GDPD2

glycerophosphodiester phosphodiesterase domain containing 2

Basic information

Region (hg38): X:70423031-70433390

Links

ENSG00000130055 ∙ NCBI:54857 ∙ OMIM:300940 ∙ HGNC:25974 ∙ Uniprot:Q9HCC8 ∙ 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 GDPD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDPD2 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				1		1
missense			19	3		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	2		3
Total	0	0	20	6	0

Variants in GDPD2

This is a list of pathogenic ClinVar variants found in the GDPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-70424991-G-A		not specified	Uncertain significance (Sep 22, 2023)
X-70424993-G-T		not specified	Uncertain significance (Mar 04, 2024)
X-70425018-G-A		not specified	Uncertain significance (Oct 03, 2022)
X-70425061-G-A		not specified	Uncertain significance (Aug 05, 2024)
X-70425777-G-A		not specified	Likely benign (Feb 01, 2023)
X-70425781-G-C		not specified	Uncertain significance (Oct 17, 2024)
X-70426071-G-A		not specified	Likely benign (Mar 16, 2022)
X-70426398-G-A		not specified	Uncertain significance (Aug 30, 2022)
X-70426402-C-T		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-70426455-C-T		not specified	Uncertain significance (Jun 18, 2024)
X-70426681-G-T		not specified	Uncertain significance (Dec 11, 2024)
X-70426693-C-A		not specified	Uncertain significance (Feb 23, 2023)
X-70426961-A-G		not specified	Uncertain significance (Jan 22, 2025)
X-70427145-C-T			Likely benign (Feb 01, 2023)
X-70427167-C-T		not specified	Uncertain significance (May 23, 2023)
X-70427185-G-A		not specified	Uncertain significance (Dec 07, 2024)
X-70427349-C-G		not specified	Uncertain significance (Jan 03, 2024)
X-70427428-C-G		not specified	Uncertain significance (Mar 03, 2025)
X-70429552-T-A		not specified	Uncertain significance (Nov 28, 2023)
X-70429557-C-T		not specified	Uncertain significance (Aug 28, 2024)
X-70429626-G-A		not specified	Uncertain significance (May 24, 2023)
X-70429940-G-A		not specified	Uncertain significance (Jul 02, 2024)
X-70429973-G-A		not specified	Uncertain significance (Jul 08, 2022)
X-70429987-C-T		not specified	Uncertain significance (Oct 24, 2024)
X-70429993-G-C		not specified	Uncertain significance (Nov 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDPD2	protein_coding	protein_coding	ENST00000453994	16	10360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.315	0.685	125739	3	4	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	142	227	0.626	0.0000177	3794
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000229	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000123	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000162	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.385
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gdpd2

Gene ontology

• Biological process: lipid metabolic process;positive regulation of osteoblast differentiation;actin filament reorganization
• Cellular component: cytoplasm;actin filament;plasma membrane;integral component of membrane;lamellipodium
• Molecular function: glycerophosphodiester phosphodiesterase activity;metal ion binding;glycerophosphoinositol inositolphosphodiesterase activity