rs536000212
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_017646.6(TRIT1):c.334del(p.Arg112GlufsTer36) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000718 in 1,609,984 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
Genomes: 𝑓 0.00034 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00076 ( 0 hom. )
Consequence
TRIT1
NM_017646.6 frameshift
NM_017646.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.33
Genes affected
TRIT1 (HGNC:20286): (tRNA isopentenyltransferase 1) This gene encodes a protein that that is targeted to the mitochondrion and modifies transfer RNAs (tRNAs) by adding a dimethylallyl group onto the adenine at position 37. This modification is important for maintaining the correct reading frame during protein translation. This gene is considered a tumor suppressor and its expression can decrease cell growth. Alternative splicing results in multiple transcripts variants, most of which are likely non-functional. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 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 1-39854049-CG-C is Pathogenic according to our data. Variant chr1-39854049-CG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 545453.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIT1 | NM_017646.6 | c.334del | p.Arg112GlufsTer36 | frameshift_variant | 3/11 | ENST00000316891.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIT1 | ENST00000316891.10 | c.334del | p.Arg112GlufsTer36 | frameshift_variant | 3/11 | 1 | NM_017646.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152104Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000427 AC: 106AN: 248326Hom.: 0 AF XY: 0.000484 AC XY: 65AN XY: 134270
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GnomAD4 exome AF: 0.000758 AC: 1105AN: 1457762Hom.: 0 Cov.: 29 AF XY: 0.000736 AC XY: 534AN XY: 725380
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GnomAD4 genome ? AF: 0.000335 AC: 51AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74426
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Epileptic encephalopathy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | Jun 01, 2017 | - - |
See cases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Apr 02, 2020 | ACMG classification criteria: PVS1, PS4, PM2, PM3 - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | TRIT1: PVS1, PM2 - |
TRIT1 Deficiency Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | DASA | Feb 05, 2022 | The c.334del;p.(Arg112Glufs*36) is a null frameshift variant (NMD) in the TRIT1 gene and predicts alteration of the nonsense-mediate decay - NMD is present in a relevant exon to the transcript - PVS1. The variant is present at low allele frequencies population databases (rs536000212– gnomAD 0.003353%; ABraOM 0.001281 frequency - http://abraom.ib.usp.br/) -PM2_supporting. In summary, the currently available evidence indicates that the variant is likely pathogenic. - |
Combined oxidative phosphorylation deficiency 35 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 05, 2024 | - - |
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