326	Q5BKZ1	495
GPANK1	TARS2	Q9BW92	483
GPANK1	GANAB	Q14697	482
GPANK1	FAM110A	Q9BQ89	451
GPANK1	LY6G6C	O95867	446
GPANK1	LRRFIP1	Q32MZ4	445
GPANK1	H1-1	Q02539	428
GPANK1	OPTN	Q96CV9	417

IntAct

302 interactions, top by confidence:

A	B	Type	Score
GPANK1	TRIM27	psi-mi:“MI:0915”(physical association)	0.780
GPANK1	TRIM23	psi-mi:“MI:0915”(physical association)	0.780
TRIM23	GPANK1	psi-mi:“MI:0915”(physical association)	0.780
TRIM27	GPANK1	psi-mi:“MI:0915”(physical association)	0.780
GPANK1	TTC19	psi-mi:“MI:0915”(physical association)	0.740
CCDC184	GPANK1	psi-mi:“MI:0915”(physical association)	0.720
GPANK1	CCDC184	psi-mi:“MI:0915”(physical association)	0.720
GOLGA2	GPANK1	psi-mi:“MI:0915”(physical association)	0.670
GPANK1	PNMA1	psi-mi:“MI:0915”(physical association)	0.670
PNMA1	GPANK1	psi-mi:“MI:0915”(physical association)	0.670
GPANK1	LZTS2	psi-mi:“MI:0915”(physical association)	0.670
TFCP2	GPANK1	psi-mi:“MI:0915”(physical association)	0.560
GPANK1	FTO	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (118): GPANK1 (Two-hybrid), GPANK1 (Two-hybrid), GPANK1 (Two-hybrid), GPANK1 (Two-hybrid), PNMA1 (Two-hybrid), CCDC184 (Two-hybrid), TGM1 (Affinity Capture-MS), TTC19 (Affinity Capture-MS), ALOX12B (Affinity Capture-MS), CCDC85B (Two-hybrid), GPANK1 (Reconstituted Complex), LZTS2 (Two-hybrid), TTC19 (Affinity Capture-MS), IL37 (Affinity Capture-MS), TGM1 (Affinity Capture-MS)

ESM2 similar proteins: A1L188, A2AMZ4, A2XK00, A7YY73, B4FGS2, B4FTR7, B8B624, C0HAV3, C5E268, G2TRP6, O13973, O75012, O95159, O95872, Q0VDN7, Q12894, Q28H71, Q2YDD3, Q3SZA2, Q3SZW4, Q3U0S6, Q3UJV1, Q49AH0, Q4G012, Q5FVV3, Q5U509, Q5U651, Q61858, Q6ASS9, Q6P0I6, Q756Q5, Q7S4Y4, Q7XAM0, Q7XK12, Q8BGD8, Q8BGX2, Q8CC36, Q8VED2, Q96BP2, Q96C34

Diamond homologs: O95872, Q09655, Q61858, Q9V7A7, Q05921, Q5E9N5, Q9H078, O97902, Q0VC93, Q1AAU6, Q28FJ2, Q3V096, Q4JHE0, Q569N2, Q5U464, Q6JAN1, Q7Z713, Q7ZUV0, Q810B6, Q96KQ7, Q9FYG2, Q9P2R3, Q9QWY8, Q9R0Z3, Q9ULH1, Q9Z148

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

803 predictions. Top by Δscore:

Variant	Effect	Δscore
6:31662711:C:CC	acceptor_gain	1.0000
6:31664932:C:CA	donor_gain	1.0000
6:31666160:G:GT	donor_gain	1.0000
6:31666205:GCCG:G	donor_gain	1.0000
6:31666206:CCGGT:C	donor_loss	1.0000
6:31666207:CGG:C	donor_loss	1.0000
6:31666207:CGGT:C	donor_loss	1.0000
6:31666208:GGT:G	donor_loss	1.0000
6:31666209:G:GG	donor_gain	1.0000
6:31666210:T:G	donor_loss	1.0000
6:31664089:T:TA	donor_gain	0.9900
6:31664209:T:TA	donor_gain	0.9900
6:31664493:C:CC	acceptor_gain	0.9900
6:31664859:AG:A	donor_gain	0.9900
6:31664878:T:TA	donor_gain	0.9900
6:31666160:G:T	donor_gain	0.9900
6:31666211:GA:G	donor_loss	0.9900
6:31662706:GAGAC:G	acceptor_gain	0.9800
6:31662708:GAC:G	acceptor_gain	0.9800
6:31663847:CCTTA:C	donor_loss	0.9800
6:31663848:CTTA:C	donor_loss	0.9800
6:31663849:TTA:T	donor_loss	0.9800
6:31663850:TA:T	donor_loss	0.9800
6:31663851:A:T	donor_loss	0.9800
6:31664004:CAG:C	donor_gain	0.9800
6:31664047:C:CT	donor_gain	0.9800
6:31664173:AT:A	donor_gain	0.9800
6:31665002:TT:T	acceptor_gain	0.9800
6:31665004:C:CC	acceptor_gain	0.9800
6:31665855:CCATA:C	donor_loss	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000552968 (6:31665533 C>T), RS1000896848 (6:31665677 C>A), RS1001235811 (6:31663052 G>A), RS1002270126 (6:31660913 C>G,T), RS1003888690 (6:31666216 T>C), RS1004416030 (6:31663266 C>T), RS1004534017 (6:31665009 C>T), RS1005016874 (6:31661876 C>A,G,T), RS1005582024 (6:31662188 G>T), RS1006077512 (6:31661356 C>T), RS1006154745 (6:31662942 G>A), RS1006213953 (6:31667323 G>T), RS1006545988 (6:31661671 G>A), RS1007206449 (6:31661037 G>C,T), RS1007344306 (6:31665940 T>C)

Disease associations

OMIM: gene MIM:142610 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

28 associations (top):

Study	Trait	p-value
GCST000984_10	Idiopathic membranous nephropathy	2.000000e-56
GCST001812_2	Epstein-Barr virus immune response (EBNA-1)	2.000000e-10
GCST002674_7	Febrile seizures (MMR vaccine-related)	2.000000e-07
GCST004131_25	Inflammatory bowel disease	2.000000e-31
GCST004133_79	Ulcerative colitis	5.000000e-65
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_117	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_126	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_154	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST004521_17	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_209	Autism spectrum disorder or schizophrenia	5.000000e-16
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_213	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST004521_224	Autism spectrum disorder or schizophrenia	5.000000e-10
GCST004521_227	Autism spectrum disorder or schizophrenia	4.000000e-12
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_281	Autism spectrum disorder or schizophrenia	5.000000e-09
GCST004521_45	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_81	Autism spectrum disorder or schizophrenia	1.000000e-14
GCST008916_111	Asthma	2.000000e-14
GCST008916_114	Asthma	1.000000e-09
GCST008916_30	Asthma	1.000000e-09
GCST008917_2	Asthma (childhood onset)	4.000000e-07
GCST008921_1	Asthma and major depressive disorder	2.000000e-16
GCST010725_43	Malaria	5.000000e-07
GCST010725_62	Malaria	3.000000e-06
GCST012227_427	Hip circumference adjusted for BMI	8.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006519	MMR-related febrile seizures
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	2
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
perfluorooctane sulfonic acid	increases expression	1
Bortezomib	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Hydrogen Peroxide	affects expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Copper Sulfate	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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