GLTPD2

Summary

GLTPD2 (glycolipid transfer protein domain containing 2, HGNC:33756) is a protein-coding gene on chromosome 17p13.2, encoding Glycolipid transfer protein domain-containing protein 2 (A6NH11).

Predicted to enable ceramide 1-phosphate binding activity and ceramide 1-phosphate transfer activity. Predicted to be involved in ceramide transport and intermembrane lipid transfer. Predicted to be located in cytoplasm. Predicted to be active in cytosol.

Source: NCBI Gene 388323 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_001014985

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33756
Approved symbol	GLTPD2
Name	glycolipid transfer protein domain containing 2
Location	17p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000182327
Ensembl biotype	protein_coding
OMIM	620824
Entrez	388323

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000331264

RefSeq mRNA: 2 — MANE Select: NM_001014985 NM_001014985, NM_001375801

CCDS: CCDS32534

Canonical transcript exons

ENST00000331264 — 4 exons

Exon	Start	End
ENSE00001299628	4789511	4789677
ENSE00001320636	4789759	4790589
ENSE00001326381	4788964	4789117
ENSE00001488620	4789226	4789290

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 94.09.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.5824 / max 90.3084, expressed in 162 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
158939	0.2920	62
158942	0.2031	107
158941	0.0550	25
158940	0.0324	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	94.09	gold quality
liver	UBERON:0002107	90.78	gold quality
adult mammalian kidney	UBERON:0000082	81.30	gold quality
duodenum	UBERON:0002114	77.87	gold quality
kidney	UBERON:0002113	74.14	gold quality
cortex of kidney	UBERON:0001225	69.95	gold quality
prefrontal cortex	UBERON:0000451	67.96	gold quality
cortical plate	UBERON:0005343	67.58	gold quality
metanephros cortex	UBERON:0010533	66.73	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	66.48	gold quality
frontal cortex	UBERON:0001870	65.78	gold quality
monocyte	CL:0000576	65.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	65.37	gold quality
superior frontal gyrus	UBERON:0002661	64.93	gold quality
cerebellum	UBERON:0002037	64.84	gold quality
cerebellar hemisphere	UBERON:0002245	64.82	gold quality
cerebellar cortex	UBERON:0002129	64.81	gold quality
Brodmann (1909) area 9	UBERON:0013540	64.81	gold quality
leukocyte	CL:0000738	64.78	gold quality
hypothalamus	UBERON:0001898	64.76	gold quality
skin of leg	UBERON:0001511	64.63	gold quality
cerebral cortex	UBERON:0000956	64.13	gold quality
nucleus accumbens	UBERON:0001882	63.82	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	63.78	gold quality
zone of skin	UBERON:0000014	63.65	gold quality
anterior cingulate cortex	UBERON:0009835	63.54	gold quality
small intestine	UBERON:0002108	63.26	gold quality
brain	UBERON:0000955	62.93	gold quality
small intestine Peyer’s patch	UBERON:0003454	62.81	gold quality
skin of abdomen	UBERON:0001416	62.79	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

2 targeting GLTPD2, 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-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	cptp	ENSDARG00000052537
danio_rerio	gltpd2a	ENSDARG00000054218
danio_rerio	gltpd2b	ENSDARG00000067889
mus_musculus	Gltpd2	ENSMUSG00000046811
rattus_norvegicus	Gltpd2	ENSRNOG00000070553
drosophila_melanogaster	CG6299	FBGN0030641
drosophila_melanogaster	CG30392	FBGN0050392
caenorhabditis_elegans		WBGENE00010666
caenorhabditis_elegans	tag-296	WBGENE00018632
caenorhabditis_elegans		WBGENE00022347
caenorhabditis_elegans	F49D11.10	WBGENE00045433

Paralogs (5): PLEKHA8 (ENSG00000106086), CERT1 (ENSG00000113163), PLEKHA3 (ENSG00000116095), GLTP (ENSG00000139433), CPTP (ENSG00000224051)

Protein

Protein identifiers

Glycolipid transfer protein domain-containing protein 2 — A6NH11 (reviewed: A6NH11)

All UniProt accessions (1): A6NH11

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GLTP family.

RefSeq proteins (2): NP_001014985, NP_001362730 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR014830	Glycolipid_transfer_prot_dom	Domain
IPR036497	GLTP_sf	Homologous_superfamily

Pfam: PF08718

UniProt features (5 total): sequence conflict 3, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NH11-F1	83.14	0.65

Functional residue map

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

Glycosylation sites (1): 276

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): GOBP_NEGATIVE_REGULATION_OF_INTERLEUKIN_1_PRODUCTION, GOBP_INTERLEUKIN_1_PRODUCTION, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_CYTOKINE_PRODUCTION, GOBP_ORGANIC_ANION_TRANSPORT, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, GOBP_LIPID_LOCALIZATION, GOBP_NEGATIVE_REGULATION_OF_CYTOKINE_PRODUCTION, GOMF_LIPID_TRANSPORTER_ACTIVITY, GOMF_AMIDE_BINDING, GOMF_PHOSPHOLIPID_TRANSPORTER_ACTIVITY, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING

GO Biological Process (4): negative regulation of interleukin-1 beta production (GO:0032691), ceramide transport (GO:0035627), intermembrane lipid transfer (GO:0120009), ceramide 1-phosphate transport (GO:1902389)

GO Molecular Function (3): ceramide 1-phosphate binding (GO:1902387), ceramide 1-phosphate transfer activity (GO:1902388), lipid transfer activity (GO:0120013)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid transport	2
cellular anatomical structure	2
interleukin-1 beta production	1
regulation of interleukin-1 beta production	1
negative regulation of interleukin-1 production	1
nitrogen compound transport	1
membrane organization	1
phospholipid transport	1
ceramide transport	1
phospholipid binding	1
anion binding	1
ceramide binding	1
phospholipid transfer activity	1
ceramide transfer activity	1
ceramide 1-phosphate transport	1
transporter activity	1
lipid carrier activity	1
intermembrane lipid transfer	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

292 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLTPD2	GLTP	Q9NZD2	588
GLTPD2	A0A1B0GU03	A0A1B0GU03	507
GLTPD2	ILKAP	Q9H0C8	506
GLTPD2	ISCA2	Q86U28	470
GLTPD2	PLEKHA8	Q96JA3	431
GLTPD2	EIF1AD	Q8N9N8	399
GLTPD2	NOL9	Q5SY16	384
GLTPD2	PGBD1	Q96JS3	360
GLTPD2	CERS4	Q9HA82	342
GLTPD2	ZNF488	Q96MN9	342
GLTPD2	OSGIN1	Q9UJX0	342
GLTPD2	KHDRBS1	Q07666	334
GLTPD2	ADAM30	Q9UKF2	321
GLTPD2	ZNF385D	Q9H6B1	320
GLTPD2	ACOXL	Q9NUZ1	320

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GLTPD2		psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A2ARS0, A6NH11, A6QQ91, C9JTQ0, D3ZVB0, D4A929, G3MZC5, O75064, O95996, P16386, P46062, P58660, Q02011, Q08DF2, Q16619, Q29RK8, Q2TBW5, Q2VPB7, Q3TAP4, Q3U0S6, Q3U1Y4, Q562E7, Q5TA50, Q5U651, Q60753, Q63086, Q64375, Q68J42, Q6P9B9, Q6ZS72, Q86YV0, Q8BH02, Q8BQU6, Q8C2K5, Q8CHT3, Q8K0R6, Q8K2B0, Q8N9M5, Q8VD26, Q92791

Diamond homologs: A6NH11, Q0VCQ0, Q5HZ92, Q5TA50, Q5XIS2, Q66JG2, Q6DBQ8, Q8BS40, Q8K0R6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

279 predictions. Top by Δscore:

Variant	Effect	Δscore
17:4789678:G:GG	donor_gain	1.0000
17:4789113:CCTAG:C	donor_loss	0.9900
17:4789114:CTAGG:C	donor_loss	0.9900
17:4789115:TAGGT:T	donor_loss	0.9900
17:4789116:AG:A	donor_loss	0.9900
17:4789117:GG:G	donor_loss	0.9900
17:4789118:GT:G	donor_loss	0.9900
17:4789119:T:A	donor_loss	0.9900
17:4789630:G:T	donor_gain	0.9900
17:4789631:G:GT	donor_gain	0.9900
17:4789631:G:T	donor_gain	0.9900
17:4789673:GTCGA:G	donor_gain	0.9900
17:4789676:GA:G	donor_gain	0.9900
17:4789110:GAGCC:G	donor_gain	0.9800
17:4789600:G:GT	donor_gain	0.9800
17:4789613:A:AG	donor_gain	0.9700
17:4789614:G:GG	donor_gain	0.9700
17:4789625:G:GT	donor_gain	0.9600
17:4789753:CCGCA:C	acceptor_loss	0.9600
17:4789754:CGCAG:C	acceptor_loss	0.9600
17:4789755:GCAG:G	acceptor_loss	0.9600
17:4789756:CAGGT:C	acceptor_loss	0.9600
17:4789757:A:T	acceptor_loss	0.9600
17:4789550:A:T	donor_gain	0.9500
17:4789120:GAGCT:G	donor_loss	0.9400
17:4789286:TCCAG:T	donor_loss	0.9400
17:4789287:CCAG:C	donor_loss	0.9400
17:4789288:CAGG:C	donor_loss	0.9400
17:4789289:AGGT:A	donor_loss	0.9400
17:4789290:GGTAC:G	donor_loss	0.9400

AlphaMissense

1809 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:4789604:T:C	F89L	0.939
17:4789606:C:A	F89L	0.939
17:4789606:C:G	F89L	0.939
17:4789893:A:T	E158V	0.934
17:4789661:T:A	W108R	0.931
17:4789661:T:C	W108R	0.931
17:4789994:T:A	W192R	0.923
17:4789994:T:C	W192R	0.923
17:4789784:T:C	F122L	0.921
17:4789786:C:A	F122L	0.921
17:4789786:C:G	F122L	0.921
17:4789816:G:C	K132N	0.919
17:4789816:G:T	K132N	0.919
17:4789663:G:C	W108C	0.913
17:4789663:G:T	W108C	0.913
17:4789996:G:C	W192C	0.905
17:4789996:G:T	W192C	0.905
17:4789613:A:C	S92R	0.899
17:4789615:T:A	S92R	0.899
17:4789615:T:G	S92R	0.899
17:4789790:T:C	F124L	0.899
17:4789792:C:A	F124L	0.899
17:4789792:C:G	F124L	0.899
17:4790132:T:C	F238L	0.899
17:4790134:C:A	F238L	0.899
17:4790134:C:G	F238L	0.899
17:4789894:G:C	E158D	0.874
17:4789894:G:T	E158D	0.874
17:4789882:G:A	M154I	0.871
17:4789882:G:C	M154I	0.871

dbSNP variants (sampled 300 via entrez): RS1000138304 (17:4788385 A>G), RS1000237291 (17:4786975 C>A,G,T), RS1000466331 (17:4788081 C>T), RS1002199595 (17:4789423 C>T), RS1002898543 (17:4790037 G>A), RS1003383245 (17:4790274 G>A), RS1003613807 (17:4790568 G>A,C), RS1003977490 (17:4788746 G>C), RS1005237270 (17:4787308 C>T), RS1006222177 (17:4788714 G>A,T), RS1006252665 (17:4787073 C>G), RS1006758422 (17:4791079 T>TTC), RS1011140136 (17:4789753 C>T), RS1013002289 (17:4789977 T>G), RS1013980289 (17:4787971 C>T)

Disease associations

OMIM: gene MIM:620824 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST001639_10	Metabolite levels	1.000000e-11
GCST006585_560	Blood protein levels	1.000000e-24
GCST008933_14	Sphingomyelin levels	2.000000e-10
GCST008933_15	Sphingomyelin levels	2.000000e-15
GCST008933_16	Sphingomyelin levels	4.000000e-13
GCST008933_17	Sphingomyelin levels	6.000000e-11
GCST008933_18	Sphingomyelin levels	9.000000e-12
GCST008933_19	Sphingomyelin levels	5.000000e-10
GCST008933_20	Sphingomyelin levels	7.000000e-10
GCST008933_21	Sphingomyelin levels	7.000000e-09
GCST008933_6	Sphingomyelin levels	8.000000e-19
GCST008933_7	Sphingomyelin levels	3.000000e-22
GCST008933_8	Sphingomyelin levels	5.000000e-20

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification
EFO:0010118	sphingomyelin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	3
Lead	affects expression, increases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases expression, affects expression	2
dicrotophos	decreases expression	1
methyleugenol	decreases expression	1
bisphenol A	increases methylation, affects cotreatment	1
titanium dioxide	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
ferrous chloride	decreases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	increases expression	1
Valproic Acid	increases methylation	1
Palmitic Acid	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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