rs1057519416
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_138773.4(SLC25A46):c.166dup(p.His56ProfsTer40) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000159 in 1,575,104 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
SLC25A46
NM_138773.4 frameshift
NM_138773.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.47
Genes affected
SLC25A46 (HGNC:25198): (solute carrier family 25 member 46) This gene encodes a mitochondrial solute carrier protein family member. It functions in promoting mitochondrial fission, and prevents the formation of hyperfilamentous mitochondria. Mutation of this gene results in neuropathy and optic atrophy. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
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Very rare variant in population databases, with high coverage;
PP5
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Variant 5-110739284-G-GC is Pathogenic according to our data. Variant chr5-110739284-G-GC is described in ClinVar as [Pathogenic]. Clinvar id is 372237.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A46 | NM_138773.4 | c.166dup | p.His56ProfsTer40 | frameshift_variant | 1/8 | ENST00000355943.8 | |
SLC25A46 | NM_001303249.3 | c.166dup | p.His56ProfsTer40 | frameshift_variant | 1/8 | ||
SLC25A46 | NM_001303250.3 | c.10+1038dup | intron_variant | ||||
SLC25A46 | NR_138151.2 | n.279dup | non_coding_transcript_exon_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A46 | ENST00000355943.8 | c.166dup | p.His56ProfsTer40 | frameshift_variant | 1/8 | 1 | NM_138773.4 | P1 | |
SLC25A46 | ENST00000447245.6 | c.166dup | p.His56ProfsTer40 | frameshift_variant | 1/8 | 2 | |||
SLC25A46 | ENST00000513807.5 | c.-204+1038dup | intron_variant | 2 | |||||
SLC25A46 | ENST00000508781.5 | n.112+1038dup | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181816Hom.: 0 AF XY: 0.0000102 AC XY: 1AN XY: 97632
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GnomAD4 exome AF: 0.0000162 AC: 23AN: 1422902Hom.: 0 Cov.: 31 AF XY: 0.0000156 AC XY: 11AN XY: 704104
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neuropathy, hereditary motor and sensory, type 6B Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 01, 2022 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 372237). This premature translational stop signal has been observed in individual(s) with clinical features of Charcot-Marie-Tooth disease (PMID: 26168012). This variant is present in population databases (no rsID available, gnomAD 0.001%). This sequence change creates a premature translational stop signal (p.His56Profs*40) in the SLC25A46 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC25A46 are known to be pathogenic (PMID: 26168012, 26951855, 27543974). - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 14, 2017 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at