GDPD3

glycerophosphodiester phosphodiesterase domain containing 3

Basic information

Region (hg38): 16:30104810-30113537

Links

ENSG00000102886 ∙ NCBI:79153 ∙ OMIM:616318 ∙ HGNC:28638 ∙ Uniprot:Q7L5L3 ∙ 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 GDPD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDPD3 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						0
missense			26	5		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	26	5	1

Variants in GDPD3

This is a list of pathogenic ClinVar variants found in the GDPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30104916-G-A		not specified	Uncertain significance (Nov 09, 2022)
16-30104936-G-A		not specified	Uncertain significance (May 30, 2023)
16-30104958-C-T		not specified	Uncertain significance (Jan 16, 2025)
16-30104981-G-A		not specified	Uncertain significance (Jan 23, 2025)
16-30105009-C-T		not specified	Uncertain significance (Sep 15, 2021)
16-30108204-C-A		not specified	Benign (Oct 09, 2017)
16-30108221-C-T		not specified	Uncertain significance (Dec 02, 2021)
16-30108226-T-G		not specified	Uncertain significance (Feb 15, 2023)
16-30108239-G-C		not specified	Uncertain significance (Aug 05, 2024)
16-30108383-C-G		not specified	Uncertain significance (Mar 04, 2025)
16-30108412-C-T		not specified	Uncertain significance (Jan 09, 2024)
16-30108415-G-A		not specified	Uncertain significance (Apr 23, 2024)
16-30111432-G-C		not specified	Uncertain significance (Sep 27, 2024)
16-30111470-G-A		not specified	Uncertain significance (Oct 01, 2024)
16-30111476-C-A		not specified	Likely benign (Mar 01, 2023)
16-30111515-C-T		not specified	Uncertain significance (Dec 01, 2022)
16-30112148-T-G		not specified	Uncertain significance (Apr 09, 2024)
16-30112167-C-T		not specified	Uncertain significance (Dec 19, 2024)
16-30112194-G-A		not specified	Uncertain significance (Mar 11, 2022)
16-30112202-C-T		not specified	Likely benign (Oct 20, 2021)
16-30112215-C-T		not specified	Uncertain significance (Aug 15, 2023)
16-30112310-C-G		not specified	Uncertain significance (Aug 04, 2024)
16-30112323-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-30112325-T-C		not specified	Uncertain significance (Oct 01, 2024)
16-30112327-C-G		not specified	Likely benign (Oct 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDPD3	protein_coding	protein_coding	ENST00000406256	10	9047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.70e-15	0.00716	125590	0	158	125748	0.000628

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.289	187	198	0.942	0.0000126	2050
Missense in Polyphen		63	71.901	0.87621		804
Synonymous	0.983	67	78.0	0.858	0.00000456	643
Loss of Function	-0.238	22	20.8	1.06	0.00000132	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00112
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000762	0.000761
Finnish	0.0000946	0.0000924
European (Non-Finnish)	0.000761	0.000756
Middle Eastern	0.000762	0.000761
South Asian	0.000656	0.000588
Other	0.000657	0.000652

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) and lysophosphatidylcholine (lyso-PC), and to a lesser extent for lysophosphatidylethanolamine (lyso-PE). Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine. {ECO:0000250|UniProtKB:Q99LY2}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Glycerophospholipid catabolism;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.699
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.144
• ghis: 0.444

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: Gdpd3

Zebrafish Information Network

• Gene name: gdpd3a
• Affected structure: pigment cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: phospholipid metabolic process;phosphatidylcholine catabolic process;glycerophospholipid catabolic process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: lysophospholipase activity;phosphoric diester hydrolase activity;metal ion binding