GPCPD1

protein-coding

glycerophosphocholine phosphodiesterase 1

Gene summary

Predicted to enable glycerophosphocholine phosphodiesterase activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within skeletal muscle tissue development. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_019593.5

Inheritance

—

ClinVar variants

U:66B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr20:5,544,404-5,611,006

External References & Databases

Ensembl (ENSG00000125772)

Transcript & Mutation Effects

hg38 • Region Span ~66.6 kb

Loading mutation effect viewer...

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 GPCPD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019593.5. 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				3 clinvar	1 clinvar	4
missense			60 clinvar	1 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	66	4	1	71

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019593.5	RefSeq	NP_062539.1	19	MANE Select
ENST00000379019.7	Ensembl	ENSP00000368305.4	19	MANE Select
ENST00000418646.5	Ensembl	ENSP00000396720.1	7	Standard
ENST00000481690.2	Ensembl	ENSP00000488635.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerophospholipid metabolism - Homo sapiens (human)
Choline metabolism in cancer - Homo sapiens (human)
Metabolism of lipids
Metabolism
Glycerophospholipid biosynthesis

Biological Process

skeletal muscle tissue development
glycerophospholipid catabolic process

Molecular Function

glycerophosphocholine phosphodiesterase activity
starch binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379019
Coding exons: 19
Length: 66588
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125747
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.05	242	350	0.692	0.0000174	4424
Missense (PolyPhen)		71	117.51	0.60419		1491
Synonymous	-0.479	125	118	1.06	0.00000608	1228
Loss of Function	4.32	9	37.6	0.240	0.00000175	500

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00031	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000046	0.000044	rare
South Asian	0	0.0	absent
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.653
RVIS EVS: -0.2
RVIS percentile EVS: 38.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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