GDPD2

protein-coding

glycerophosphodiester phosphodiesterase domain containing 2

Gene summary

This gene encodes a member of the glycerophosphodiester phosphodiesterase enzyme family. The encoded protein hydrolyzes glycerophosphoinositol to produce inositol 1-phosphate and glycerol. This protein may have a role in osteoblast differentiation and growth. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2010]

MANE transcript

NM_017711.4

Inheritance

—

ClinVar variants

U:103B:5

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chrX:70,423,031-70,433,390

External References & Databases

Ensembl (ENSG00000130055)

Transcript & Mutation Effects

hg38 • Region Span ~10.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GDPD2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 4

Abnormality of neuronal migrationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017711.4. 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			9 clinvar	1 clinvar		10
missense			71 clinvar	3 clinvar	1 clinvar	75
nonsense			4 clinvar			4
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			18 clinvar			18
Total	0	0	103	4	1	108

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017711.4	RefSeq	NP_060181.2	15	MANE Select
ENST00000374382.4	Ensembl	ENSP00000363503.3	15	MANE Select
NM_001171191.2	RefSeq	NP_001164662.1	13	Standard
NM_001171192.2	RefSeq	NP_001164663.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid metabolic process
positive regulation of osteoblast differentiation
actin filament reorganization

Molecular Function

glycerophosphodiester phosphodiesterase activity
metal ion binding
glycerophosphoinositol inositolphosphodiesterase activity

Cellular Component

cytoplasm
actin filament
plasma membrane
integral component of membrane
lamellipodium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000453994
Coding exons: 16
Length: 10360
Individuals with no LoFs: 125739
Homozygous LoFs: 3
Heterozygous LoFs: 4
Defined: 125746
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.00	142	227	0.626	0.0000177	3794
Missense (PolyPhen)		28	67.323	0.41591		1183
Synonymous	0.729	83	91.9	0.903	0.00000705	1216
Loss of Function	3.63	6	25.9	0.231	0.00000210	363

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00023	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000012	0.0000088	rare
South Asian	0.00016	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has glycerophosphoinositol inositolphosphodiesterase activity and specifically hydrolyzes glycerophosphoinositol, with no activity for other substrates such as glycerophosphoinositol 4- phosphate, glycerophosphocholine, glycerophosphoethanolamine, and glycerophosphoserine. Accelerates the program of osteoblast differentiation and growth. May play a role in remodeling of the actin cytoskeleton (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0939

Intolerance Scores

LoFtool: 0.701
RVIS EVS: 0.06
RVIS percentile EVS: 58.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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