NM_017875.4:c.324_325delCT
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_017875.4(SLC25A38):c.324_325delCT(p.Tyr109LeufsTer43) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000273 in 1,613,754 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_017875.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 151926Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251474Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135910
GnomAD4 exome AF: 0.000283 AC: 413AN: 1461828Hom.: 0 AF XY: 0.000303 AC XY: 220AN XY: 727210
GnomAD4 genome AF: 0.000184 AC: 28AN: 151926Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74198
ClinVar
Submissions by phenotype
not provided Pathogenic:4
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This sequence change creates a premature translational stop signal (p.Tyr109Leufs*43) in the SLC25A38 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC25A38 are known to be pathogenic (PMID: 19412178, 25985931). This variant is present in population databases (rs535344665, gnomAD 0.04%). This premature translational stop signal has been observed in individuals with congenital sideroblastic anemia (PMID: 19412178, 21393332). ClinVar contains an entry for this variant (Variation ID: 1119). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects SLC25A38 function (PMID: 19412178). For these reasons, this variant has been classified as Pathogenic. -
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 28772256, 19412178, 27753142, 21393332, 31589614) -
SLC25A38: PM3:Very Strong, PVS1, PM2:Supporting -
Sideroblastic anemia 2 Pathogenic:4
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.017%). The variant is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic without evidence for the classification (ClinVar ID: VCV000001119 / PMID: 19412178). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
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SLC25A38-related disorder Pathogenic:1
The SLC25A38 c.324_325delCT (p.Tyr109LeufsTer43) frameshift variant is also reported as c.698_699delCT (p.Leu108fs) in literature. This variant has been reported in at least two studies, in which it is found in a total of six unrelated individuals with congenital sideroblastic anemia, including in two in a homozygous state and in four in a compound heterozygous state with a second missense or truncating variant (Guernsey et al. 2009; Kannengiesser et al. 2011). This variant is not reported in individuals with pyridoxine-refractory sideroblastic anemia. Control data are unavailable for this variant, which is reported at a frequency of 0.001454 in the European American population of the Exome Sequencing Project. Based on the collective evidence, the p.Tyr109LeufsTer43 variant is classified as likely pathogenic for SLC25A38-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at