SLC25A20

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Introduction

The SLC25A20 gene, solute carrier family 25 member 20, is located on chromosome 3p21.31 and has 9 exons spanning ~16.5kb (1). It encodes a 302 amino acid protein that is one of several closely related mitochondrial-membrane carrier proteins shuttling substrates between cytosol and the intramitochondrial matrix space.

The SLC25A20 protein mediates the transport of acylcarnitines into mitochondrial matrix for oxidation by the mitochondrial fatty acid-oxidation pathway (2). It also mediates the electroneutral exchange of acylcarnitines (O-acyl-(R)-carnitine or L-acylcarnitine) of different acyl chain lengths (ranging from O-acetyl-(R)-carnitine to long-chain O-acyl-(R)-carnitines) with free carnitine ((R)-carnitine or L-carnitine) across the mitochondrial inner membrane (3,4).

Variations in this gene are associated with carnitine-acylcarnitine translocase deficiency, which can cause a variety of pathological conditions such as hypoglycemia, cardiac arrest, hepatomegaly, hepatic dysfunction and muscle weakness, and is usually lethal in newborns and infants (1). The protein is expressed in liver, duodenum and other tissues (5).

More than 58 disease-causing variants in the SLC25A20 gene have been identified in patients and are represented in this database. The variants occur across the entire length of the gene and include frameshift, splice site, copy-number, nonsense and missense variants (6).

Variant List

To see more information, click on the Variant in the table. Hover on the Variant in the table to see its location on the gene. For more information on table headers, HGVS nomenclature, and ACMG classification please use the following links here.

Gene Structure

Variant ID	Variant	Amino Acid Change	Gene Symbol	Variant Type	Effect Type	Display ACMG Call	Disease Subtype	Times Observed Range	Phenotype	PMID	Location

SLC25A20_0059	NC_000003.11:g.(?_48900092)_(48895143_?)del		SLC25A20			Pathogenic	CACT	<3		21605995
SLC25A20_0002	c.897dup	p.Asn300Glnfs*24	SLC25A20	Duplication	Frameshift	Pathogenic	CACT	3-5	Abnormal liver morph....	11162577, 36109795, 9399886	Exon 9
SLC25A20_0003	c.868G>A	p.Ala290Thr	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3			Exon 9
SLC25A20_0004	c.843+4_843+50del	Intronic	SLC25A20	Deletion	Splice region	Likely Pathogenic	CACT	3-5	Abnormal liver morph....	10472533, 15365988	Intron 8
SLC25A20_0005	c.843+4A>G	Intronic	SLC25A20	SNV	Splice region	Uncertain Significance	CACT	<3			Intron 8
SLC25A20_0006	c.842C>T	p.Ala281Val	SLC25A20	SNV	Missense	Pathogenic	CACT	3-5	Cardiac-other, Coma,....	15365988	Exon 8
SLC25A20_0007	c.824G>A	p.Arg275Gln	SLC25A20	SNV	Missense	Likely Pathogenic	CACT	6-10	Abnormal liver morph....	32337051	Exon 8
SLC25A20_0008	c.823C>T	p.Arg275*	SLC25A20	SNV	Nonsense	Pathogenic	CACT	<3	Hyperammonemia, Hypoketotic hypoglycemia	21605995	Exon 8
SLC25A20_0009	c.804del	p.Phe269Serfs*4	SLC25A20	Deletion	Frameshift	Pathogenic	CACT	6-10	Encephalopathy, Hepatic failure	12559850, 21605995, 24088670, 31156707, 35360862	Exon 8
SLC25A20_0010	c.673_782del	p.Ala225Serfs*27	SLC25A20	Copy Number Loss		Likely Pathogenic	CACT	<3	Abnormal liver morph....	21605995, 9686371	Exon 7-8, Intron 7
SLC25A20_0011	c.779_781del	p.Glu260del	SLC25A20	Deletion	Deletion	Uncertain Significance	CACT	<3	Abnormality of metab....	21605995	Exon 8
SLC25A20_0012	c.752_761del	p.Asp251Glyfs*3	SLC25A20	Deletion	Frameshift	Pathogenic	CACT	<3	Abnormality of metab....	21605995	Exon 8
SLC25A20_0013	c.719-9_719-1dup	Intronic	SLC25A20	Insertion	Intronic	Uncertain Significance	CACT	<3	Arrhythmia, Cardiomy....	31108048, 33194920	Intron 7
SLC25A20_0014	c.718+1G>C	Intronic	SLC25A20	SNV	Splice donor	Pathogenic	CACT	<3	Abnormal liver morph....	15365988	Intron 7
SLC25A20_0015	c.715A>C	p.Thr239Pro	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3		31319225	Exon 7
SLC25A20_0016	c.713A>G	p.Gln238Arg	SLC25A20	SNV	Missense	Pathogenic	CACT	21-30	Arrhythmia, Cardiomy....	15057979, 23867825, 32906206	Exon 7
SLC25A20_0017	c.706C>T	p.Arg236*	SLC25A20	SNV	Nonsense	Pathogenic	CACT	<3		34626609	Exon 7
SLC25A20_0018	c.691G>C	p.Asp231His	SLC25A20	SNV	Missense	Pathogenic	CACT	3-5	Hepatic failure, Hyperammonemia, Hypoglycemia	12559850, 15365988	Exon 7
SLC25A20_0019	c.689C>G	p.Pro230Arg	SLC25A20	SNV	Missense	Likely Pathogenic	CACT	<3		12559850	Exon 7
SLC25A20_0020	c.658G>A	p.Gly220Arg	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3	Encephalopathy, Hype....	32905135	Exon 7
SLC25A20_0021	c.609-1G>A	Intronic	SLC25A20	SNV	Splice acceptor	Pathogenic	CACT	<3		12559850	Intron 6
SLC25A20_0022	c.609-3C>G	Intronic	SLC25A20	SNV		Pathogenic	CACT	3-5	Abnormal liver morph....	16919490, 25604974	Intron 6
SLC25A20_0023	c.576G>A	p.Trp192*	SLC25A20	SNV	Nonsense	Pathogenic	CACT	<3	Asphyxia, Cardiac ar....	24088670	Exon 6
SLC25A20_0024	c.536A>G	p.Asp179Gly	SLC25A20	SNV	Missense	Uncertain Significance	CACT	3-5	Abnormality of metab....	25614308	Exon 6
SLC25A20_0025	c.533G>A	p.Arg178Gln	SLC25A20	SNV	Missense	Pathogenic	CACT	3-5		12559850	Exon 5
SLC25A20_0026	c.532C>T	p.Arg178*	SLC25A20	SNV	Nonsense	Pathogenic	CACT	6-10	Abnormal liver morph....	12559850, 12801121, 15365988, 25614308	Exon 5
SLC25A20_0027	c.528del	p.Met177Cysfs*12	SLC25A20	Deletion	Frameshift	Pathogenic	CACT	<3		21605995	Exon 5
SLC25A20_0028	c.516T>C	p.Thr172=	SLC25A20	SNV	Silent	Uncertain Significance	CACT	<3		24088670	Exon 5
SLC25A20_0029	c.496C>T	p.Arg166*	SLC25A20	SNV	Nonsense	Pathogenic	CACT	3-5	Abnormal liver morph....	10384384, 10653336, 12559850, 21605995	Exon 5
SLC25A20_0030	c.463T>C	p.Cys155Arg	SLC25A20	SNV	Missense	Likely Pathogenic	CACT	<3	Discoloured stools, Jaundice	31561269	Exon 5
SLC25A20_0031	c.417+1G>T	Intronic	SLC25A20	SNV	Splice donor	Pathogenic	CACT	<3		23322164, 23850792	Intron 4
SLC25A20_0032	c.397C>T	p.Arg133Trp	SLC25A20	SNV	Missense	Pathogenic	CACT	3-5	Abnormal liver morph....	15365988, 21605995, 32905135	Exon 4
SLC25A20_0033	c.261_388del	p.Val88Trpfs*53	SLC25A20	Copy Number Loss		Pathogenic	CACT	<3	Abnormal liver morph....	21605995, 9686371	Exon 3-4, Intron 3
SLC25A20_0034	c.383T>A	p.Met128Lys	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3		26589311	Exon 4
SLC25A20_0035	c.364G>A	p.Val122Ile	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3			Exon 4
SLC25A20_0036	c.326+1del	Intronic	SLC25A20	Deletion	Splice donor	Pathogenic	CACT	6-10	Abnormal liver morph....	11592821, 15365988, 16919490, 25604974, 32070364, 36109795, 9290607	Intron 3
SLC25A20_0037	c.270del	p.Phe91Leufs*38	SLC25A20	Deletion	Frameshift	Pathogenic	CACT	3-5	Abnormal liver morph....	11592821, 35360862, 8450053	Exon 3
SLC25A20_0038	c.269T>G	p.Phe90Cys	SLC25A20	SNV	Missense	Likely Pathogenic	CACT	<3	Hypoglycemia	36109795	Exon 3
SLC25A20_0039	c.241G>A	p.Gly81Arg	SLC25A20	SNV	Missense	Pathogenic	CACT	3-5		23322164, 23850792	Exon 3
SLC25A20_0040	c.226G>C	p.Ala76Pro	SLC25A20	SNV	Missense	Uncertain Significance	CACT	30+			Exon 3
SLC25A20_0041	c.199-10T>G	Intronic	SLC25A20	SNV	Intronic	Likely Pathogenic	CACT	30+	Abnormal liver morph....	11592821, 12559850, 1598097, 24088670, 25459972, 25604974, 26117549, 27066551, 29137068, 31108048, 33194920, 34626609, 35314707, 35360862, 36419912, 8739960, 9290607	Intron 2
SLC25A20_0042	c.198+4G>A	Intronic	SLC25A20	SNV	Splice region	Uncertain Significance	CACT	<3			Intron 2
SLC25A20_0043	c.160_163delinsTGGG	p.Gly54_Thr55delinsTrpAla	SLC25A20	Delins	Missense	Pathogenic	CACT	6-10	Abnormal liver morph....	15365988, 21605995, 25614308	Exon 2
SLC25A20_0044	c.110G>C	p.Arg37Pro	SLC25A20	SNV	Missense	Likely Pathogenic	CACT	<3	Hyperaminoaciduria	31575911	Exon 2
SLC25A20_0045	c.109C>T	p.Arg37*	SLC25A20	SNV	Nonsense	Pathogenic	CACT	<3		34626609	Exon 2
SLC25A20_0046	c.106-2A>T	Intronic	SLC25A20	SNV	Splice acceptor	Pathogenic	CACT	<3	Cardiac arrest	24088670	Intron 1
SLC25A20_0047	c.94G>A	p.Asp32Asn	SLC25A20	SNV	Missense	Likely Pathogenic	CACT	<3		12559850	Exon 1
SLC25A20_0048	c.84del	p.His29Thrfs*100	SLC25A20	Deletion	Frameshift	Pathogenic	CACT	<3	Abnormal liver morph....	11592821, 1598097	Exon 1
SLC25A20_0049	c.82G>T	p.Gly28Cys	SLC25A20	SNV	Missense	Pathogenic	CACT	6-10	Abnormality of metab....	12559850, 33123633, 34374989, 9544911	Exon 1
SLC25A20_0050	c.67T>C	p.Cys23Arg	SLC25A20	SNV	Missense	Likely Pathogenic	CACT	3-5	Cardiomyopathy, Hypoglycemia	21605995	Exon 1
SLC25A20_0051	c.65_69dup	p.Leu24Cysfs*107	SLC25A20	Insertion	Frameshift	Pathogenic	CACT	<3		12559850	Exon 1
SLC25A20_0052	c.59G>A	p.Gly20Asp	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3	Abnormal liver morph....	25614308	Exon 1
SLC25A20_0053	c.50G>C	p.Gly17Ala	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3	Attention deficit hy....	32070364	Exon 1
SLC25A20_0054	c.47C>T	p.Ala16Val	SLC25A20	SNV	Missense	Uncertain Significance	CACT	<3	Discoloured stools, Jaundice	31561269	Exon 1
SLC25A20_0055	c.10C>T	p.Gln4*	SLC25A20	SNV	Nonsense	Pathogenic	CACT	<3	Abnormality of metab....	36109795	Exon 1
SLC25A20_0056	c.3G>A	Intronic	SLC25A20	SNV	Missense	Pathogenic	CACT	<3		23322164, 23850792	Exon 1
SLC25A20_0058	c.1A>G	p.Met1?	SLC25A20	SNV	Missense	Pathogenic	CACT	<3		35360862	Exon 1
SLC25A20_0057	c.1A>G	Intronic	SLC25A20	SNV	Missense	Pathogenic	CACT	<3	Cardiac-other, Cyano....	29137068	Exon 1

Notes:

* Click the PMID number to go to the corresponding publication.
* All variants are referencing NM_000387.6 and there is no change between these versions with respect to the coding sequence.
* Genomic coordinates are calculated based on variant data provided: in some cases coordinates are estimated in order to allow users to sort the variants linearly, by approximation.

Definition of acronyms:

"*": Referenced a stop codon insertion when listed under amino acid change.
ACMG: American College of Medical Genetics and Genomics
CNV: Copy number variant which here describes a change 100 DNA nucleotides or larger.
SNV: Single DNA nucleotide variant
del: Deletion
dup: Duplication
fs: Frameshift
ins: Insertion

References:

Iacobazzi, V. et al., The structure and organization of the human carnitine/acylcarnitine translocase (CACT1) gene. Biochem Biophys Res Commun. 1998 Nov 27;252(3):770-4.
https://www.ncbi.nlm.nih.gov/gene/788
Pérez. P. et al. Functional analysis of mutations in the human carnitine/acylcarnitine translocase in Aspergillus nidulans. Fungal Genet Biol. 2003 Aug;39(3):211-20.
De Lucas, J. R. et al., Functional characterization of residues within the carnitine/acylcarnitine translocase RX2PANAAXF distinct motif. Mol Membr Biol. 2008 Feb;25(2):152-63.
https://www.uniprot.org/uniprotkb/O43772/entry#
Richbourg et al. (2023) Phenotype associations from a comprehensive database of long-chain fatty acid oxidation disorder gene variants (Abstract and poster presentation, ASHG 2023).

Introduction

Variant List

Gene Structure

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