PCTP

phosphatidylcholine transfer protein, the group of StAR related lipid transfer domain containing

Basic information

Region (hg38): 17:55751051-55842830

Links

ENSG00000141179 ∙ NCBI:58488 ∙ OMIM:606055 ∙ HGNC:8752 ∙ Uniprot:Q9UKL6 ∙ 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 PCTP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCTP 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						0
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	17	1	0

Variants in PCTP

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

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

Position	Type	Phenotype	Significance	ClinVar
17-55751116-G-A		not specified	Uncertain significance (Apr 22, 2024)
17-55751126-T-C		not specified	Uncertain significance (Dec 01, 2022)
17-55751153-G-T		not specified	Uncertain significance (Jan 29, 2025)
17-55767339-C-A		not specified	Uncertain significance (May 30, 2024)
17-55767372-T-C		not specified	Uncertain significance (Sep 03, 2024)
17-55767408-A-G		not specified	Uncertain significance (Jul 13, 2021)
17-55771177-A-G		not specified	Uncertain significance (Feb 28, 2024)
17-55773772-A-T		not specified	Uncertain significance (Feb 27, 2025)
17-55773791-G-A		not specified	Likely benign (Jan 24, 2024)
17-55773802-A-G		not specified	Likely benign (Mar 03, 2025)
17-55773832-A-G		not specified	Uncertain significance (Apr 25, 2023)
17-55773835-C-T		not specified	Uncertain significance (Jun 22, 2021)
17-55773836-G-A		not specified	Uncertain significance (Jun 05, 2023)
17-55773857-G-A		not specified	Uncertain significance (Aug 01, 2024)
17-55773878-G-C		not specified	Uncertain significance (May 31, 2023)
17-55774799-G-A		not specified	Uncertain significance (Dec 13, 2023)
17-55774801-A-G		not specified	Uncertain significance (Nov 10, 2024)
17-55774831-C-T		not specified	Uncertain significance (Sep 30, 2024)
17-55774851-G-A		not specified	Uncertain significance (Dec 27, 2022)
17-55776071-G-A		not specified	Uncertain significance (Oct 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCTP	protein_coding	protein_coding	ENST00000268896	6	91852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.76e-12	0.0215	125655	0	93	125748	0.000370

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.259	126	118	1.07	0.00000643	1387
Missense in Polyphen		34	26.71	1.2729		316
Synonymous	-0.326	47	44.2	1.06	0.00000246	384
Loss of Function	-0.418	16	14.3	1.12	7.93e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000585	0.000573
Ashkenazi Jewish	0.00	0.00
East Asian	0.00218	0.00218
Finnish	0.00	0.00
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.00218	0.00218
South Asian	0.000787	0.000784
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of phosphatidylcholine between membranes. Binds a single lipid molecule. {ECO:0000269|PubMed:12055623}.
• Pathway: Metabolism of lipids;Mitochondrial Fatty Acid Beta-Oxidation;Metabolism;Fatty acid metabolism;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.594
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.0426
• hipred: N
• hipred_score: 0.167
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.332

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pctp
• Phenotype: immune system phenotype; normal phenotype; hematopoietic system phenotype; liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: pctp
• Affected structure: pancreas
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: phosphatidylcholine biosynthetic process;lipid transport;phospholipid transport;negative regulation of cold-induced thermogenesis
• Cellular component: cytosol
• Molecular function: protein binding;phospholipid transporter activity;phosphatidylcholine transporter activity;phosphatidylcholine binding