rs754871147
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Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PM4_Supporting
The NM_000387.6(SLC25A20):c.779_781del(p.Glu260del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000379 in 1,614,106 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00039 ( 0 hom. )
Consequence
SLC25A20
NM_000387.6 inframe_deletion
NM_000387.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.00
Genes affected
SLC25A20 (HGNC:1421): (solute carrier family 25 member 20) This gene product is one of several closely related mitochondrial-membrane carrier proteins that shuttle substrates between cytosol and the intramitochondrial matrix space. This protein mediates the transport of acylcarnitines into mitochondrial matrix for their oxidation by the mitochondrial fatty acid-oxidation pathway. Mutations 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 new born and infants. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM1
?
In a repeat Solcar 3 (size 86) in uniprot entity MCAT_HUMAN there are 6 pathogenic changes around while only 1 benign (86%) in NM_000387.6
PM2
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Very rare variant in population databases, with high coverage;
PM4
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Nonframeshift variant in NON repetitive region in NM_000387.6. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A20 | NM_000387.6 | c.779_781del | p.Glu260del | inframe_deletion | 8/9 | ENST00000319017.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A20 | ENST00000319017.5 | c.779_781del | p.Glu260del | inframe_deletion | 8/9 | 1 | NM_000387.6 | P1 | |
SLC25A20 | ENST00000430379.5 | c.560_562del | p.Glu187del | inframe_deletion | 6/7 | 3 | |||
SLC25A20 | ENST00000479050.1 | n.98_100del | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
SLC25A20 | ENST00000440964.1 | c.*609_*611del | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152212Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000274 AC: 69AN: 251446Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135890
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GnomAD4 exome AF: 0.000392 AC: 573AN: 1461894Hom.: 0 AF XY: 0.000407 AC XY: 296AN XY: 727248
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GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74356
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Carnitine acylcarnitine translocase deficiency Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2022 | This variant, c.779_781del, results in the deletion of 1 amino acid(s) of the SLC25A20 protein (p.Glu260del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs754871147, gnomAD 0.2%), including at least one homozygous and/or hemizygous individual. This variant has been observed in individual(s) with carnitine-acylcarnitine translocase deficiency (PMID: 21605995). ClinVar contains an entry for this variant (Variation ID: 345940). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | The SLC25A20 c.779_781delAAG (p.Glu260del) variant has been identified in a compound heterozygous state with a missense variant in one individual with elevated long chain fatty acids and an acylcarnitine profile consistent with carnitine-acylcarnitine translocase deficiency (Wang et al. 2011). Control data are unavailable for this variant, which is reported at a frequency of 0.001814 in the European (Finnish) population of the Exome Aggregation Consortium. In silico modelling experiments showed that the Glu260 amino acid residue is conserved and critical for maintaining the enzyme cavity and substrate recognition. The evidence for this variant is limited. The p.Glu260del variant is therefore classified as a variant of unknown significance but suspicious for pathogenicity for carnitine-acylcarnitine translocase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 29, 2021 | In-frame deletion of 1 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21605995, 32340404) - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 29, 2022 | Variant summary: SLC25A20 c.779_781delAAG (p.Glu260del) results in an in-frame deletion that is predicted to remove one amino acid from the encoded protein. The variant allele was found at a frequency of 0.00029 in 282850 control chromosomes, predominantly at a frequency of 0.0018 within the Finnish subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within Finnish control individuals in the gnomAD database is approximately two fold of the estimated maximal expected allele frequency for a pathogenic variant in SLC25A20 causing Carnitine-Acylcarnitine Translocase Deficiency phenotype (0.0011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Finnish origin. c.779_781delAAG has been reported in the literature in at least one individual affected with Carnitine-Acylcarnitine Translocase Deficiency (Wang_2011). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign. - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at