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.

not_specified (34 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000016641.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			34 clinvar			34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	0	1

Loading clinvar variants...

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