rs143747297
Variant names:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2PP3_ModeratePP5_Very_Strong
The NM_012123.4(MTO1):c.1282G>A(p.Ala428Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000061 ( 0 hom. )
Consequence
MTO1
NM_012123.4 missense
NM_012123.4 missense
Scores
11
7
1
Clinical Significance
Conservation
PhyloP100: 9.54
Genes affected
MTO1 (HGNC:19261): (mitochondrial tRNA translation optimization 1) This gene encodes a mitochondrial protein thought to be involved in mitochondrial tRNA modification. The encoded protein may also play a role in the expression of the non-syndromic and aminoglycoside-induced deafness phenotypes associated with a specific mutation in the mitochondrial 12S rRNA gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.935
PP5
Variant 6-73482061-G-A is Pathogenic according to our data. Variant chr6-73482061-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 35496.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-73482061-G-A is described in Lovd as [Pathogenic]. Variant chr6-73482061-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152052Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251484Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135914
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GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727248
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74260
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:10
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency Pathogenic:5
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | Jan 14, 2020 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Oct 03, 2022 | PS3_Moderate, PM3_Strong, PM2 - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2013 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 13, 2025 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 428 of the MTO1 protein (p.Ala428Thr). This variant is present in population databases (rs143747297, gnomAD 0.009%). This missense change has been observed in individuals with oxidative phosphorylation deficiency (PMID: 22608499, 23929671, 25058219). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 35496). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MTO1 protein function. Experimental studies have shown that this missense change affects MTO1 function (PMID: 22608499, 23929671). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 11, 2022 | - - |
not provided Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 14, 2022 | Reported in multiple unrelated individuals with clinical features are consistent with COXPD10 who were homozygous for A428T or heterozygous for A428T and another variant in MTO1 (Ghezzi et al., 2012; Baruffini et al., 2013; O'Byrne et al., 2018); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23929671, 22608499, 25058219, 29440775, 29331171, 31589614) - |
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 31, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Nov 17, 2023 | PP3, PM2, PM3_strong, PS3 - |
Mitochondrial oxidative phosphorylation disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 12, 2017 | The p.Ala468Thr variant in MTO1 has been reported in 1 homozygous and 2 compound heterozygous individuals with infantile-onset HCM, lactic acidosis, and defecti ve mitochondrial respiratory chain activity in muscle biopsies, and segregated w ith disease in 1 affected relative (Ghezzi 2012, Baruffini 2013). This variant h as been identified in 12/126720 European chromosomes by the Genome Aggregation D atabase (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs143747297). Although this variant has been seen in the general population, its frequency is low enoug h to be consistent with a recessive carrier frequency. Yeast studies provide som e evidence that the p.Ala468Thr variant may impact protein function (Ghezzi 2012 , Baruffini 2013). However, these types of assays may not accurately represent b iological function in humans. Computational prediction tools and conservation an alysis suggest that the p.Ala468Thr variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, alt hough additional studies are required to fully establish its clinical significan ce, the p.Ala468Thr variant is likely pathogenic. ACMG/AMP Criteria applied: PM2 ,PM3,PS3_M, PP3 - |
Global developmental delay Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Génétique des Maladies du Développement, Hospices Civils de Lyon | Nov 01, 2019 | homozygous - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
.;.;.;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;.;.;H
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
D;D;.;D
Vest4
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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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