CPTP

ceramide-1-phosphate transfer protein

Basic information

Region (hg38): 1:1324756-1328896

Previous symbols: [ "GLTPD1" ]

Links

ENSG00000224051 ∙ NCBI:80772 ∙ OMIM:615467 ∙ HGNC:28116 ∙ Uniprot:Q5TA50 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPTP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPTP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			29	6		35
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	7	0

Variants in CPTP

This is a list of pathogenic ClinVar variants found in the CPTP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-1326921-C-T		not specified	Likely benign (Feb 17, 2023)
1-1326951-T-C		not specified	Uncertain significance (Jan 22, 2024)
1-1326986-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-1327001-C-T		not specified	Uncertain significance (Sep 27, 2024)
1-1327302-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-1327303-G-A		not specified	Likely benign (Nov 21, 2022)
1-1327311-G-T			Uncertain significance (Apr 27, 2019)
1-1327315-G-A		not specified	Uncertain significance (Jan 21, 2025)
1-1327317-C-T		not specified	Uncertain significance (May 11, 2022)
1-1327348-G-A		not specified	Uncertain significance (Nov 21, 2022)
1-1327364-G-T		not specified	Uncertain significance (May 31, 2023)
1-1327371-C-T		not specified	Likely benign (Feb 06, 2023)
1-1327374-G-A		not specified	Uncertain significance (Jun 04, 2024)
1-1327387-G-A		not specified	Likely benign (Dec 08, 2023)
1-1327413-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-1327416-C-G		not specified	Uncertain significance (Oct 20, 2021)
1-1327425-T-A		not specified	Uncertain significance (Mar 28, 2024)
1-1327434-C-T		not specified	Uncertain significance (Aug 27, 2024)
1-1327446-C-T		not specified	Uncertain significance (Apr 14, 2022)
1-1327447-G-A		not specified	Uncertain significance (Nov 26, 2024)
1-1327488-G-A		not specified	Uncertain significance (Nov 11, 2024)
1-1327494-C-T		not specified	Uncertain significance (Jul 20, 2022)
1-1327506-G-A		not specified	Uncertain significance (Apr 14, 2022)
1-1327512-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-1327515-C-T		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPTP	protein_coding	protein_coding	ENST00000343938	2	4142

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0225	0.778	125497	0	18	125515	0.0000717

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0932	158	155	1.02	0.0000115	1357
Missense in Polyphen		53	53.078	0.99853		511
Synonymous	-1.01	88	76.7	1.15	0.00000602	464
Loss of Function	0.928	3	5.31	0.565	2.26e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000886	0.0000886
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000384	0.0000353
Middle Eastern	0.000112	0.000109
South Asian	0.000297	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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 (PubMed:28011644). Regulates autophagy, inflammasome mediated IL1B and IL18 processing, and pyroptosis, but not apoptosis (PubMed:29164996). {ECO:0000269|PubMed:23863933, ECO:0000269|PubMed:28011644, ECO:0000269|PubMed:29164996}.
• Pathway: Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Intolerance Scores

• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.292
• ghis: 0.444

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cptp

Gene ontology

• Biological process: glycosphingolipid metabolic process;negative regulation of autophagy;ceramide transport;glycolipid transport;negative regulation of interleukin-1 beta secretion;intermembrane lipid transfer;negative regulation of NLRP3 inflammasome complex assembly;ceramide 1-phosphate transport
• Cellular component: nuclear outer membrane;Golgi apparatus;cytosol;plasma membrane;endosome membrane;membrane
• Molecular function: phospholipid binding;phospholipid transporter activity;lipid binding;intermembrane lipid transfer activity;ceramide 1-phosphate binding;ceramide 1-phosphate transporter activity