GPD2

glycerol-3-phosphate dehydrogenase 2, the group of EF-hand domain containing

Basic information

Region (hg38): 2:156435290-156613735

Links

ENSG00000115159 ∙ NCBI:2820 ∙ OMIM:138430 ∙ HGNC:4456 ∙ Uniprot:P43304 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diabetes mellitus, noninsulin-dependent (No Known Disease Relationship), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPD2 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				6		6
missense			39	2	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	8	1

Variants in GPD2

This is a list of pathogenic ClinVar variants found in the GPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-156476134-C-T		not specified	Uncertain significance (Dec 22, 2023)
2-156476181-C-G		not specified	Uncertain significance (Mar 01, 2024)
2-156496063-A-C		not specified	Uncertain significance (May 16, 2024)
2-156496076-C-T		GPD2-related disorder	Likely benign (Aug 19, 2023)
2-156496164-A-G		Type 2 diabetes mellitus	Conflicting classifications of pathogenicity (Jun 01, 2024)
2-156496174-G-A			Uncertain significance (Apr 06, 2018)
2-156496195-C-T		not specified	Uncertain significance (Oct 27, 2022)
2-156510813-G-C		not specified	Uncertain significance (Mar 30, 2024)
2-156510824-T-G		not specified	Uncertain significance (Jul 19, 2022)
2-156510884-T-C			Likely benign (Mar 29, 2018)
2-156512228-G-A		not specified	Uncertain significance (Jan 09, 2023)
2-156513364-A-G		not specified	Uncertain significance (Dec 08, 2023)
2-156513414-T-C		GPD2-related disorder	Likely benign (Dec 09, 2019)
2-156513415-G-A		GPD2-related disorder	Benign (Dec 18, 2019)
2-156513449-C-T			Conflicting classifications of pathogenicity (Jun 01, 2024)
2-156513451-A-G		not specified	Uncertain significance (Apr 12, 2023)
2-156513467-A-G		not specified	Uncertain significance (Aug 17, 2022)
2-156513488-A-G		not specified	Uncertain significance (Jan 08, 2024)
2-156549618-C-G		not specified	Uncertain significance (Jan 03, 2022)
2-156549619-G-A		not specified	Uncertain significance (Apr 28, 2022)
2-156549643-G-C		not specified	Uncertain significance (Mar 31, 2024)
2-156549704-T-C		not specified	Uncertain significance (Nov 14, 2023)
2-156549713-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-156550627-A-G		not specified	Likely benign (Apr 01, 2016)
2-156550656-C-G		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPD2	protein_coding	protein_coding	ENST00000310454	16	178446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.13e-11	0.970	125488	0	260	125748	0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.724	361	402	0.898	0.0000219	4748
Missense in Polyphen		141	166.97	0.84444		1884
Synonymous	-0.714	150	139	1.08	0.00000736	1426
Loss of Function	2.23	22	36.5	0.602	0.00000180	454

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00150	0.00150
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000490	0.000489
Finnish	0.000324	0.000323
European (Non-Finnish)	0.00161	0.00160
Middle Eastern	0.000490	0.000489
South Asian	0.000523	0.000523
Other	0.000980	0.000978

dbNSFP

Source: dbNSFP

• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Mitochondrial Electron Transport Chain;Familial lipoprotein lipase deficiency;Glycerol Phosphate Shuttle;Glycerolipid Metabolism;Glycerol Kinase Deficiency;Phospholipid Biosynthesis;D-glyceric acidura;Fatty Acid Beta Oxidation;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Metabolism of lipids;Metabolism;glycerol-3-phosphate shuttle;Glycerophospholipid metabolism;Triglyceride catabolism;Triglyceride metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA;glycerol degradation (Consensus)

Recessive Scores

• pRec: 0.514

Intolerance Scores

• loftool: 0.356
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.49

Haploinsufficiency Scores

• pHI: 0.436
• hipred: Y
• hipred_score: 0.591
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.847

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpd2
• Phenotype: vision/eye 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); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: gluconeogenesis;glycerophosphate shuttle;glycerol catabolic process;multicellular organism growth;camera-type eye development;glycerol-3-phosphate catabolic process
• Cellular component: mitochondrion;mitochondrial inner membrane;glycerol-3-phosphate dehydrogenase complex
• Molecular function: glycerol-3-phosphate dehydrogenase [NAD+] activity;glycerol-3-phosphate dehydrogenase (quinone) activity;calcium ion binding;sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity