CHPT1

choline phosphotransferase 1

Basic information

Region (hg38): 12:101696946-101744140

Links

ENSG00000111666 ∙ NCBI:56994 ∙ OMIM:616747 ∙ HGNC:17852 ∙ Uniprot:Q8WUD6 ∙ 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 CHPT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHPT1 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			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	1	4	12
Total	0	0	22	1	6

Variants in CHPT1

This is a list of pathogenic ClinVar variants found in the CHPT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-101697886-T-G		not specified	Uncertain significance (Aug 08, 2022)
12-101697908-C-A		not specified	Uncertain significance (May 26, 2024)
12-101697937-C-G		not specified	Uncertain significance (Dec 09, 2023)
12-101697952-G-C		not specified	Uncertain significance (Mar 28, 2022)
12-101697988-G-C		not specified	Uncertain significance (Oct 13, 2023)
12-101698118-C-G		not specified	Uncertain significance (Apr 24, 2023)
12-101714097-A-G		not specified	Uncertain significance (Dec 03, 2021)
12-101714234-A-G		not specified	Uncertain significance (May 30, 2023)
12-101716732-G-T		not specified	Uncertain significance (Mar 25, 2024)
12-101716735-G-A		not specified	Uncertain significance (Dec 06, 2022)
12-101716792-G-C		not specified	Uncertain significance (May 27, 2022)
12-101716793-C-T		not specified	Uncertain significance (Jul 21, 2022)
12-101720150-A-T		not specified	Uncertain significance (Jul 20, 2021)
12-101720156-C-G		not specified	Uncertain significance (Dec 14, 2022)
12-101723182-G-T		not specified	Uncertain significance (May 30, 2023)
12-101723803-T-C			Benign (Jun 22, 2018)
12-101726326-T-G		not specified	Uncertain significance (Nov 09, 2023)
12-101726327-A-G		not specified	Uncertain significance (Feb 16, 2023)
12-101726357-C-G		not specified	Uncertain significance (Mar 16, 2024)
12-101726374-C-T			Benign (Jun 11, 2018)
12-101728682-TAGAG-T		Spermatogenic Failure	Likely benign (Jun 14, 2016)
12-101728684-G-C		Spermatogenic failure 4	Uncertain significance (Jan 12, 2018)
12-101728722-C-T		Spermatogenic failure 4	Benign (Jan 12, 2018)
12-101728729-C-T		Spermatogenic failure 4	Uncertain significance (Jan 13, 2018)
12-101728744-T-C		Spermatogenic failure 4	Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHPT1	protein_coding	protein_coding	ENST00000229266	9	47194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000243	0.984	125720	0	22	125742	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.823	161	193	0.833	0.00000868	2582
Missense in Polyphen		65	69.91	0.92977		920
Synonymous	0.0911	71	72.0	0.986	0.00000339	795
Loss of Function	2.13	9	19.0	0.473	8.03e-7	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000160	0.000157
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000830	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000269	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes phosphatidylcholine biosynthesis from CDP- choline. It thereby plays a central role in the formation and maintenance of vesicular membranes.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Phosphonate and phosphinate metabolism - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Lamivudine Metabolism Pathway;Phospholipid Biosynthesis;Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Metabolism of lipids;phosphatidylcholine biosynthesis;Metabolism;Synthesis of PC;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0901

Intolerance Scores

• loftool: 0.648
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.0824
• hipred: N
• hipred_score: 0.450
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chpt1

Gene ontology

• Biological process: regulation of cell growth;lipid metabolic process;phosphatidylcholine biosynthetic process;CDP-choline pathway;platelet activating factor biosynthetic process
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;Golgi apparatus;membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: diacylglycerol cholinephosphotransferase activity;phosphotransferase activity, for other substituted phosphate groups;diacylglycerol binding;metal ion binding