GDPD1

protein-coding

glycerophosphodiester phosphodiesterase domain containing 1

Gene summary

This gene encodes a member of the glycerophosphodiester phosphodiesterase family of enzymes that catalyze the hydrolysis of deacylated glycerophospholipids to glycerol phosphate and alcohol. The encoded protein is localized to the cytoplasm and concentrates near the perinuclear region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

MANE transcript

NM_182569.4

Inheritance

ClinVar variants

U:24B:1

Top phenotype

GDPD1-related condition

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr17:59,220,467-59,275,970

External References & Databases

Ensembl (ENSG00000153982)

Transcript & Mutation Effects

hg38 • Region Span ~55.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Franklin by Genoox

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GDPD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

GDPD1-related conditionTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182569.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			23 clinvar			23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	1	0	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182569.4	RefSeq	NP_872375.2	10	MANE Select
ENST00000284116.9	Ensembl	ENSP00000284116.4	10	MANE Select
NM_001165993.2	RefSeq	NP_001159465.1	10	Standard
NM_001165994.2	RefSeq	NP_001159466.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ether lipid metabolism - Homo sapiens (human)
Metabolism of lipids
Metabolism
Glycerophospholipid catabolism
PI Metabolism

Biological Process

phospholipid metabolic process
glycerophospholipid catabolic process
N-acylethanolamine metabolic process

Molecular Function

lysophospholipase activity
phosphoric diester hydrolase activity
metal ion binding
alkylglycerophosphoethanolamine phosphodiesterase activity

Cellular Component

endoplasmic reticulum membrane
membrane
integral component of membrane
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000284116
Coding exons: 10
Length: 55501
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125745
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.56	106	162	0.654	0.00000777	2045
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.546
RVIS EVS: -0.19
RVIS percentile EVS: 39.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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