GPAM

glycerol-3-phosphate acyltransferase, mitochondrial, the group of Glycerol-3-phosphate acyltransferases

Basic information

Region (hg38): 10:112149864-112215377

Links

ENSG00000119927 ∙ NCBI:57678 ∙ OMIM:602395 ∙ HGNC:24865 ∙ Uniprot:Q9HCL2 ∙ 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 GPAM gene.

• Inborn genetic diseases (27 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPAM 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			26	1	2	29
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	26	1	3

Variants in GPAM

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

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

Position	Type	Phenotype	Significance	ClinVar
10-112153638-A-C		not specified	Uncertain significance (May 23, 2023)
10-112155893-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-112155897-T-C		not specified	Likely benign (Mar 31, 2022)
10-112155905-T-C		not specified	Uncertain significance (Feb 10, 2023)
10-112158342-G-T		not specified	Uncertain significance (Nov 17, 2023)
10-112159957-G-A		not specified	Uncertain significance (May 27, 2022)
10-112159964-G-C		not specified	Uncertain significance (May 17, 2023)
10-112160630-T-C		not specified	Uncertain significance (Feb 15, 2023)
10-112160694-T-C		not specified	Uncertain significance (Oct 14, 2023)
10-112160706-C-G		not specified	Uncertain significance (Dec 07, 2021)
10-112160814-G-C		not specified	Uncertain significance (Nov 10, 2021)
10-112160820-C-T		not specified	Uncertain significance (Jun 26, 2023)
10-112160864-A-G		not specified	Uncertain significance (Dec 14, 2023)
10-112161671-C-G		not specified	Uncertain significance (Mar 02, 2023)
10-112163799-T-C		not specified	Uncertain significance (Aug 02, 2021)
10-112164561-A-G		not specified	Uncertain significance (Aug 01, 2022)
10-112164573-G-A			Benign (Jul 23, 2018)
10-112164589-G-T		not specified	Uncertain significance (Dec 27, 2023)
10-112164616-G-GA			Benign (Jul 23, 2018)
10-112166426-A-G			Benign (Jul 23, 2018)
10-112168352-T-C		not specified	Uncertain significance (Mar 31, 2023)
10-112168440-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-112168443-A-G		not specified	Uncertain significance (Jul 25, 2023)
10-112168505-C-T		not specified	Uncertain significance (Nov 12, 2021)
10-112168910-C-G		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPAM	protein_coding	protein_coding	ENST00000348367	20	65512

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-9	1.00	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	359	440	0.816	0.0000228	5425
Missense in Polyphen		80	139.29	0.57434		1766
Synonymous	-1.37	184	162	1.14	0.00000828	1595
Loss of Function	3.36	23	48.1	0.478	0.00000277	531

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000601	0.000600
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000272	0.000272
Finnish	0.000462	0.000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000272	0.000272
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Esterifies acyl-group from acyl-ACP to the sn-1 position of glycerol-3-phosphate, an essential step in glycerolipid biosynthesis. {ECO:0000250|UniProtKB:P97564, ECO:0000269|PubMed:18238778}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Metformin Pathway, Pharmacodynamic;Familial lipoprotein lipase deficiency;Glycerolipid Metabolism;Glycerol Kinase Deficiency;Phospholipid Biosynthesis;D-glyceric acidura;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Activation of gene expression by SREBF (SREBP);Estrogen Receptor Pathway;Nuclear Receptors Meta-Pathway;Triacylglyceride Synthesis;Transcriptional regulation by RUNX1;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Metabolism of lipids;RNA Polymerase II Transcription;Regulation of cholesterol biosynthesis by SREBP (SREBF);Metabolism;CDP-diacylglycerol biosynthesis;Metabolism of steroids;Glycerophospholipid metabolism;Triglyceride biosynthesis;Triglyceride metabolism;triacylglycerol biosynthesis;Signaling by Nuclear Receptors;Glycerophospholipid biosynthesis;Phospholipid metabolism;Estrogen-dependent gene expression;Activation of gene expression by SREBF (SREBP);Synthesis of PA;RUNX1 regulates estrogen receptor mediated transcription;ESR-mediated signaling;Transcriptional regulation by RUNX1;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.375

Intolerance Scores

• loftool: 0.581
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.23

Haploinsufficiency Scores

• pHI: 0.222
• hipred: Y
• hipred_score: 0.524
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpam
• Phenotype: liver/biliary system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: glycerol-3-phosphate metabolic process;fatty acid metabolic process;acyl-CoA metabolic process;phosphatidic acid biosynthetic process;phospholipid biosynthetic process;response to glucose;CDP-diacylglycerol biosynthetic process;triglyceride biosynthetic process;regulation of intracellular estrogen receptor signaling pathway;positive regulation of multicellular organism growth;positive regulation of activated T cell proliferation;regulation of cholesterol biosynthetic process;regulation of cytokine secretion;defense response to virus;fatty acid homeostasis;phospholipid homeostasis;negative regulation of activation-induced cell death of T cells;interleukin-2 secretion
• Cellular component: mitochondrial outer membrane;plasma membrane;integral component of membrane;mitochondrial membrane
• Molecular function: glycerol-3-phosphate O-acyltransferase activity;sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity