GDPD1

glycerophosphodiester phosphodiesterase domain containing 1

Basic information

Region (hg38): 17:59220467-59275970

Links

ENSG00000153982

∙ NCBI:284161 ∙ OMIM:616317 ∙ HGNC:20883 ∙ Uniprot:Q8N9F7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GDPD1 gene.

not_specified (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDPD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000182569.4. 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						0
missense			19 clinvar			19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	19	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDPD1	protein_coding	protein_coding	ENST00000284116	10	55501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00262	0.995	125720	0	25	125745	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	106	162	0.654	0.00000777	2045
Missense in Polyphen		28	60.696	0.46132		754
Synonymous	0.0215	60	60.2	0.996	0.00000283	589
Loss of Function	2.62	8	20.9	0.382	0.00000117	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000522	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000668	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylethanolamine (lyso-PE) and lysophosphatidylcholine (lyso-PC). May be involved in bioactive N-acylethanolamine biosynthesis. Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine. {ECO:0000250|UniProtKB:Q9CRY7}.;
Pathway: Ether lipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Glycerophospholipid catabolism;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

loftool: 0.546
rvis_EVS: -0.19
rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

pHI: 0.288
hipred: Y
hipred_score: 0.554
ghis: 0.642

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gdpd1
Phenotype

Gene ontology

Biological process: phospholipid metabolic process;glycerophospholipid catabolic process;N-acylethanolamine metabolic process
Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane;perinuclear region of cytoplasm
Molecular function: lysophospholipase activity;phosphoric diester hydrolase activity;metal ion binding;alkylglycerophosphoethanolamine phosphodiesterase activity