GDPD5

glycerophosphodiester phosphodiesterase domain containing 5

Basic information

Region (hg38): 11:75434640-75525941

Links

ENSG00000158555 ∙ NCBI:81544 ∙ OMIM:609632 ∙ HGNC:28804 ∙ Uniprot:Q8WTR4 ∙ 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 GDPD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDPD5 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				2	1	3
missense			54	4		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	54	6	1

Variants in GDPD5

This is a list of pathogenic ClinVar variants found in the GDPD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-75435512-G-A		not specified	Uncertain significance (Apr 13, 2022)
11-75435598-T-G		not specified	Uncertain significance (May 26, 2025)
11-75436974-C-T		not specified	Uncertain significance (Sep 28, 2021)
11-75436975-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-75436983-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-75436992-G-A		not specified	Uncertain significance (Mar 06, 2023)
11-75437029-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-75437043-C-T		not specified	Uncertain significance (Mar 22, 2023)
11-75439886-G-A		not specified	Likely benign (Jan 18, 2023)
11-75439890-G-A			Likely benign (Jul 01, 2022)
11-75439895-T-C		not specified	Uncertain significance (Aug 19, 2023)
11-75439923-G-T		not specified	Uncertain significance (Nov 26, 2024)
11-75439926-G-A			Likely benign (Jul 01, 2022)
11-75439952-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-75441165-T-C		not specified	Uncertain significance (Jun 27, 2023)
11-75441203-G-A		not specified	Uncertain significance (Apr 23, 2024)
11-75441203-G-C		not specified	Uncertain significance (Oct 20, 2024)
11-75441233-G-A		not specified	Uncertain significance (Mar 15, 2024)
11-75441264-C-T		not specified	Uncertain significance (Apr 08, 2025)
11-75441651-C-G		not specified	Uncertain significance (Jan 06, 2023)
11-75441658-C-T		not specified	Uncertain significance (Jan 21, 2025)
11-75441716-C-T		not specified	Likely benign (Oct 24, 2023)
11-75441745-T-C		not specified	Uncertain significance (Dec 30, 2024)
11-75441751-C-T		not specified	Uncertain significance (Jan 26, 2023)
11-75441752-C-T		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDPD5	protein_coding	protein_coding	ENST00000336898	15	91264

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000250	1.00	125722	2	24	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	298	393	0.759	0.0000259	3885
Missense in Polyphen		100	143.62	0.69626		1527
Synonymous	-0.679	179	168	1.07	0.0000115	1245
Loss of Function	3.31	12	32.3	0.372	0.00000139	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000101	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.000404	0.000359
Other	0.000352	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes neurite formation. Cooperates with PRDX1 to drive postmitotic motor neuron differentiation. The glycerophosphodiester phosphodiesterase activity may be required for its role in neuronal differentiation. May contribute to the osmotic regulation of cellular glycerophosphocholine.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid catabolism;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.593
• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.11

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.756
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gdpd5
• Phenotype: cellular phenotype; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: gdpd5a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: lipid metabolic process;spinal cord motor neuron differentiation;cerebral cortex neuron differentiation;neuron projection development;positive regulation of neuron differentiation;negative regulation of Notch signaling pathway;positive regulation of cell cycle;regulation of timing of cell differentiation
• Cellular component: integral component of membrane;growth cone;neuronal cell body;perinuclear endoplasmic reticulum
• Molecular function: phosphatidylinositol phospholipase C activity;protein binding;glycerophosphodiester phosphodiesterase activity;glycerophosphocholine phosphodiesterase activity