GPCPD1

glycerophosphocholine phosphodiesterase 1

Basic information

Region (hg38): 20:5544438-5611006

Links

ENSG00000125772 ∙ NCBI:56261 ∙ OMIM:614124 ∙ HGNC:26957 ∙ Uniprot:Q9NPB8 ∙ 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 GPCPD1 gene.

• Inborn genetic diseases (13 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPCPD1 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	2
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	1

Variants in GPCPD1

This is a list of pathogenic ClinVar variants found in the GPCPD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-5547675-C-T		not specified	Uncertain significance (Feb 28, 2023)
20-5547740-C-T		not specified	Likely benign (Jan 23, 2024)
20-5547794-C-T		not specified	Uncertain significance (Sep 27, 2021)
20-5547795-G-A		not specified	Uncertain significance (Nov 08, 2022)
20-5557994-T-C		not specified	Uncertain significance (Jun 23, 2023)
20-5558005-T-C		not specified	Uncertain significance (Nov 07, 2023)
20-5558059-A-C		not specified	Uncertain significance (Feb 02, 2024)
20-5558719-T-C		not specified	Uncertain significance (Feb 15, 2023)
20-5558725-T-C		not specified	Uncertain significance (Nov 06, 2023)
20-5558757-T-A		not specified	Uncertain significance (Mar 23, 2023)
20-5561515-G-C		not specified	Uncertain significance (Dec 16, 2023)
20-5567500-G-T		not specified	Uncertain significance (May 15, 2023)
20-5567556-A-G		not specified	Uncertain significance (Oct 12, 2022)
20-5573946-G-C			Uncertain significance (Jan 01, 2024)
20-5575917-C-T		not specified	Uncertain significance (Dec 28, 2023)
20-5575950-C-T		not specified	Uncertain significance (Dec 21, 2022)
20-5578430-T-C		not specified	Uncertain significance (Jan 23, 2023)
20-5578558-G-C		not specified	Uncertain significance (Sep 26, 2023)
20-5578575-G-A			Benign (May 03, 2018)
20-5586216-T-C			Likely benign (Aug 01, 2022)
20-5586264-G-C		not specified	Uncertain significance (Feb 07, 2023)
20-5598734-G-A		not specified	Uncertain significance (Jan 10, 2022)
20-5598750-G-T		not specified	Uncertain significance (Jul 27, 2023)
20-5598806-A-G		not specified	Uncertain significance (Jan 04, 2024)
20-5598808-C-T		not specified	Likely benign (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPCPD1	protein_coding	protein_coding	ENST00000379019	19	66588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.202	0.798	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	242	350	0.692	0.0000174	4424
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000501	0.000487
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000459	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity. {ECO:0000250}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC;Hydrolysis of LPE (Consensus)

Intolerance Scores

• loftool: 0.653
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.639
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpcpd1

Gene ontology

• Biological process: skeletal muscle tissue development;glycerophospholipid catabolic process
• Cellular component: cytosol
• Molecular function: glycerophosphocholine phosphodiesterase activity;starch binding