GPAM

protein-coding

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

Gene summary

This gene encodes a mitochondrial enzyme which prefers saturated fatty acids as its substrate for the synthesis of glycerolipids. This metabolic pathway's first step is catalyzed by the encoded enzyme. Two forms for this enzyme exist, one in the mitochondria and one in the endoplasmic reticulum. Two alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_001244949.2

Inheritance

—

ClinVar variants

U:99B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr10:112,149,865-112,215,377

External References & Databases

Ensembl (ENSG00000119927)

Transcript & Mutation Effects

hg38 • Region Span ~65.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GPAM variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 93

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001244949.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			96 clinvar	3 clinvar	1 clinvar	100
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	99	3	2	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001244949.2	RefSeq	NP_001231878.1	20	MANE Select
ENST00000348367.9	Ensembl	ENSP00000265276.4	20	MANE Select
NM_020918.6	RefSeq	NP_065969.3	20	Standard
ENST00000369425.5	Ensembl	ENSP00000358433.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerolipid metabolism - Homo sapiens (human)
Glycerophospholipid metabolism - Homo sapiens (human)
Metformin Pathway, Pharmacodynamic
Familial lipoprotein lipase deficiency
Glycerolipid Metabolism

Biological Process

glycerol-3-phosphate metabolic process
fatty acid metabolic process
acyl-CoA metabolic process
phosphatidic acid biosynthetic process
phospholipid biosynthetic process

Molecular Function

glycerol-3-phosphate O-acyltransferase activity
sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity

Cellular Component

mitochondrial outer membrane
plasma membrane
integral component of membrane
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000348367
Coding exons: 20
Length: 65512
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125748
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.37	359	440	0.816	0.0000228	5425
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00027	0.00027	rare
Finnish	0.00046	0.00046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.375

Intolerance Scores

LoFtool: 0.581
RVIS EVS: -0.24
RVIS percentile EVS: 36.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.969

Gene Damage Prediction

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