GDPD4

glycerophosphodiester phosphodiesterase domain containing 4

Basic information

Region (hg38): 11:77216558-77301687

Links

ENSG00000178795 ∙ NCBI:220032 ∙ ∙ HGNC:24849 ∙ Uniprot:Q6W3E5 ∙ 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 GDPD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDPD4 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			41	2		43
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	3	1

Variants in GDPD4

This is a list of pathogenic ClinVar variants found in the GDPD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-77217003-T-C			Likely benign (Apr 01, 2023)
11-77217312-T-C		not specified	Uncertain significance (Jul 15, 2024)
11-77227914-C-T		not specified	Uncertain significance (Dec 06, 2023)
11-77229153-T-C		not specified	Uncertain significance (Jul 08, 2022)
11-77229172-C-A		not specified	Uncertain significance (Feb 08, 2023)
11-77233128-T-C		not specified	Uncertain significance (Jan 10, 2023)
11-77233128-T-G		not specified	Uncertain significance (Dec 20, 2024)
11-77233129-T-C		not specified	Uncertain significance (Oct 29, 2024)
11-77233141-C-T		not specified	Uncertain significance (Feb 12, 2024)
11-77233161-G-C		not specified	Uncertain significance (Feb 27, 2024)
11-77233170-T-C		not specified	Uncertain significance (Aug 27, 2024)
11-77243721-T-C		not specified	Uncertain significance (Mar 29, 2022)
11-77243727-A-G		not specified	Uncertain significance (Nov 10, 2024)
11-77243743-T-TA			Benign (Oct 16, 2019)
11-77243755-C-T		not specified	Likely benign (Oct 25, 2024)
11-77243779-G-A		not specified	Uncertain significance (Feb 17, 2024)
11-77243797-C-A		not specified	Uncertain significance (Mar 02, 2023)
11-77243806-C-A		not specified	Uncertain significance (Mar 11, 2022)
11-77243815-C-T		not specified	Uncertain significance (Nov 14, 2024)
11-77243824-T-C		not specified	Uncertain significance (Aug 02, 2023)
11-77245289-G-T		not specified	Uncertain significance (May 09, 2023)
11-77245304-C-A		not specified	Uncertain significance (Jan 26, 2022)
11-77245319-C-T		not specified	Uncertain significance (May 29, 2024)
11-77245327-C-T		not specified	Uncertain significance (Feb 01, 2025)
11-77245328-G-A		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDPD4	protein_coding	protein_coding	ENST00000315938	15	85130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.80e-13	0.249	124985	9	754	125748	0.00304

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00145	272	272	1.00	0.0000133	3429
Missense in Polyphen		74	82.377	0.89831		1130
Synonymous	0.444	92	97.6	0.943	0.00000499	963
Loss of Function	1.09	23	29.4	0.782	0.00000125	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00281	0.00268
Ashkenazi Jewish	0.00615	0.00607
East Asian	0.0314	0.0315
Finnish	0.00	0.00
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.0314	0.0315
South Asian	0.00110	0.00108
Other	0.00312	0.00310

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0392

Intolerance Scores

• loftool: 0.950
• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.57

Haploinsufficiency Scores

• pHI: 0.0159
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 1.87e-7

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Gdpd4

Gene ontology

• Biological process: lipid metabolic process
• Cellular component: integral component of membrane
• Molecular function: glycerophosphodiester phosphodiesterase activity;metal ion binding