GLTP

Summary

GLTP (glycolipid transfer protein, HGNC:24867) is a protein-coding gene on chromosome 12q24.11, encoding Glycolipid transfer protein (Q9NZD2). Accelerates the intermembrane transfer of various glycolipids.

The protein encoded by this gene is similar to bovine and porcine proteins which accelerate transfer of certain glycosphingolipids and glyceroglycolipids between membranes. It is thought to be a cytoplasmic protein.

Source: NCBI Gene 51228 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 48 total
• MANE Select transcript: NM_016433

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24867
Approved symbol	GLTP
Name	glycolipid transfer protein
Location	12q24.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000139433
Ensembl biotype	protein_coding
OMIM	608949
Entrez	51228

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 nonsense_mediated_decay

ENST00000318348, ENST00000536390, ENST00000537066, ENST00000540772, ENST00000544393, ENST00000885089, ENST00000928213, ENST00000965361, ENST00000965362

RefSeq mRNA: 1 — MANE Select: NM_016433 NM_016433

CCDS: CCDS9136

Canonical transcript exons

ENST00000318348 — 5 exons

Exon	Start	End
ENSE00001277972	109850945	109852737
ENSE00001277979	109880272	109880541
ENSE00003464018	109858683	109858741
ENSE00003602203	109855619	109855769
ENSE00003658956	109857526	109857659

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 99.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.4416 / max 1257.2362, expressed in 1808 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
133204	14.8428	1789
133205	11.9810	1738
133201	5.9999	1571
133203	2.8615	1423
133202	0.7563	451

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	99.79	gold quality
gingival epithelium	UBERON:0001949	99.73	gold quality
gingiva	UBERON:0001828	99.68	gold quality
penis	UBERON:0000989	99.67	gold quality
upper leg skin	UBERON:0004262	99.61	gold quality
mammalian vulva	UBERON:0000997	99.59	gold quality
pharyngeal mucosa	UBERON:0000355	99.51	gold quality
oral cavity	UBERON:0000167	99.34	gold quality
lower esophagus mucosa	UBERON:0035834	99.28	gold quality
skin of hip	UBERON:0001554	99.22	gold quality
esophagus squamous epithelium	UBERON:0006920	99.20	gold quality
nasal cavity epithelium	UBERON:0005384	99.19	gold quality
ileal mucosa	UBERON:0000331	99.13	gold quality
nipple	UBERON:0002030	98.95	gold quality
pancreatic ductal cell	CL:0002079	98.77	gold quality
inferior vagus X ganglion	UBERON:0005363	98.66	gold quality
esophagus mucosa	UBERON:0002469	98.65	gold quality
body of tongue	UBERON:0011876	98.65	gold quality
zone of skin	UBERON:0000014	98.48	gold quality
skin of abdomen	UBERON:0001416	98.47	gold quality
skin of leg	UBERON:0001511	98.32	gold quality
spinal cord	UBERON:0002240	98.19	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.17	gold quality
endothelial cell	CL:0000115	98.04	gold quality
subthalamic nucleus	UBERON:0001906	97.81	gold quality
kidney epithelium	UBERON:0004819	97.79	gold quality
medial globus pallidus	UBERON:0002477	97.71	gold quality
globus pallidus	UBERON:0001875	97.69	gold quality
tongue	UBERON:0001723	97.63	gold quality
cartilage tissue	UBERON:0002418	97.63	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	1596.41
E-HCAD-1	yes	218.55
E-CURD-114	yes	53.89
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1, SP3

miRNA regulators (miRDB)

68 targeting GLTP, 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-1252-5P	100.00	69.80	2774
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-8087	99.90	69.55	1351

Literature-anchored findings (GeneRIF, showing 25)

• This paper shows that the rate at which glycolipid transfer protein catalyzes the intermembrane transfer of glycolipids is greatly diminished by increasing the charged lipid content of membranes. (PMID:10653652)
• This paper describes the first cloning of the cDNAs encoding the glycolipid transfer proteins of bovine and porcine brain. The cDNAs are highly homologous to the human cDNA (AF209704). (PMID:10671554)
• First insights into human GLTP structural dynamics by fluorescence spectroscopy, including global conformational changes that accompany GLTP folding into an active conformational state. (PMID:15287756)
• crystal structures of apo-GLTP (1.65 A resolution) and lactosylceramide-bound (1.95 A) GLTP, in which the bound glycosphingolipid is sandwiched, after adaptive recognition, within a previously unknown two-layer all-alpha-helical topology (PMID:15329726)
• The rate-limiting step for glycolipid transfer protein (GLTP) action appears to be the surface processes leading to the GLTP-glycosphingolipid complex formation and release associated with a shuttle/carrier mode of action. (PMID:15504043)
• analysis of the liganding site in human glycolipid transfer protein (PMID:15901739)
• GLTP is not likely involved in the de novo synthesis of glycosphingolipids, but could rather have a role as a glycolipid sensor for the cellular levels of glucosylceramide. (PMID:17980653)
• A single-copy 5-exon/4-intron GLTP gene at 12q24.11 was the highly conserved, transcript source of active GLTP in human and vertebrate cells. An intronless GLTP gene at 11p15.1 was transcriptionally silent, primate-specific, and yielded inactive protein. (PMID:18261224)
• Active transcription was found for 12q24.11 GLTP but 11p15.1 GLTP was transcriptionally silent. (PMID:18261224)
• transgenic expression in Arabidopsis thaliana of human GLTP partially suppressed the phenotype of the acd11 null mutant, resulting in delayed programmed cell death development and plant survival (PMID:18657186)
• Glycolipid acquisition by human glycolipid transfer protein dramatically alters intrinsic tryptophan fluorescence: insights into glycolipid binding affinity. (PMID:19270338)
• GLTP and VAP-A were shown to interact. (PMID:19665998)
• remarkable versatility for Trp, providing three distinct intramolecular functions in the novel amphitropic GLTP fold (PMID:20959104)
• This study represents the first characterization of any Gltp gene promoter and links human GLTP expression to sphingolipid homeostasis through ceramide (PMID:20974858)
• findings represent the first known phenotypic changes triggered by GLTP overexpression and regulated by direct interaction with a p120-catenin protein family member (PMID:21625605)
• The paper describes the complete primary amino acid sequence of glycolipid transfer protein (GLTP) from porcine brain. The sequence was determined by Edman degradation. (PMID:2190982)
• Comprehensive analysis of the dimerization interfaces discloses -helices 6 and 2 and the protein C-terminus (C-end) as three specific structural elements that are simultaneously involved in dimer formation and ligand binding by GLTP. (PMID:23519669)
• GLTP mediates non-vesicular transport of ganglioside GM1 between native membranes (PMID:23555818)
• GLTP not only could be a significant player in cellular sphingolipid metabolism, but also could have a much broader role in the overall lipid metabolism. (PMID:24824606)
• GLTP was specifically labeled by either XLA or XLB GlcCer cross-linker during this process, together with a (the same) small subset of microsomal proteins. These cross-linkers will serve to probe physiologically relevant GlcCer-interacting cellular proteins (PMID:27412675)
• HOXA5, HOXB6, and GLTP were direct target genes of MIR196B in CRC cells. (PMID:29532406)
• Four bulky, conserved hydrophobic residues involved in “sensor-like” interactions with lipid chains in protein hydrophobic pockets and FF motifs in GLTP and FAPP2. (PMID:30206120)
• Emerging roles for human glycolipid transfer protein superfamily members in the regulation of autophagy, inflammation, and cell death. (PMID:32339554)
• Glycolipid transfer protein knockout disrupts vesicle trafficking to the plasma membrane. (PMID:36924944)
• Role of Gltp in Maturation of Oligodendrocytes Under the Regulation of Nkx2.2. (PMID:37191854)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	gltpa	ENSDARG00000061921
danio_rerio	gltpb	ENSDARG00000077962
mus_musculus	Gltp	ENSMUSG00000011884
rattus_norvegicus	Gltp	ENSRNOG00000001192
drosophila_melanogaster	CG6299	FBGN0030641
caenorhabditis_elegans	tag-296	WBGENE00018632
caenorhabditis_elegans		WBGENE00022347
caenorhabditis_elegans	F49D11.10	WBGENE00045433

Paralogs (5): PLEKHA8 (ENSG00000106086), CERT1 (ENSG00000113163), PLEKHA3 (ENSG00000116095), GLTPD2 (ENSG00000182327), CPTP (ENSG00000224051)

Protein

Protein identifiers

Glycolipid transfer protein — Q9NZD2 (reviewed: Q9NZD2)

All UniProt accessions (4): Q9NZD2, F5GZ49, F5H0U5, H0YFS9

UniProt curated annotations — full annotation on UniProt →

Function. Accelerates the intermembrane transfer of various glycolipids. Catalyzes the transfer of various glycosphingolipids between membranes but does not catalyze the transfer of phospholipids. May be involved in the intracellular translocation of glucosylceramides.

Subunit / interactions. Monomer.

Subcellular location. Cytoplasm.

Tissue specificity. Detected in fibroblasts (at protein level). Detected in fibroblasts and in various cancer cell lines.

Similarity. Belongs to the GLTP family.

RefSeq proteins (1): NP_057517* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR014830	Glycolipid_transfer_prot_dom	Domain
IPR036497	GLTP_sf	Homologous_superfamily

Pfam: PF08718

UniProt features (40 total): helix 14, mutagenesis site 13, turn 3, binding site 3, repeat 2, initiator methionine 1, chain 1, strand 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

22 structures.

PDB	Method	Resolution (Å)
3RZN	X-RAY DIFFRACTION	1.1
4GH0	X-RAY DIFFRACTION	1.35
3S0K	X-RAY DIFFRACTION	1.4
4H2Z	X-RAY DIFFRACTION	1.45
3RWV	X-RAY DIFFRACTION	1.5
3S0I	X-RAY DIFFRACTION	1.5
1SWX	X-RAY DIFFRACTION	1.65
4GIX	X-RAY DIFFRACTION	1.8
2EUK	X-RAY DIFFRACTION	1.85
4GHP	X-RAY DIFFRACTION	1.9
1SX6	X-RAY DIFFRACTION	1.95
2EVT	X-RAY DIFFRACTION	1.99
2EVD	X-RAY DIFFRACTION	2
4GJQ	X-RAY DIFFRACTION	2
3RIC	X-RAY DIFFRACTION	2.1
4GXD	X-RAY DIFFRACTION	2.1
2EVL	X-RAY DIFFRACTION	2.2
2EVS	X-RAY DIFFRACTION	2.2
2EUM	X-RAY DIFFRACTION	2.3
4GXG	X-RAY DIFFRACTION	2.4
4GVT	X-RAY DIFFRACTION	2.9
4GHS	X-RAY DIFFRACTION	3.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NZD2-F1	94.52	0.87

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 (3): 48–55; 140; 207

Post-translational modifications (1): 2

Mutagenesis-validated functional residues (13):

Position	Phenotype
48	significant inactivation; 15% residual activity.
52	significant inactivation; 15% residual activity.
55	no loss of activity; 90-97% residual activity.
96	almost complete inactivation; 1-3% residual activity. no effect on autophagy.
96	partial inactivation; 63% residual activity.
103	about 25% decrease in activity.
136	significant inactivation; 5% residual acti vity.
140	almost complete inactivation; 1-3% residual activity.
148	about 50% decrease in activity.
165	46% decrease in activity.
183	no loss of activity; 90% residual activity.
207	no loss of activity; 90-97% residual activity.
45	18% decrease in activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9845576	Glycosphingolipid transport

MSigDB gene sets: 169 (showing top): GCM_MAP4K4, GOBP_RESPONSE_TO_IMMOBILIZATION_STRESS, HUMMERICH_SKIN_CANCER_PROGRESSION_UP, BEIER_GLIOMA_STEM_CELL_DN, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, BILD_HRAS_ONCOGENIC_SIGNATURE, GOBP_ORGANIC_ANION_TRANSPORT, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, HNF4_01, PPAR_DR1_Q2, GOBP_PHOSPHOLIPID_TRANSPORT, MILI_PSEUDOPODIA_CHEMOTAXIS_UP, GOBP_MEMBRANE_ORGANIZATION, WALLACE_PROSTATE_CANCER_RACE_DN, GOBP_LIPID_LOCALIZATION

GO Biological Process (6): ceramide transport (GO:0035627), response to immobilization stress (GO:0035902), intermembrane lipid transfer (GO:0120009), lipid transport (GO:0006869), glycolipid transport (GO:0046836), ceramide 1-phosphate transport (GO:1902389)

GO Molecular Function (8): lipid binding (GO:0008289), glycolipid transfer activity (GO:0017089), identical protein binding (GO:0042802), glycolipid binding (GO:0051861), lipid transfer activity (GO:0120013), ceramide 1-phosphate binding (GO:1902387), ceramide 1-phosphate transfer activity (GO:1902388), protein binding (GO:0005515)

GO Cellular Component (2): cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid transport	3
binding	2
cellular anatomical structure	2
nitrogen compound transport	1
response to stress	1
membrane organization	1
transport	1
lipid localization	1
carbohydrate derivative transport	1
phospholipid transport	1
ceramide transport	1
glycolipid transport	1
glycolipid binding	1
lipid transfer activity	1
protein binding	1
lipid binding	1
carbohydrate derivative binding	1
transporter activity	1
lipid carrier activity	1
intermembrane lipid transfer	1
phospholipid binding	1
anion binding	1
ceramide binding	1
phospholipid transfer activity	1
ceramide transfer activity	1
ceramide 1-phosphate transport	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

632 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLTP	PLEKHA3	Q9HB20	902
GLTP	CPTP	Q5TA50	709
GLTP	CERT1	Q9Y5P4	657
GLTP	CEL	P19835	638
GLTP	PLEK2	Q9NYT0	610
GLTP	PLEK	P08567	599
GLTP	GLTPD2	A6NH11	588
GLTP	UGCG	Q16739	572
GLTP	CERK	Q8TCT0	424
GLTP	RFLNA	Q6ZTI6	418
GLTP	MMAB	Q96EY8	418
GLTP	VAPA	Q9P0L0	411
GLTP	ZDHHC9	Q9Y397	402
GLTP	PTPRN	Q16849	401
GLTP	OSBP	P22059	400

IntAct

17 interactions, top by confidence:

A	B	Type	Score
CMTM5	GLTP	psi-mi:“MI:0915”(physical association)	0.670
GLTP	CMTM5	psi-mi:“MI:0915”(physical association)	0.670
GLTP	GLTP	psi-mi:“MI:0407”(direct interaction)	0.560
GLTP	AMD1	psi-mi:“MI:0914”(association)	0.530
STX17	A2ML1	psi-mi:“MI:0914”(association)	0.350
HCN1	A2ML1	psi-mi:“MI:0914”(association)	0.350
CCR1	UBA6	psi-mi:“MI:0914”(association)	0.350
FNDC5	A2ML1	psi-mi:“MI:0914”(association)	0.350
MBNL1	A2ML1	psi-mi:“MI:0914”(association)	0.350
GLTP	POF1B	psi-mi:“MI:0914”(association)	0.350
SMPD2	A2ML1	psi-mi:“MI:0914”(association)	0.350
GLTP		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (34): CMTM5 (Two-hybrid), GLTP (Two-hybrid), STARD7 (Affinity Capture-MS), ASPSCR1 (Affinity Capture-MS), SHKBP1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), GLTP (Affinity Capture-MS), GLTP (Affinity Capture-MS), SHKBP1 (Affinity Capture-MS), STARD7 (Affinity Capture-MS), ASPSCR1 (Affinity Capture-MS), GLTP (Affinity Capture-MS), GLTP (Affinity Capture-MS), AMD1 (Affinity Capture-MS), GLTP (Affinity Capture-MS)

ESM2 similar proteins: A0A223HDI2, A2BG43, B0BLT4, B0BNM9, B0YN54, O22797, O64587, O94360, P40124, P68265, P68266, Q01518, Q08163, Q0VCQ0, Q2WBN3, Q3SYV4, Q3T1J9, Q4R4I6, Q54XJ0, Q5F495, Q5HZ92, Q5RAE0, Q5RDB1, Q5TA50, Q5XIS2, Q63ZQ3, Q66JG2, Q6DBQ8, Q6NLQ3, Q6NU44, Q6PEB6, Q6Z6S1, Q70IA6, Q7L9L4, Q8BPB0, Q8BS40, Q8GYX0, Q8VI63, Q921Y0, Q949G5

Diamond homologs: A0A223HDI2, A2BG43, B0BLT4, B0BNM9, B0YN54, D2KC46, D3ZY60, F1MS15, O95397, P68265, P68266, Q5U3N0, Q63ZQ3, Q6NU44, Q80W71, Q96JA3, Q9JL62, Q9NZD2, O22797, O14340, P16258, P22059, P35845, Q12451, Q3B7Z2, Q5M7Y0, Q5QNQ6, Q5R6M6, Q6NRZ4, Q6NTN5, Q6P3Q6, Q6VVX2, Q8C115, Q8IVE3, Q969R2, Q9EQG9, Q9ERS4, Q9GKI7, Q9HB20, Q9SAF0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1271 predictions. Top by Δscore:

Variant	Effect	Δscore
12:109852750:A:T	acceptor_gain	1.0000
12:109855614:CTCA:C	donor_loss	1.0000
12:109855615:TCACC:T	donor_loss	1.0000
12:109855616:CACC:C	donor_loss	1.0000
12:109855617:A:AC	donor_gain	1.0000
12:109855618:C:CC	donor_gain	1.0000
12:109855768:CT:C	acceptor_gain	1.0000
12:109855770:C:CC	acceptor_gain	1.0000
12:109855778:C:CT	acceptor_gain	1.0000
12:109855778:C:T	acceptor_gain	1.0000
12:109855779:A:T	acceptor_gain	1.0000
12:109857559:A:AC	donor_gain	1.0000
12:109857560:C:CC	donor_gain	1.0000
12:109857582:CATTT:C	donor_gain	1.0000
12:109880266:GCTCA:G	donor_loss	1.0000
12:109880267:CTCAC:C	donor_loss	1.0000
12:109880268:TCACC:T	donor_loss	1.0000
12:109880269:CAC:C	donor_loss	1.0000
12:109880270:A:AC	donor_gain	1.0000
12:109880271:C:CC	donor_gain	1.0000
12:109852502:G:A	donor_gain	0.9900
12:109852734:CTGC:C	acceptor_gain	0.9900
12:109852737:CC:C	acceptor_loss	0.9900
12:109852738:C:CC	acceptor_gain	0.9900
12:109852739:T:C	acceptor_gain	0.9900
12:109852739:T:TC	acceptor_gain	0.9900
12:109852745:C:CT	acceptor_gain	0.9900
12:109852746:A:T	acceptor_gain	0.9900
12:109852749:C:CT	acceptor_gain	0.9900
12:109855613:GCTCA:G	donor_loss	0.9900

AlphaMissense

1376 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:109855769:T:A	R99S	0.998
12:109855769:T:G	R99S	0.998
12:109857526:C:G	R99T	0.997
12:109857532:A:G	L97P	0.997
12:109857534:C:A	W96C	0.997
12:109857534:C:G	W96C	0.997
12:109857536:A:G	W96R	0.997
12:109857536:A:T	W96R	0.997
12:109855659:A:T	L136H	0.996
12:109855764:A:G	L101P	0.996
12:109855622:G:C	F148L	0.995
12:109855622:G:T	F148L	0.995
12:109855624:A:G	F148L	0.995
12:109855648:G:C	H140D	0.995
12:109855743:A:G	L108P	0.995
12:109852733:G:T	A151E	0.994
12:109855648:G:T	H140N	0.994
12:109855674:G:T	A131D	0.994
12:109855683:G:T	A128D	0.994
12:109855757:G:C	F103L	0.994
12:109855757:G:T	F103L	0.994
12:109855759:A:G	F103L	0.994
12:109857526:C:A	R99I	0.994
12:109857541:A:G	L94P	0.994
12:109857592:T:A	E77V	0.994
12:109858702:T:A	D48V	0.994
12:109858703:C:G	D48H	0.994
12:109858719:A:C	F42L	0.994
12:109858719:A:T	F42L	0.994
12:109858721:A:G	F42L	0.994

dbSNP variants (sampled 300 via entrez): RS1000163398 (12:109865887 T>C), RS1000181545 (12:109873887 T>G), RS1000249621 (12:109865913 G>T), RS1000363546 (12:109855342 C>T), RS1000394898 (12:109855621 G>A), RS1000529423 (12:109871249 A>G,T), RS1000544389 (12:109877044 G>A,C), RS1000625233 (12:109864401 G>A), RS1000672934 (12:109870112 A>C), RS1000700568 (12:109856872 A>G), RS1000731378 (12:109857243 C>T), RS1000760641 (12:109863953 G>C), RS1000810403 (12:109880688 C>T), RS1000919728 (12:109863712 G>A), RS1000967818 (12:109872566 A>G)

Disease associations

OMIM: gene MIM:608949 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST000753_3	Metabolic syndrome	3.000000e-06
GCST008103_145	Bipolar disorder	3.000000e-06
GCST90002384_315	Hemoglobin	8.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0000195	metabolic syndrome
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004509	hemoglobin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic Trioxide	affects binding, decreases reaction, decreases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Valproic Acid	affects expression, increases expression	2
Aflatoxin B1	increases expression	2
shuanghuang shengbai	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenite	increases expression	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	increases methylation	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Furaldehyde	affects cotreatment, affects localization, increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Progesterone	affects cotreatment, increases expression	1
Rotenone	increases expression	1
Smoke	decreases expression	1
Sodium Chloride	affects cotreatment, affects localization, increases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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