CPTP

Summary

CPTP (ceramide-1-phosphate transfer protein, HGNC:28116) is a protein-coding gene on chromosome 1p36.33, encoding Ceramide-1-phosphate transfer protein (Q5TA50). Mediates the intracellular transfer of ceramide-1-phosphate (C1P) between organelle membranes and the cell membrane.

Enables ceramide 1-phosphate binding activity and ceramide 1-phosphate transfer activity. Involved in several processes, including ceramide 1-phosphate transport; negative regulation of NLRP3 inflammasome complex assembly; and negative regulation of interleukin-1 beta production. Is active in cytosol and trans-Golgi network membrane.

Source: NCBI Gene 80772 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 64 total
• GTEx eGene: eQTL in 21 tissues, sQTL in 4 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.75 (unconstrained)
• MANE Select transcript: NM_001029885
• Notable: 64 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28116
Approved symbol	CPTP
Name	ceramide-1-phosphate transfer protein
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Aliases	MGC10334
Ensembl gene	ENSG00000224051
Ensembl biotype	protein_coding
OMIM	615467
Entrez	80772

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000343938

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 2: 3

ENST00000343938, ENST00000464957, ENST00000488011, ENST00000900278, ENST00000900279, ENST00000900280, ENST00000900281, ENST00000900282, ENST00000900283, ENST00000956293, ENST00001144607

RefSeq mRNA: 1 — MANE Select: NM_001029885 NM_001029885

CCDS: CCDS30555

Canonical transcript exons

ENST00000343938 — 3 exons

Exon	Start	End
ENSE00001714593	1327241	1328896
ENSE00001831550	1324802	1325102
ENSE00002725815	1326836	1327032

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 97.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.3689 / max 189.8881, expressed in 1810 samples.

Highest expression (Bgee): apex of heart, lower esophagus mucosa, heart left ventricle, cardiac ventricle, testis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CPTP is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 21 tissues and its splicing (sQTL) in 4 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 25 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Brain Cerebellar Hemisphere	eqtl	2.5e-11	-0.34	1:1318756:G:A
Cells Cultured fibroblasts	eqtl	1.6e-10	-0.28	1:1330080:T:C
Brain Cerebellum	eqtl	2.9e-08	-0.46	1:1357046:C:G
Whole Blood	eqtl	7.7e-08	+0.17	1:1341362:GAC:G
Cells EBV-transformed lymphocytes	eqtl	2.2e-07	-0.44	1:1353443:A:G
Nerve Tibial	eqtl	8.5e-07	-0.22	1:1359943:G:A
Muscle Skeletal	eqtl	1.3e-05	+0.14	1:1331945:G:GC
Colon Sigmoid	eqtl	2.5e-05	-0.70	1:1445234:C:G
Esophagus Muscularis	eqtl	5.2e-05	-0.21	1:1330080:T:C
Testis	eqtl	2.1e-04	-0.19	1:1327211:C:T
Lung	eqtl	5.9e-04	-0.43	1:1217168:G:A
Whole Blood	sqtl	1.7e-03	+0.38	1:1359138:C:T
Esophagus Mucosa	eqtl	3.3e-03	-0.17	1:1486396:C:G
Artery Aorta	eqtl	4.0e-03	+0.19	1:1281640:G:C
Skin Sun Exposed Lower leg	eqtl	5.5e-03	-0.27	1:1458485:G:A
Adipose Visceral Omentum	eqtl	8.7e-03	-0.40	1:933401:A:C
Uterus	eqtl	1.6e-02	-1.38	1:2311038:C:T
Artery Tibial	eqtl	1.8e-02	+0.14	1:1331945:G:GC
Brain Nucleus accumbens basal ganglia	eqtl	2.1e-02	-0.12	1:2320508:G:A
Adipose Subcutaneous	eqtl	3.1e-02	+0.20	1:1235349:G:A

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
84	28.2937	1810
87	0.0752	3

Top tissues by expression

showing 100 of 287 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	97.48	gold quality
lower esophagus mucosa	UBERON:0035834	95.85	gold quality
heart left ventricle	UBERON:0002084	94.77	gold quality
cardiac ventricle	UBERON:0002082	94.64	gold quality
left testis	UBERON:0004533	94.37	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.16	gold quality
mucosa of transverse colon	UBERON:0004991	94.12	gold quality
right testis	UBERON:0004534	93.97	gold quality
parotid gland	UBERON:0001831	92.73	gold quality
right lobe of liver	UBERON:0001114	92.55	gold quality
testis	UBERON:0000473	92.28	gold quality
triceps brachii	UBERON:0001509	91.92	gold quality
diaphragm	UBERON:0001103	91.25	gold quality
heart right ventricle	UBERON:0002080	90.99	gold quality
esophagus mucosa	UBERON:0002469	90.64	gold quality
gluteal muscle	UBERON:0002000	90.45	gold quality
tendon of biceps brachii	UBERON:0008188	90.25	gold quality
heart	UBERON:0000948	89.94	gold quality
vastus lateralis	UBERON:0001379	89.70	gold quality
buccal mucosa cell	CL:0002336	89.62	gold quality
cervix squamous epithelium	UBERON:0006922	89.57	gold quality
metanephros cortex	UBERON:0010533	89.52	gold quality
body of stomach	UBERON:0001161	89.14	gold quality
saliva-secreting gland	UBERON:0001044	89.01	gold quality
transverse colon	UBERON:0001157	88.94	gold quality
quadriceps femoris	UBERON:0001377	88.86	gold quality
corpus epididymis	UBERON:0004359	88.84	gold quality
left ventricle myocardium	UBERON:0006566	88.63	gold quality
skin of leg	UBERON:0001511	88.62	gold quality
gastrocnemius	UBERON:0001388	88.48	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	88.35	gold quality
minor salivary gland	UBERON:0001830	88.15	gold quality
muscle organ	UBERON:0001630	88.12	gold quality
biceps brachii	UBERON:0001507	88.03	gold quality
muscle of leg	UBERON:0001383	88.02	gold quality
skin of abdomen	UBERON:0001416	87.88	gold quality
right atrium auricular region	UBERON:0006631	87.75	gold quality
mouth mucosa	UBERON:0003729	87.66	gold quality
skeletal muscle tissue	UBERON:0001134	87.30	gold quality
liver	UBERON:0002107	87.29	gold quality
esophagus	UBERON:0001043	87.20	gold quality
cardiac atrium	UBERON:0002081	87.20	gold quality
right frontal lobe	UBERON:0002810	86.99	gold quality
lateral nuclear group of thalamus	UBERON:0002736	86.88	gold quality
stomach	UBERON:0000945	86.68	gold quality
zone of skin	UBERON:0000014	86.56	gold quality
adult mammalian kidney	UBERON:0000082	86.53	gold quality
myocardium	UBERON:0002349	86.42	gold quality
cingulate cortex	UBERON:0003027	86.18	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.18	gold quality
anterior cingulate cortex	UBERON:0009835	86.18	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.06	gold quality
fundus of stomach	UBERON:0001160	85.85	gold quality
right adrenal gland cortex	UBERON:0035827	85.79	gold quality
muscle tissue	UBERON:0002385	85.73	gold quality
right adrenal gland	UBERON:0001233	85.58	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.32	gold quality
small intestine	UBERON:0002108	85.29	gold quality
colon	UBERON:0001155	84.99	gold quality
left adrenal gland	UBERON:0001234	84.91	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	84.81	gold quality
left adrenal gland cortex	UBERON:0035825	84.76	gold quality
type B pancreatic cell	CL:0000169	84.69	gold quality
large intestine	UBERON:0000059	84.68	gold quality
prefrontal cortex	UBERON:0000451	84.62	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	84.57	gold quality
ectocervix	UBERON:0012249	84.54	gold quality
body of tongue	UBERON:0011876	84.52	gold quality
adrenal cortex	UBERON:0001235	84.47	gold quality
intestine	UBERON:0000160	84.37	gold quality
spleen	UBERON:0002106	84.35	gold quality
pharyngeal mucosa	UBERON:0000355	84.22	gold quality
neocortex	UBERON:0001950	84.19	gold quality
olfactory bulb	UBERON:0002264	84.19	gold quality
amniotic fluid	UBERON:0000173	84.10	gold quality
adult organism	UBERON:0007023	84.02	gold quality
frontal cortex	UBERON:0001870	84.00	gold quality
vagina	UBERON:0000996	83.98	gold quality
cerebellar vermis	UBERON:0004720	83.91	silver quality
lower esophagus	UBERON:0013473	83.91	gold quality
lower esophagus muscularis layer	UBERON:0035833	83.86	gold quality
granulocyte	CL:0000094	83.81	gold quality
cervix epithelium	UBERON:0004801	83.76	gold quality
amygdala	UBERON:0001876	83.67	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	83.67	gold quality
cortical plate	UBERON:0005343	83.64	gold quality
jejunum	UBERON:0002115	83.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.57	gold quality
duodenum	UBERON:0002114	83.55	gold quality
cerebral cortex	UBERON:0000956	83.51	gold quality
colonic mucosa	UBERON:0000317	83.39	gold quality
upper arm skin	UBERON:0004263	83.38	gold quality
substantia nigra pars compacta	UBERON:0001965	83.30	gold quality
nasal cavity epithelium	UBERON:0005384	83.24	gold quality
gingiva	UBERON:0001828	83.22	gold quality
muscle layer of sigmoid colon	UBERON:0035805	83.19	gold quality
nasal cavity mucosa	UBERON:0001826	83.06	gold quality
left coronary artery	UBERON:0001626	83.02	gold quality
male germ cell	CL:0000015	83.00	silver quality
jejunal mucosa	UBERON:0000399	82.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.30

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 71 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Skeletal muscle	tissue	51.8	low
Salivary gland	tissue	35.0	not detected
Medulla oblongata	tissue	28.1
Hippocampus	tissue	27.6	not detected
Choroid plexus	tissue	27.3
Substantia nigra	tissue	27.3
Retrosplenial cortex	tissue	24.3
Vagina	tissue	24.0	not detected
Spinal cord	tissue	23.9
Testis	tissue	23.4	low
Hypothalamus	tissue	23.0
Pons	tissue	22.9
Locus coeruleus	tissue	22.9
Midbrain	tissue	22.6
Postcentral gyrus	tissue	22.5
Tongue	tissue	21.3
Thalamus	tissue	20.5
Putamen	tissue	19.2
Duodenum	tissue	18.7	medium
Basal ganglia	tissue	18.6	not detected
Septum	tissue	18.6
Cerebral cortex	tissue	16.6	low
Frontal cortex	tissue	16.6
Nucleus accumbens	tissue	16.6
Retrosplenial and cingulate cortex	tissue	16.5
Cerebellum	tissue	16.4	not detected
Somatosensory cortex	tissue	16.1
Ventral forebrain	tissue	15.9
Occipital cortex	tissue	15.7
Liver	tissue	15.6	not detected
Hippocampal formation	tissue	15.3
Amygdala	tissue	15.0
Small intestine	tissue	14.2	medium
Stomach 1	tissue	14.0	low
Heart muscle	tissue	13.9	low
Caudate putamen	tissue	13.8
Entorhinal cortex	tissue	13.6
Olfactory bulb	tissue	13.6
Parathyroid gland	tissue	13.2	not detected
Corpus callosum	tissue	13.0
Colon	tissue	11.2	low
Skin 1	tissue	10.2	low
Spleen	tissue	8.7	not detected
Adipose tissue	tissue	8.5	not detected
Pancreas	tissue	8.1	not detected
Epididymis	tissue	8.0	low
Pituitary gland	tissue	7.9
Kidney	tissue	7.3	low
Esophagus	tissue	7.2	low
Seminal vesicle	tissue	6.2	not detected
Adrenal gland	tissue	5.9	low
Appendix	tissue	5.7	low
Ovary	tissue	5.6	not detected
Prostate	tissue	5.5	low
Lung	tissue	5.3	not detected
Lymph node	tissue	5.1	not detected
Rectum	tissue	4.5	low
Cervix	tissue	4.3	not detected
Placenta	tissue	4.3	not detected
Fallopian tube	tissue	4.3	low

Brain sub-regions (HPA Brain Atlas): detected in 185; highest nTPM — Nuclei of the trapezoid body (33.4), Nucleus raphe magnus (31.1), Motor facial nucleus (30.1), Ventral posterolateral thalamic nucleus (29.9), Pontine nuclei (29.3).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CPTP by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 34 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-499A-3P	99.18	69.20	1392
HSA-MIR-499B-3P	99.18	69.27	1391
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-3184-5P	98.56	67.13	1491
HSA-MIR-615-5P	98.10	63.76	591
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-4469	97.93	65.81	1319
HSA-MIR-6787-3P	97.75	66.17	1233
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4675	97.69	64.82	774
HSA-MIR-4741	97.69	64.14	883
HSA-MIR-4430	97.47	65.61	1813

Functional genomics

gnomAD constraint: pLI 0.00015, LOEUF 1.75, missense Z -1.04 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000343938 — one region, missense o/e 1.09.

Literature-anchored findings (GeneRIF, showing 6)

• a ubiquitously expressed lipid transfer protein, human GLTPD1, named here CPTP, is shown to specifically transfer C1P between membranes. (PMID:23863933)
• These findings identify human CPTP as an endogenous regulator of early-stage autophagosome assembly and inflammasome-driven, pro-inflammatory cytokine generation and release. (PMID:29164996)
• Ceramide-1-phosphate transfer protein (CPTP) regulation by phosphoinositides. (PMID:33781749)
• Ceramide-1-phosphate and its transfer proteins in eukaryotes. (PMID:34499882)
• Ceramide-1-phosphate transfer protein promotes sphingolipid reorientation needed for binding during membrane interaction. (PMID:34808193)
• Human CPTP promotes growth and metastasis via sphingolipid metabolite ceramide and PI4KA/AKT signaling in pancreatic cancer cells. (PMID:35982909)

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	cptp	ENSDARG00000052537
danio_rerio	gltpd2a	ENSDARG00000054218
danio_rerio	gltpd2b	ENSDARG00000067889
mus_musculus	Cptp	ENSMUSG00000029073
rattus_norvegicus	Cptp	ENSRNOG00000022455
rattus_norvegicus		ENSRNOG00000064148
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), GLTP (ENSG00000139433), GLTPD2 (ENSG00000182327)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Xenopus laevis	Q5HZ92	87.9%	Diamond
Xenopus tropicalis	Q66JG2	87.9%	Diamond
Bos taurus	Q0VCQ0	81.8%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
SNORD167	snoRNA	109623456
ACAP3	protein-coding	116983
PUSL1	protein-coding	126789
DVL1	protein-coding	1855
INTS11	protein-coding	54973
TAS1R3	protein-coding	83756
MXRA8	protein-coding	54587
AURKAIP1	protein-coding	54998
MIR6726	ncRNA	102465434
MIR6727	ncRNA	102465435
MIR6808	ncRNA	102466740

Protein

Protein identifiers

Ceramide-1-phosphate transfer protein — Q5TA50 (reviewed: Q5TA50)

Alternative names: Glycolipid transfer protein domain-containing protein 1

All UniProt accessions (3): Q5TA50, J3KST3, S4S694

UniProt curated annotations — full annotation on UniProt →

Function. Mediates the intracellular transfer of ceramide-1-phosphate (C1P) between organelle membranes and the cell membrane. Required for normal structure of the Golgi stacks. Can bind phosphoceramides with a variety of aliphatic chains, but has a preference for lipids with saturated C16:0 or monounsaturated C18:1 aliphatic chains, and is inefficient with phosphoceramides containing lignoceryl (C24:0). Plays a role in the regulation of the cellular levels of ceramide-1-phosphate, and thereby contributes to the regulation of phospholipase PLA2G4A activity and the release of arachidonic acid. Has no activity with galactosylceramide, lactosylceramide, sphingomyelin, phosphatidylcholine, phosphatidic acid and ceramide. C1P transfer is stimulated by phosphatidylserine in C1P source vesicles. Regulates autophagy, inflammasome mediated IL1B and IL18 processing, and pyroptosis, but not apoptosis.

Subcellular location. Cytoplasm. Cytosol. Golgi apparatus. trans-Golgi network membrane. Cell membrane. Endosome membrane. Nucleus outer membrane.

Tissue specificity. Ubiquitous. Detected in heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon and peripheral blood leukocytes.

Similarity. Belongs to the GLTP family.

RefSeq proteins (1): NP_001025056* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR014830	Glycolipid_transfer_prot_dom	Domain
IPR036497	GLTP_sf	Homologous_superfamily

Pfam: PF08718

Catalyzed reactions (Rhea)

• N-(hexadecanoyl)-sphing-4-enine-1-phosphate(in) = N-(hexadecanoyl)-sphing-4-enine-1-phosphate(out) (RHEA:45680)
• N-(9Z-octadecenoyl)-sphing-4-enine-1-phosphate(in) = N-(9Z-octadecenoyl)-sphing-4-enine-1-phosphate(out) (RHEA:45688)

UniProt features (36 total): mutagenesis site 14, helix 14, binding site 5, strand 2, chain 1

Structure

Experimental structures (PDB)

6 structures by resolution:

PDB	Title	Method	Resolution (Å)
4K84	Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with …	X-RAY DIFFRACTION	1.9
4KBS	Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with …	X-RAY DIFFRACTION	1.9
4K85	Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with …	X-RAY DIFFRACTION	1.9
4K80	Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with …	X-RAY DIFFRACTION	2.05
4K8N	Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with …	X-RAY DIFFRACTION	3.1
4KF6	Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with …	X-RAY DIFFRACTION	3.19

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TA50-F1	93.93	0.87

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; flagellar centriole; mid piece; perinuclear theca

Antibody reliability (HPA): IH approved · IF supported

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 (5)

Position	Role
56	an N-acylsphingoid base 1-phosphate
60	an N-acylsphingoid base 1-phosphate
106	an N-acylsphingoid base 1-phosphate
110	an N-acylsphingoid base 1-phosphate
150	an N-acylsphingoid base 1-phosphate

Mutagenesis-validated functional residues (14)

Position	Phenotype
56	slightly decreases phosphoceramide transfer.
60	nearly abolishes phosphoceramide transfer. induces autophagy in a dominant negative manner.
97	no effect.
106	nearly abolishes phosphoceramide transfer. induces autophagy in a dominant negative manner.
110	reduces phosphoceramide transfer.
113	strongly reduces phosphoceramide transfer.
117	slightly reduces phosphoceramide transfer.
118	abolishes phosphoceramide transfer.
149	reduces phosphoceramide transfer.
158	abolishes phosphoceramide transfer.
42	increases phosphoceramide transfer.
43	nearly abolishes phosphoceramide transfer.
50	slightly reduces phosphoceramide transfer.
53	slightly decreases phosphoceramide transfer.

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 2; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

2 pathways:

ID	Pathway	Evidence
R-HSA-9845576	Glycosphingolipid transport	curated
R-HSA-382551	Transport of small molecules	—

MSigDB gene sets: 149 (showing top): GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_NEGATIVE_REGULATION_OF_INTERLEUKIN_1_PRODUCTION, GOBP_INFLAMMATORY_RESPONSE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_INTERLEUKIN_1_PRODUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_NEGATIVE_REGULATION_OF_AUTOPHAGY, GOBP_REGULATION_OF_IMMUNE_RESPONSE

GO Biological Process (7): negative regulation of autophagy (GO:0010507), negative regulation of interleukin-1 beta production (GO:0032691), ceramide transport (GO:0035627), intermembrane lipid transfer (GO:0120009), negative regulation of NLRP3 inflammasome complex assembly (GO:1900226), ceramide 1-phosphate transport (GO:1902389), lipid transport (GO:0006869)

GO Molecular Function (5): phospholipid binding (GO:0005543), ceramide 1-phosphate binding (GO:1902387), ceramide 1-phosphate transfer activity (GO:1902388), lipid binding (GO:0008289), lipid transfer activity (GO:0120013)

GO Cellular Component (7): nuclear outer membrane (GO:0005640), cytosol (GO:0005829), plasma membrane (GO:0005886), endosome membrane (GO:0010008), trans-Golgi network membrane (GO:0032588), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794)

Reactome top-level categories

1 top-level categories:

Category	Pathways
Transport of small molecules	1

GO top-level categories

43 GO namespaces:

Category	Terms
lipid transport	2
cytoplasm	2
cellular anatomical structure	2
autophagy	1
negative regulation of catabolic process	1
regulation of autophagy	1
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
negative regulation of protein-containing complex assembly	1
NLRP3 inflammasome complex assembly	1
negative regulation of inflammasome-mediated signaling pathway	1
regulation of NLRP3 inflammasome complex assembly	1
phospholipid transport	1
ceramide transport	1
transport	1
lipid localization	1
lipid binding	1
phospholipid binding	1
anion binding	1
ceramide binding	1
phospholipid transfer activity	1
ceramide transfer activity	1
ceramide 1-phosphate transport	1
binding	1
transporter activity	1
lipid carrier activity	1
intermembrane lipid transfer	1
nuclear membrane	1
organelle outer membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
membrane	1
cell periphery	1
endosome	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
trans-Golgi network	1
organelle membrane	1
intracellular anatomical structure	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 9 of 19 annotations. The rest are phylogenetic / computational / electronic (IEA).

9 experimentally-supported GO terms:

GO term	NS	Evidence
ceramide 1-phosphate transport	BP	direct assay
negative regulation of NLRP3 inflammasome complex assembly	BP	mutant phenotype
negative regulation of autophagy	BP	mutant phenotype
negative regulation of interleukin-1 beta production	BP	mutant phenotype
cytosol	CC	direct assay
trans-Golgi network membrane	CC	experiment
ceramide 1-phosphate binding	MF	direct assay
ceramide 1-phosphate transfer activity	MF	direct assay
phospholipid binding	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 294 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPTP	GLTP	Q9NZD2	700
CPTP	CERK	Q8TCT0	596
CPTP	CERT1	Q9Y5P4	520
CPTP	NOL9	Q5SY16	429
CPTP	ZBTB48	P10074	407
CPTP	TAS1R3	Q7RTX0	404
CPTP	ALDH4A1	P30038	401
CPTP	ACER1	Q8TDN7	393
CPTP	SPTLC3	Q9NUV7	376
CPTP	SPTLC2	O15270	371
CPTP	SPTLC1	O15269	370
CPTP	PAX7	P23759	368
CPTP	PAX3	P23760	368
CPTP	UGCG	Q16739	366
CPTP	TAS1R2	Q8TE23	359

IntAct

Human interaction partners of CPTP in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

8 partners by confidence:

Partner	Interaction type	MIscore	Records
LRRK2	direct interaction	0.440	1
CD7	physical association	0.370	1
ECM1	physical association	0.370	1
ELOC	physical association	0.370	1
INPP5K	physical association	0.370	1
PHF13	physical association	0.370	1
SMAD3	physical association	0.370	1
ZNF451	physical association	0.370	1

BioGRID (10 interactions; top human partners by supporting records): CD7 (Two-hybrid), ECM1 (Two-hybrid), INPP5K (Two-hybrid), PHF13 (Two-hybrid), SMAD3 (Two-hybrid), TCEB1 (Two-hybrid), TOP3B (Affinity Capture-RNA), TRIM71 (Affinity Capture-RNA), ZNF451 (Two-hybrid)

Disease & clinical

Genetic variants

Variant evidence for CPTP: 64 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	9
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 29 predictions of 287):

Position(s)	Effect	Δscore	Sites
1:1326829–1326831	acceptor_gain	0.9800	2
1:1326904	acceptor_gain	0.9800
1:1326907	acceptor_gain	0.9800
1:1327239–1327240	acceptor_loss	0.9800	6
1:1325103–1325104	donor_loss	0.9700	5
1:1326834–1326835	acceptor_loss	0.9700	6
1:1327033–1327034	donor_loss	0.9700	5
1:1326833	acceptor_gain	0.9600
1:1327282	acceptor_gain	0.9600
1:1327034	donor_loss	0.9500

AlphaMissense

376 missense substitutions predicted likely pathogenic (of 1,381 scored), across 112 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
H150	8	0.930	0.981
F121	8	0.872	0.959
F50	8	0.870	0.969
D56	8	0.855	0.945
F171	8	0.841	0.960
F42	8	0.832	0.968
H112	8	0.798	0.930
W36	7	0.920	0.985
E86	7	0.916	0.972
W117	7	0.889	0.977
F162	7	0.796	0.924
K60	6	0.923	0.965
M82	6	0.897	0.934
G47	6	0.873	0.954
Y142	6	0.868	0.962
C138	6	0.864	0.961
M175	6	0.850	0.910
P166	6	0.835	0.900
F17	6	0.813	0.892
W152	6	0.784	0.880

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Papillary Cell Carcinoma (TCGA)	favorable	2.56e-05
Rectum Adenocarcinoma (TCGA)	unfavorable	0.000236

Disease associations

OMIM: gene MIM:615467 | disease phenotypes:

GWAS associations

2 associations:

Study	Trait	p-value
GCST004131_103	Inflammatory bowel disease	2e-7
GCST004133_8	Ulcerative colitis	3e-6

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	2
bisphenol A	affects cotreatment, decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
ferrous chloride	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
eprenetapopt	affects expression, affects reaction	1
MT19c compound	decreases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Arsenic	increases expression, affects cotreatment, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Indomethacin	decreases expression, affects cotreatment	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Plant Extracts	affects cotreatment, decreases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.