GPLD1

glycosylphosphatidylinositol specific phospholipase D1

Basic information

Region (hg38): 6:24424565-24495205

Links

ENSG00000112293 ∙ NCBI:2822 ∙ OMIM:602515 ∙ HGNC:4459 ∙ Uniprot:P80108 ∙ 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 GPLD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPLD1 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			44	5		49
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	6	1

Variants in GPLD1

This is a list of pathogenic ClinVar variants found in the GPLD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-24429067-C-T		not specified	Uncertain significance (Dec 07, 2021)
6-24429069-G-C		not specified	Uncertain significance (Jul 26, 2022)
6-24429112-CT-C			Benign (Aug 05, 2018)
6-24433226-C-G		not specified	Uncertain significance (Sep 21, 2023)
6-24436589-C-A		not specified	Uncertain significance (Apr 12, 2024)
6-24436619-G-A		not specified	Uncertain significance (Jun 13, 2024)
6-24436622-A-G		not specified	Uncertain significance (Dec 17, 2023)
6-24436623-T-C		not specified	Uncertain significance (Mar 07, 2024)
6-24436640-T-C		not specified	Uncertain significance (Jan 04, 2022)
6-24437127-T-C		not specified	Uncertain significance (Sep 16, 2021)
6-24437170-G-A		not specified	Uncertain significance (Jun 18, 2021)
6-24437178-C-A		not specified	Uncertain significance (Feb 21, 2024)
6-24437229-A-G		not specified	Uncertain significance (Apr 19, 2024)
6-24437232-C-T		not specified	Uncertain significance (May 09, 2023)
6-24437260-C-T		not specified	Likely benign (Dec 13, 2021)
6-24445620-G-A		not specified	Uncertain significance (Jun 09, 2022)
6-24445758-C-A		not specified	Likely benign (Dec 13, 2023)
6-24445782-C-G		not specified	Uncertain significance (Dec 01, 2022)
6-24445808-C-T		not specified	Uncertain significance (Jan 31, 2022)
6-24445816-T-G		not specified	Likely benign (Oct 02, 2023)
6-24446881-T-G		not specified	Uncertain significance (Sep 07, 2022)
6-24446907-A-C		not specified	Uncertain significance (Jun 11, 2021)
6-24446974-G-C		not specified	Uncertain significance (Dec 13, 2021)
6-24447918-A-G		not specified	Uncertain significance (Sep 22, 2023)
6-24447951-G-C		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPLD1	protein_coding	protein_coding	ENST00000230036	25	70641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.59e-15	0.980	124426	8	1314	125748	0.00527

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.296	505	487	1.04	0.0000272	5455
Missense in Polyphen		178	174.36	1.0209		1949
Synonymous	0.104	198	200	0.991	0.0000132	1651
Loss of Function	2.53	32	51.6	0.620	0.00000270	583

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00327	0.00327
Ashkenazi Jewish	0.00357	0.00358
East Asian	0.000598	0.000598
Finnish	0.0217	0.0216
European (Non-Finnish)	0.00579	0.00577
Middle Eastern	0.000598	0.000598
South Asian	0.00152	0.00150
Other	0.00410	0.00392

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein hydrolyzes the inositol phosphate linkage in proteins anchored by phosphatidylinositol glycans (GPI-anchor) thus releasing these proteins from the membrane.
• Pathway: Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Homo sapiens (human);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;adp-ribosylation factor;Phosphatidylinositol phosphate metabolism;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.962
• rvis_EVS: 0.28
• rvis_percentile_EVS: 70.78

Haploinsufficiency Scores

• pHI: 0.295
• hipred: N
• hipred_score: 0.431
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpld1
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: ossification;cell migration involved in sprouting angiogenesis;chondrocyte differentiation;complement receptor mediated signaling pathway;C-terminal protein lipidation;GPI anchor release;negative regulation of cell population proliferation;insulin receptor signaling pathway;response to glucose;positive regulation of endothelial cell migration;positive regulation of alkaline phosphatase activity;positive regulation of triglyceride biosynthetic process;negative regulation of triglyceride catabolic process;positive regulation of glucose metabolic process;positive regulation of high-density lipoprotein particle clearance;cellular response to insulin stimulus;cellular response to drug;hematopoietic stem cell migration;positive regulation of insulin secretion involved in cellular response to glucose stimulus;positive regulation of apoptotic process;positive regulation of cytolysis;phosphatidylcholine metabolic process;positive regulation of membrane protein ectodomain proteolysis;positive regulation of secretion;transepithelial transport;cellular response to calcium ion;cellular response to cholesterol;cellular response to triglyceride;cellular response to pH;hematopoietic stem cell migration to bone marrow;regulation of cellular response to insulin stimulus
• Cellular component: extracellular region;extracellular space;cytoplasm;lysosomal membrane;extracellular matrix;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: glycosylphosphatidylinositol phospholipase D activity;phospholipase D activity;sodium channel regulator activity