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.

• not_specified (88 variants)
• not_provided (9 variants)
• GPD2-related_disorder (7 variants)
• Type_2_diabetes_mellitus (3 variants)

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. These statistics are base on transcript: NM_000000408.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6		6
missense	1		92	4	1	98
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6			6
Total	1	0	99	10	1

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
		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

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

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