GTPBP6

Summary

GTPBP6 (GTP binding protein 6, HGNC:30189) is a protein-coding gene on chromosome Xp22.33 and Yp11.32, encoding Putative GTP-binding protein 6 (O43824).

This gene encodes a GTP binding protein and is located in the pseudoautosomal region (PAR) at the end of the short arms of the X and Y chromosomes.

Source: NCBI Gene 8225 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_012227

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30189
Approved symbol	GTPBP6
Name	GTP binding protein 6
Location	Xp22.33 and Yp11.32
Locus type	gene with protein product
Status	Approved
Aliases	PGPL, FLJ20977
Ensembl gene	ENSG00000178605
Ensembl biotype	protein_coding
OMIM	300124
Entrez	8225

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000326153, ENST00000485332, ENST00000850592, ENST00000900013, ENST00000900014, ENST00000900015, ENST00000914511, ENST00000966877

RefSeq mRNA: 1 — MANE Select: NM_012227 NM_012227

CCDS: CCDS75943

Canonical transcript exons

ENST00000326153 — 10 exons

Exon	Start	End
ENSE00001288218	311419	311627
ENSE00001793174	312766	312924
ENSE00003449454	314150	314217
ENSE00003581203	307360	307512
ENSE00003654058	307732	307880
ENSE00003714129	314890	315020
ENSE00003733507	316914	317051
ENSE00003733593	315229	315299
ENSE00004282261	304759	305197
ENSE00004282262	318439	318796

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 95.74.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ovary	UBERON:0002119	95.74	gold quality
right ovary	UBERON:0002118	95.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.68	gold quality
tibial nerve	UBERON:0001323	95.01	gold quality
body of stomach	UBERON:0001161	94.93	gold quality
gastrocnemius	UBERON:0001388	94.87	gold quality
body of uterus	UBERON:0009853	94.82	gold quality
sural nerve	UBERON:0015488	94.59	gold quality
cerebellar hemisphere	UBERON:0002245	94.55	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.45	gold quality
cerebellar cortex	UBERON:0002129	94.42	gold quality
left uterine tube	UBERON:0001303	94.30	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.24	gold quality
right uterine tube	UBERON:0001302	94.22	gold quality
lower esophagus	UBERON:0013473	94.22	gold quality
left coronary artery	UBERON:0001626	94.17	gold quality
muscle of leg	UBERON:0001383	94.13	gold quality
right lobe of thyroid gland	UBERON:0001119	94.07	gold quality
metanephros cortex	UBERON:0010533	94.07	gold quality
body of pancreas	UBERON:0001150	94.04	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.02	gold quality
endocervix	UBERON:0000458	94.01	gold quality
left lobe of thyroid gland	UBERON:0001120	93.98	gold quality
right lung	UBERON:0002167	93.96	gold quality
popliteal artery	UBERON:0002250	93.96	gold quality
tibial artery	UBERON:0007610	93.95	gold quality
right atrium auricular region	UBERON:0006631	93.90	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.84	gold quality
mucosa of transverse colon	UBERON:0004991	93.77	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.77	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting GTPBP6, 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-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-6090	91.01	62.65	222

Literature-anchored findings (GeneRIF, showing 1)

• Dual function of GTPBP6 in biogenesis and recycling of human mitochondrial ribosomes. (PMID:33264405)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	gtpbp6	ENSDARG00000061091
mus_musculus	Gtpbp6	ENSMUSG00000033434
rattus_norvegicus	Gtpbp6	ENSRNOG00000062521
drosophila_melanogaster	CG5116	FBGN0039339

Protein

Protein identifiers

Putative GTP-binding protein 6 — O43824 (reviewed: O43824)

Alternative names: Pseudoautosomal GTP-binding protein-like

All UniProt accessions (1): O43824

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Ubiquitously expressed.

Miscellaneous. The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes.

Similarity. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. HflX GTPase family.

RefSeq proteins (1): NP_036359* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006073	GTP-bd	Domain
IPR016496	GTPase_HflX	Family
IPR025121	GTPase_HflX_N	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR030394	G_HFLX_dom	Domain
IPR032305	GTP-bd_M	Domain
IPR042108	GTPase_HflX_N_sf	Homologous_superfamily

Pfam: PF01926, PF13167, PF16360

UniProt features (18 total): binding site 7, sequence conflict 5, compositionally biased region 3, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
7OF6	ELECTRON MICROSCOPY	2.6
7OF2	ELECTRON MICROSCOPY	2.7
7OF4	ELECTRON MICROSCOPY	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43824-F1	77.92	0.38

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 (7): 349–352; 418–421; 437–439; 301–308; 308; 327–331; 329

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 98 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_RIBOSOME_BIOGENESIS, GOBP_RIBOSOME_ASSEMBLY, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN, SANSOM_APC_TARGETS_REQUIRE_MYC, NUYTTEN_NIPP1_TARGETS_DN, MODULE_159, GOMF_RIBONUCLEOPROTEIN_COMPLEX_BINDING, GOMF_RIBOSOME_BINDING

GO Biological Process (1): mitochondrial large ribosomal subunit assembly (GO:1902775)

GO Molecular Function (5): GTP binding (GO:0005525), ribosome binding (GO:0043022), ribosomal large subunit binding (GO:0043023), metal ion binding (GO:0046872), nucleotide binding (GO:0000166)

GO Cellular Component (2): cytoplasm (GO:0005737), mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribosomal large subunit assembly	1
mitochondrial ribosome assembly	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoprotein complex binding	1
ribosome binding	1
cation binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1694 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GTPBP6	GTPBP4	Q9BZE4	832
GTPBP6	MALSU1	Q96EH3	769
GTPBP6	GTPBP10	A4D1E9	763
GTPBP6	PLCXD1	Q9NUJ7	754
GTPBP6	MTG2	Q9H4K7	747
GTPBP6	ASMTL	O95671	728
GTPBP6	PPP2R3B	Q9Y5P8	698
GTPBP6	DDX28	Q9NUL7	691
GTPBP6	MTG1	Q9BT17	690
GTPBP6	GTPBP8	Q8N3Z3	667
GTPBP6	AKAP17A	Q02040	666
GTPBP6	DHRSX	Q8N5I4	630
GTPBP6	MTERF4	Q7Z6M4	616
GTPBP6	NSUN4	Q96CB9	602
GTPBP6	MRRF	Q96E11	595

IntAct

44 interactions, top by confidence:

A	B	Type	Score
CD79A	METTL15	psi-mi:“MI:0914”(association)	0.530
SDF4	GTPBP6	psi-mi:“MI:0914”(association)	0.530
BPNT1	GTPBP10	psi-mi:“MI:0914”(association)	0.530
YBEY	NME4	psi-mi:“MI:0914”(association)	0.530
PSME1	POLR3A	psi-mi:“MI:0914”(association)	0.530
ATP5F1D	NDUFB5	psi-mi:“MI:0914”(association)	0.530
EMILIN1	METTL15	psi-mi:“MI:0914”(association)	0.530
ZNRD2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
GTPBP6	RPL24	psi-mi:“MI:0915”(physical association)	0.400
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
RIPK4	VWA8	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
MRPL12		psi-mi:“MI:0914”(association)	0.350
	AP3B1	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
ATG16L1		psi-mi:“MI:0914”(association)	0.350
HLA-DRA	TMEM223	psi-mi:“MI:0914”(association)	0.350
PIPSL	C1orf226	psi-mi:“MI:0914”(association)	0.350
LURAP1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
MAGEA9	CIBAR1	psi-mi:“MI:0914”(association)	0.350
FAXC	METTL15	psi-mi:“MI:0914”(association)	0.350
DGCR2	CCDC85C	psi-mi:“MI:0914”(association)	0.350
DKK3	MYO9A	psi-mi:“MI:0914”(association)	0.350
THBS3	APBB1	psi-mi:“MI:0914”(association)	0.350
MRPS17	POLRMT	psi-mi:“MI:0914”(association)	0.350
MRPL23	GTPBP6	psi-mi:“MI:0914”(association)	0.350

BioGRID (86): GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-RNA), GTPBP6 (Affinity Capture-RNA), GTPBP6 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B3PEJ0, A0A2K3DU55, A2XFU5, A2XU53, A2YQ58, A4HUY0, A4I1F7, A4RPM5, A8I2V9, B6TN12, B8A031, B8AA76, B8B016, B9FK36, C0PN26, C5XKZ1, C5Y9R0, E1BRE2, E2RDZ6, O43824, P18080, P52506, P52507, P84172, Q0D3F2, Q0J705, Q10MI9, Q2KIF8, Q2KNB4, Q2QMG2, Q3U6U5, Q5AQE4, Q5R6G3, Q5ZAQ2, Q5ZHX9, Q6H4G3, Q6L534, Q6NZB1, Q6Z4A7, Q74ZW4

Diamond homologs: A0L4B2, A0LPF9, A1RY30, A2BLW4, A5EY43, A5GNK6, A5IKX2, A6H294, A6TQJ6, A7HIF8, A8FRU4, A9A623, A9H253, B0K414, B0KAB8, B0T310, B1I5V8, B1KGH1, B1LA53, B1ZZ37, B2FNR1, B2U9V3, B2UPE7, B3QZ96, B3R1J8, B4RD64, B4SSW8, B4UIU2, B5EJF7, B7JC34, B8FUR9, B8I179, B8JBP2, B9DNE7, B9KZ43, C0QLE9, C1F407, C5BLV6, C6E2H7, D3FTV4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 57 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Translation	6	10.6×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
translation	6	12.3×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

761 predictions. Top by Δscore:

Variant	Effect	Δscore
X:305211:CGCGT:C	acceptor_gain	1.0000
X:305213:CGT:C	acceptor_gain	1.0000
X:305215:T:C	acceptor_gain	1.0000
X:305215:T:TC	acceptor_gain	1.0000
X:307355:CTCA:C	donor_loss	1.0000
X:307356:TCA:T	donor_loss	1.0000
X:307357:CACCT:C	donor_loss	1.0000
X:307358:AC:A	donor_loss	1.0000
X:307728:TCA:T	donor_loss	1.0000
X:307729:CACCC:C	donor_loss	1.0000
X:307730:AC:A	donor_gain	1.0000
X:307731:CC:C	donor_gain	1.0000
X:305194:CCAG:C	acceptor_gain	0.9900
X:305195:CAGC:C	acceptor_gain	0.9900
X:305196:A:T	acceptor_gain	0.9900
X:305205:CAGA:C	acceptor_gain	0.9900
X:305208:A:AC	acceptor_gain	0.9900
X:305208:A:C	acceptor_gain	0.9900
X:305214:G:GC	acceptor_gain	0.9900
X:305217:G:GC	acceptor_gain	0.9900
X:305219:A:AC	acceptor_gain	0.9900
X:305219:A:C	acceptor_gain	0.9900
X:307508:TGTAC:T	acceptor_gain	0.9900
X:307510:TAC:T	acceptor_gain	0.9900
X:307511:AC:A	acceptor_gain	0.9900
X:307512:CC:C	acceptor_gain	0.9900
X:307513:C:CC	acceptor_gain	0.9900
X:307513:C:CG	acceptor_loss	0.9900
X:307514:T:C	acceptor_loss	0.9900
X:307730:A:AC	donor_gain	0.9900

AlphaMissense

6586 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
Y:311563:A:C	F327L	0.993
Y:311563:A:T	F327L	0.993
Y:311565:A:G	F327L	0.993
Y:311449:G:C	F365L	0.992
Y:311449:G:T	F365L	0.992
Y:311451:A:G	F365L	0.992
Y:305181:C:G	A482P	0.991
Y:311485:G:C	F353L	0.991
Y:311485:G:T	F353L	0.991
Y:311487:A:G	F353L	0.991
Y:307749:C:A	K419N	0.989
Y:307749:C:G	K419N	0.989
Y:311486:A:G	F353S	0.989
Y:312780:C:T	G301E	0.989
Y:315266:A:T	V174D	0.989
Y:311565:A:T	F327I	0.988
Y:311627:C:T	G306E	0.988
Y:311564:A:C	F327C	0.985
Y:311627:C:A	G306V	0.985
Y:312781:C:G	G301R	0.985
Y:312781:C:T	G301R	0.985
Y:315002:A:G	W193R	0.985
Y:315002:A:T	W193R	0.985
Y:317031:C:G	A124P	0.985
Y:305174:A:T	V484D	0.984
Y:311499:C:G	D349H	0.984
Y:311623:C:A	K307N	0.984
Y:311623:C:G	K307N	0.984
Y:314944:G:T	A212D	0.984
Y:311498:T:A	D349V	0.983

dbSNP variants (sampled 300 via entrez): RS1000079997 (X:307386 A>G), RS1000157476 (X:310832 A>G), RS1000637681 (X:310951 G>A,C), RS1000675767 (X:306377 C>T), RS1001171690 (X:306183 G>A), RS1001798100 (X:306138 A>C,G), RS1002005441 (X:309641 C>T), RS1002516783 (X:309382 T>C), RS1002580836 (X:313229 C>T), RS1002909325 (X:305375 G>A,C), RS1002940360 (X:305481 C>G), RS1003112505 (X:308590 G>A,C), RS1003427511 (X:308774 A>G), RS1004146563 (X:308515 C>T), RS1005802417 (X:304472 A>G,T)

Disease associations

OMIM: gene MIM:300124 | 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

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
chromium hexavalent ion	increases expression, decreases expression, increases abundance	2
Cadmium Chloride	increases expression	2
trichostatin A	affects expression	1
zinc chromate	decreases expression, increases abundance	1
potassium chromate(VI)	increases expression	1
cupric chloride	increases expression	1
nickel sulfate	increases expression	1
2,3-dimethoxy-1,4-naphthoquinone	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Air Pollutants	increases abundance, affects expression	1
Antimony	increases expression	1
Antimony Potassium Tartrate	increases expression	1
Cadmium	increases expression	1
Cisplatin	decreases expression	1
Estradiol	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Ouabain	increases expression	1
Ozone	affects expression, increases abundance	1
Potassium Dichromate	increases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Toluene	decreases methylation, increases expression	1
Valproic Acid	increases methylation	1
Sodium Selenite	increases expression	1

Clinical trials (associated diseases)

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