GIMAP2

Summary

GIMAP2 (GTPase, IMAP family member 2, HGNC:21789) is a protein-coding gene on chromosome 7q36.1, encoding GTPase IMAP family member 2 (Q9UG22). The heterodimer formed by GIMAP2 and GIMAP7 has GTPase activity.

This gene encodes a protein belonging to the GTP-binding superfamily and to the immuno-associated nucleotide (IAN) subfamily of nucleotide-binding proteins. In humans, the IAN subfamily genes are located in a cluster at 7q36.1.

Source: NCBI Gene 26157 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_015660

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21789
Approved symbol	GIMAP2
Name	GTPase, IMAP family member 2
Location	7q36.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp586D0824, HIMAP2, IMAP2, IAN12
Ensembl gene	ENSG00000106560
Ensembl biotype	protein_coding
OMIM	608085
Entrez	26157

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000223293, ENST00000474605, ENST00000487388

RefSeq mRNA: 1 — MANE Select: NM_015660 NM_015660

CCDS: CCDS5905

Canonical transcript exons

ENST00000223293 — 3 exons

Exon	Start	End
ENSE00000729852	150687052	150687087
ENSE00000872368	150685706	150685785
ENSE00000872369	150692315	150693641

Expression profiles

Bgee: expression breadth ubiquitous, 207 present calls, max score 97.54.

FANTOM5 (CAGE): breadth broad, TPM avg 14.8359 / max 602.9430, expressed in 803 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
81961	14.6355	802
81962	0.2003	98

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
leukocyte	CL:0000738	97.54	gold quality
monocyte	CL:0000576	97.52	gold quality
granulocyte	CL:0000094	96.59	gold quality
vermiform appendix	UBERON:0001154	94.54	gold quality
blood	UBERON:0000178	93.78	gold quality
lymph node	UBERON:0000029	93.71	gold quality
spleen	UBERON:0002106	93.49	gold quality
epithelium of nasopharynx	UBERON:0001951	88.99	gold quality
ileal mucosa	UBERON:0000331	88.24	gold quality
gall bladder	UBERON:0002110	87.66	gold quality
epithelial cell of pancreas	CL:0000083	87.18	silver quality
caecum	UBERON:0001153	87.04	gold quality
superficial temporal artery	UBERON:0001614	86.91	gold quality
right lung	UBERON:0002167	86.36	gold quality
rectum	UBERON:0001052	86.20	gold quality
lower lobe of lung	UBERON:0008949	85.95	silver quality
calcaneal tendon	UBERON:0003701	85.68	gold quality
lung	UBERON:0002048	84.97	gold quality
bone marrow	UBERON:0002371	84.69	gold quality
upper lobe of lung	UBERON:0008948	84.44	gold quality
germinal epithelium of ovary	UBERON:0001304	84.32	gold quality
upper lobe of left lung	UBERON:0008952	84.32	gold quality
smooth muscle tissue	UBERON:0001135	83.97	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.74	gold quality
colonic epithelium	UBERON:0000397	83.41	gold quality
jejunal mucosa	UBERON:0000399	83.00	gold quality
skin of hip	UBERON:0001554	82.99	gold quality
small intestine	UBERON:0002108	82.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.65	gold quality
omental fat pad	UBERON:0010414	82.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.87
E-MTAB-5061	no	2.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting GIMAP2, 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-656-3P	100.00	72.15	2788
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-199A-3P	99.75	70.48	929
HSA-MIR-199B-3P	99.75	70.48	929
HSA-MIR-3129-5P	99.75	70.46	914
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-190B-3P	99.33	68.29	1382
HSA-MIR-4528	99.18	69.77	1936
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-376A-3P	99.06	69.17	1128
HSA-MIR-376B-3P	99.06	69.17	1128
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-936	98.87	70.51	1124
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-222-5P	98.75	69.17	1242
HSA-MIR-506-5P	98.02	67.41	1065
HSA-MIR-892B	98.00	67.11	821
HSA-MIR-4693-5P	97.35	67.02	1234
HSA-MIR-921	97.09	66.45	562
HSA-MIR-4301	95.00	65.22	554
HSA-MIR-3174	94.63	63.64	577

Literature-anchored findings (GeneRIF, showing 1)

• GDP-bound GIMAP2(21-260) and GDP-bound GIMAP2(1-234) crystallized in space group P2(1)2(1)2(1) and the crystals diffracted X-rays to 2.9 and 1.7 A resolution, respectively. (PMID:20516611)

Cross-species orthologs

0 orthologs

Paralogs (7): GIMAP6 (ENSG00000133561), GIMAP4 (ENSG00000133574), GIMAP8 (ENSG00000171115), GIMAP7 (ENSG00000179144), GIMAP5 (ENSG00000196329), GIMAP1 (ENSG00000213203), GIMD1 (ENSG00000250298)

Protein

Protein identifiers

GTPase IMAP family member 2 — Q9UG22 (reviewed: Q9UG22)

Alternative names: Immunity-associated protein 2

All UniProt accessions (3): Q9UG22, A0A090N8H4, C9JND7

UniProt curated annotations — full annotation on UniProt →

Function. The heterodimer formed by GIMAP2 and GIMAP7 has GTPase activity. In contrast, GIMAP2 has no GTPase activity by itself.

Subunit / interactions. Monomer in the presence of bound GDP and in the absence of bound nucleotide. Homodimer in the presence of bound GTP. Can form linear oligomers. Heterodimer with GIMAP7.

Subcellular location. Lipid droplet.

Tissue specificity. Detected in T-cells.

Similarity. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. AIG1/Toc34/Toc159-like paraseptin GTPase family. IAN subfamily.

RefSeq proteins (1): NP_056475* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006703	G_AIG1	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR045058	GIMA/IAN/Toc	Family

Pfam: PF04548

UniProt features (37 total): helix 11, binding site 6, strand 6, region of interest 5, sequence variant 3, mutagenesis site 2, turn 2, chain 1, domain 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
2XTP	X-RAY DIFFRACTION	1.5
2XTM	X-RAY DIFFRACTION	1.7
2XTN	X-RAY DIFFRACTION	1.9
3P1J	X-RAY DIFFRACTION	2.58
2XTO	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UG22-F1	89.04	0.71

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (6): 147–149; 184; 318–320; 31–37; 50; 57–58

Mutagenesis-validated functional residues (2):

Position	Phenotype
54	abolishes gtp-induced dimerization.
117	abolishes gtp-induced dimerization.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 76 (showing top): FUJII_YBX1_TARGETS_UP, RIGGI_EWING_SARCOMA_PROGENITOR_UP, GOMF_GTPASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, LEE_DIFFERENTIATING_T_LYMPHOCYTE, GENTLES_LEUKEMIC_STEM_CELL_UP, GOCC_LIPID_DROPLET, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_PINK_DN, MIR582_5P, MIR1252_3P, MIR380_3P, MIR4528, MIR659_3P, MIR222_5P

GO Biological Process (0):

GO Molecular Function (5): GTPase activity (GO:0003924), GTP binding (GO:0005525), identical protein binding (GO:0042802), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (4): nucleoplasm (GO:0005654), endoplasmic reticulum (GO:0005783), lipid droplet (GO:0005811), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
ribonucleoside triphosphate phosphatase activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
protein binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
nuclear lumen	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1086 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GIMAP2	AIG1	Q9NVV5	589
GIMAP2	C2orf78	A6NCI8	573
GIMAP2	ZNF775	Q96BV0	500
GIMAP2	GIMAP7	Q8NHV1	439
GIMAP2	UBAC2	Q8NBM4	434
GIMAP2	KLRC4	O43908	397
GIMAP2	C7orf33	Q8WU49	370
GIMAP2	TMEM176B	Q3YBM2	363
GIMAP2	DRC11L	A6NCM1	360
GIMAP2	SSC5D	A1L4H1	354
GIMAP2	MELTF	P08582	354
GIMAP2	GPR37	O15354	339
GIMAP2	SETX	Q7Z333	333
GIMAP2	ZBED11	P0CF97	325
GIMAP2	C1orf50	Q9BV19	321

IntAct

17 interactions, top by confidence:

A	B	Type	Score
GIMAP2	GIMAP2	psi-mi:“MI:0407”(direct interaction)	0.620
HTT	GIMAP2	psi-mi:“MI:0915”(physical association)	0.560
GIMAP2	TOR1B	psi-mi:“MI:0914”(association)	0.530
GIMAP2	STOM	psi-mi:“MI:0914”(association)	0.530
GIMAP7	GIMAP2	psi-mi:“MI:0407”(direct interaction)	0.440
TRIM54	GIMAP2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): TOR1B (Affinity Capture-MS), STOM (Affinity Capture-MS), TOR1B (Affinity Capture-MS), STOM (Affinity Capture-MS), FBP1 (Affinity Capture-MS), PRMT8 (Affinity Capture-MS), GIMAP2 (Two-hybrid), TOR1B (Affinity Capture-MS), PRMT8 (Affinity Capture-MS), STOM (Affinity Capture-MS), ARFIP1 (Affinity Capture-MS), TMEM159 (Affinity Capture-MS), PNPLA2 (Affinity Capture-MS)

ESM2 similar proteins: A4D126, A5PK43, A5PKB7, A6H603, C3VPR6, D2GU20, E9PW74, G1T469, G3MZQ6, O60294, O75578, O75616, P38570, P56201, P70224, Q149M9, Q17QI8, Q17QJ3, Q1JPJ9, Q2HJ51, Q53B87, Q53B88, Q5EBA0, Q5FVI9, Q5FVN6, Q5R6H6, Q5RJG7, Q5S6T3, Q5W0U4, Q643R3, Q6AYF9, Q6E804, Q6P5Z2, Q6P9H5, Q8BWF2, Q8BYR1, Q8K045, Q8K2J0, Q8K349, Q8K3L6

Diamond homologs: A5PKB7, F4HT21, G3X987, O23680, O81025, P54120, P70224, Q41009, Q4KLG2, Q5FVN6, Q6P9H5, Q75N62, Q8BWF2, Q8K349, Q8K3K9, Q8K3L6, Q8ND71, Q8NHV1, Q8WWP7, Q96F15, Q99JY3, Q99MI6, Q9C8U2, Q9C8V0, Q9C8V2, Q9NUV9, Q9T0F2, Q9T0F3, Q9T0F4, Q9UG22, E9PW74, Q9C8U5, Q9C8U6, Q9C8U7, Q9C8U8, Q9LVT3, O81283, Q6S5G3, D2GU20, O75616

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

511 predictions. Top by Δscore:

Variant	Effect	Δscore
7:150685784:AGGT:A	donor_loss	0.9900
7:150685785:GGTAA:G	donor_loss	0.9900
7:150685786:GTAA:G	donor_loss	0.9900
7:150685787:T:A	donor_loss	0.9900
7:150689592:AT:A	donor_gain	0.9800
7:150687046:TCTCA:T	acceptor_loss	0.9600
7:150687047:CTCA:C	acceptor_loss	0.9600
7:150687048:TCA:T	acceptor_loss	0.9600
7:150687049:CAGG:C	acceptor_loss	0.9600
7:150687085:GGG:G	donor_gain	0.9600
7:150687086:GGG:G	donor_gain	0.9600
7:150685754:G:GT	donor_gain	0.9500
7:150687086:GG:G	donor_gain	0.9500
7:150687087:GG:G	donor_gain	0.9500
7:150687089:T:TC	donor_loss	0.9500
7:150685786:G:GG	donor_gain	0.9400
7:150689588:TGTA:T	donor_gain	0.9300
7:150689597:A:AG	donor_gain	0.9200
7:150689587:GT:G	donor_gain	0.9100
7:150689593:T:G	donor_gain	0.9100
7:150690220:G:GA	donor_gain	0.9000
7:150690345:C:T	donor_gain	0.9000
7:150685782:TCAG:T	donor_gain	0.8900
7:150687048:TCAGG:T	donor_loss	0.8900
7:150687050:AGG:A	donor_loss	0.8900
7:150687050:A:AG	acceptor_gain	0.8800
7:150687051:G:GG	acceptor_gain	0.8800
7:150687088:G:GG	donor_gain	0.8800
7:150687100:C:G	donor_gain	0.8700
7:150690319:TGG:T	donor_gain	0.8700

AlphaMissense

2242 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:150692428:T:C	F48L	0.961
7:150692430:T:A	F48L	0.961
7:150692430:T:G	F48L	0.961
7:150692683:T:C	F133L	0.937
7:150692685:T:A	F133L	0.937
7:150692685:T:G	F133L	0.937
7:150692714:T:A	V143D	0.912
7:150692719:T:C	F145L	0.912
7:150692721:T:A	F145L	0.912
7:150692721:T:G	F145L	0.912
7:150692530:T:C	F82L	0.911
7:150692532:T:A	F82L	0.911
7:150692532:T:G	F82L	0.911
7:150692830:T:C	F182L	0.895
7:150692832:T:A	F182L	0.895
7:150692832:T:G	F182L	0.895
7:150692392:A:C	S36R	0.894
7:150692394:T:A	S36R	0.894
7:150692394:T:G	S36R	0.894
7:150692720:T:C	F145S	0.865
7:150692360:T:C	I25T	0.848
7:150692391:A:C	K35N	0.848
7:150692391:A:T	K35N	0.848
7:150692372:G:T	G29V	0.843
7:150692411:T:C	I42T	0.838
7:150692517:C:A	D77E	0.832
7:150692517:C:G	D77E	0.832
7:150692390:A:T	K35I	0.822
7:150692411:T:G	I42S	0.820
7:150692819:G:C	R178P	0.817

dbSNP variants (sampled 300 via entrez): RS1000242562 (7:150689255 T>C), RS1000485732 (7:150689099 C>T), RS1000574537 (7:150688114 T>C), RS1000642566 (7:150689595 T>C), RS1001082075 (7:150688837 A>C), RS1001416847 (7:150687735 G>C), RS1002159761 (7:150687969 C>T), RS1002579753 (7:150685361 G>A), RS1002993817 (7:150692082 G>A), RS1003040165 (7:150685051 A>G), RS1003063998 (7:150691470 T>C), RS1003421492 (7:150685034 C>G,T), RS1004164599 (7:150685291 C>A,G), RS1004652349 (7:150685721 G>T), RS1004975999 (7:150689143 A>G)

Disease associations

OMIM: gene MIM:608085 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001113_18	Age at smoking initiation in chronic obstructive pulmonary disease	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005670	smoking initiation

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
bisphenol S	decreases methylation	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	increases expression	1
Calcitriol	increases expression	1
Cisplatin	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Methotrexate	decreases expression	1
Ozone	affects expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases methylation, decreases expression	1
Cyclosporine	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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