GDE1

glycerophosphodiester phosphodiesterase 1

Basic information

Region (hg38): 16:19501693-19522123

Links

ENSG00000006007 ∙ NCBI:51573 ∙ OMIM:605943 ∙ HGNC:29644 ∙ Uniprot:Q9NZC3 ∙ 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 GDE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDE1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	1

Variants in GDE1

This is a list of pathogenic ClinVar variants found in the GDE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-19503482-T-G		not specified	Uncertain significance (Sep 20, 2023)
16-19503487-A-C		not specified	Uncertain significance (Oct 27, 2023)
16-19503513-T-C		not specified	Uncertain significance (May 18, 2023)
16-19503543-C-G		not specified	Uncertain significance (Sep 22, 2022)
16-19503597-G-A		not specified	Uncertain significance (Feb 17, 2024)
16-19504903-T-A		not specified	Uncertain significance (Nov 02, 2021)
16-19504957-C-G		not specified	Uncertain significance (May 08, 2024)
16-19504966-T-C		not specified	Uncertain significance (Feb 27, 2024)
16-19507722-C-A		not specified	Uncertain significance (May 24, 2023)
16-19510910-T-C		not specified	Uncertain significance (Oct 14, 2021)
16-19517015-T-C		not specified	Uncertain significance (Jul 07, 2022)
16-19517077-C-T		not specified	Uncertain significance (Apr 04, 2024)
16-19517123-A-C		not specified	Uncertain significance (Jul 09, 2021)
16-19521775-G-C		not specified	Uncertain significance (Dec 18, 2023)
16-19521776-G-C		not specified	Uncertain significance (Feb 27, 2024)
16-19521790-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-19521830-G-T		not specified	Uncertain significance (Oct 04, 2022)
16-19521861-G-C		not specified	Uncertain significance (Feb 16, 2023)
16-19521870-C-G		not specified	Uncertain significance (Feb 06, 2023)
16-19521872-G-C			Benign (Feb 16, 2018)
16-19521885-C-T		not specified	Uncertain significance (Nov 10, 2022)
16-19521894-A-G		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDE1	protein_coding	protein_coding	ENST00000353258	6	20453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000612	0.709	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.788	155	185	0.837	0.00000891	2176
Missense in Polyphen		44	68.57	0.64168		784
Synonymous	1.34	58	72.5	0.800	0.00000368	628
Loss of Function	1.09	10	14.5	0.691	7.94e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000598	0.000598
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000334	0.000334
Middle Eastern	0.000111	0.000109
South Asian	0.000238	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has glycerophosphoinositol phosphodiesterase activity. Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity). {ECO:0000250|UniProtKB:Q9JL55, ECO:0000250|UniProtKB:Q9JL56}.
• Pathway: Phospholipid Biosynthesis;Metabolism of lipids;Metabolism;Glycerophospholipid catabolism;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.659
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.557
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.788

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gde1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: lipid metabolic process;phospholipid metabolic process;glycerophospholipid catabolic process;N-acylethanolamine metabolic process
• Cellular component: plasma membrane;integral component of membrane;cytoplasmic vesicle membrane
• Molecular function: lysophospholipase activity;glycerophosphodiester phosphodiesterase activity;metal ion binding;glycerophosphoinositol glycerophosphodiesterase activity