6-73492103-CAAAAAA-CA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_012123.4(MTO1):c.1638-120_1638-116delAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000872 in 344,160 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000087 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MTO1
NM_012123.4 intron
NM_012123.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.464
Publications
0 publications found
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]
EEF1A1 (HGNC:3189): (eukaryotic translation elongation factor 1 alpha 1) This gene encodes an isoform of the alpha subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This isoform (alpha 1) is expressed in brain, placenta, lung, liver, kidney, and pancreas, and the other isoform (alpha 2) is expressed in brain, heart and skeletal muscle. This isoform is identified as an autoantigen in 66% of patients with Felty syndrome. This gene has been found to have multiple copies on many chromosomes, some of which, if not all, represent different pseudogenes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012123.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MTO1 | NM_012123.4 | MANE Select | c.1638-120_1638-116delAAAAA | intron | N/A | NP_036255.2 | Q9Y2Z2-4 | ||
| MTO1 | NM_001123226.2 | c.1758-120_1758-116delAAAAA | intron | N/A | NP_001116698.1 | Q9Y2Z2-6 | |||
| MTO1 | NM_133645.3 | c.1713-120_1713-116delAAAAA | intron | N/A | NP_598400.1 | Q9Y2Z2-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MTO1 | ENST00000498286.6 | TSL:1 MANE Select | c.1638-120_1638-116delAAAAA | intron | N/A | ENSP00000419561.2 | Q9Y2Z2-4 | ||
| MTO1 | ENST00000415954.6 | TSL:1 | c.1758-120_1758-116delAAAAA | intron | N/A | ENSP00000402038.2 | Q9Y2Z2-6 | ||
| MTO1 | ENST00000370300.8 | TSL:1 | c.1713-120_1713-116delAAAAA | intron | N/A | ENSP00000359323.4 | Q9Y2Z2-1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 141258Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
141258
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000872 AC: 30AN: 344160Hom.: 0 AF XY: 0.0000970 AC XY: 18AN XY: 185574 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
30
AN:
344160
Hom.:
AF XY:
AC XY:
18
AN XY:
185574
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
8782
American (AMR)
AF:
AC:
3
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
9178
East Asian (EAS)
AF:
AC:
1
AN:
21060
South Asian (SAS)
AF:
AC:
2
AN:
41206
European-Finnish (FIN)
AF:
AC:
0
AN:
19102
Middle Eastern (MID)
AF:
AC:
0
AN:
1422
European-Non Finnish (NFE)
AF:
AC:
23
AN:
210102
Other (OTH)
AF:
AC:
0
AN:
18052
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.255
Heterozygous variant carriers
0
3
7
10
14
17
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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Age
GnomAD4 genome 0.00 AC: 0AN: 141258Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 68112
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
141258
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
68112
African (AFR)
AF:
AC:
0
AN:
37670
American (AMR)
AF:
AC:
0
AN:
14048
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3370
East Asian (EAS)
AF:
AC:
0
AN:
4894
South Asian (SAS)
AF:
AC:
0
AN:
4492
European-Finnish (FIN)
AF:
AC:
0
AN:
8648
Middle Eastern (MID)
AF:
AC:
0
AN:
304
European-Non Finnish (NFE)
AF:
AC:
0
AN:
65026
Other (OTH)
AF:
AC:
0
AN:
1932
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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