CHPT1

protein-coding

choline phosphotransferase 1

Gene summary

Enables diacylglycerol cholinephosphotransferase activity. Involved in phosphatidylcholine biosynthetic process and platelet activating factor biosynthetic process. Is active in Golgi membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020244.3

Inheritance

—

ClinVar variants

U:52B:3

Top phenotype

Spermatogenic failure 4

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr12:101,696,947-101,744,140

External References & Databases

Ensembl (ENSG00000111666)

Transcript & Mutation Effects

hg38 • Region Span ~47.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHPT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 3

Spermatogenic failure 4Total: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020244.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			49 clinvar	1 clinvar	1 clinvar	51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	52	1	2	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020244.3	RefSeq	NP_064629.2	9	MANE Select
ENST00000229266.8	Ensembl	ENSP00000229266.3	9	MANE Select
ENST00000546873.1	Ensembl	ENSP00000448369.1	2	Standard
ENST00000549128.5	Ensembl	ENSP00000446994.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

regulation of cell growth
lipid metabolic process
phosphatidylcholine biosynthetic process
CDP-choline pathway
platelet activating factor biosynthetic process

Molecular Function

diacylglycerol cholinephosphotransferase activity
phosphotransferase activity, for other substituted phosphate groups
diacylglycerol binding
metal ion binding

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
Golgi apparatus
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000229266
Coding exons: 9
Length: 47194
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125742
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.823	161	193	0.833	0.00000868	2582
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000096	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000083	0.000079	rare
South Asian	0.00027	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes phosphatidylcholine biosynthesis from CDP- choline. It thereby plays a central role in the formation and maintenance of vesicular membranes.;

Recessive Scores

pRec: 0.0901

Intolerance Scores

LoFtool: 0.648
RVIS EVS: -0.03
RVIS percentile EVS: 51.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.168

Gene Damage Prediction

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