1-155610313-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_018116.4(MSTO1):c.65C>A(p.Ala22Glu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 26)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MSTO1
NM_018116.4 missense
NM_018116.4 missense
Scores
4
7
2
Clinical Significance
Conservation
PhyloP100: 4.15
Genes affected
MSTO1 (HGNC:29678): (misato mitochondrial distribution and morphology regulator 1) Involved in mitochondrion distribution. Located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.808
PP5
?
Variant 1-155610313-C-A is Pathogenic according to our data. Variant chr1-155610313-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1693163.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTO1 | NM_018116.4 | c.65C>A | p.Ala22Glu | missense_variant | 1/14 | ENST00000245564.8 | |
LOC105371452 | XR_922171.2 | n.77-421G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTO1 | ENST00000245564.8 | c.65C>A | p.Ala22Glu | missense_variant | 1/14 | 1 | NM_018116.4 | P1 | |
ENST00000456382.2 | n.68G>T | non_coding_transcript_exon_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 26
GnomAD3 genomes
?
Cov.:
26
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 912646Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0AN XY: 457514
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
912646
Hom.:
Cov.:
12
AF XY:
AC XY:
0
AN XY:
457514
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
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Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
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Gnomad4 OTH exome
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GnomAD4 genome ? Cov.: 26
GnomAD4 genome
?
Cov.:
26
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
See cases Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Laboratory of Genetics in Ophthalmology, Institut Imagine | Jun 17, 2022 | The c.65C>A (p.22AlaGlu) variant in MSTO1 is absent from large population studies. It has been identified in compound heterozygosity with the c.220+5 splice variant (induces exon skipping; nonsense-mediated mRNA decay highly suspected from mRNA analysis in patient cells) in three siblings affected with typical MSTO1-associated myopathy, cerebellar atrophy and corticospinal involvement associated with a previously unreported optic neuropathy responsible for a profound central visual loss. Biallelism has been experimentally demonstrated. Multiple line of computational evidence support deleterious effect of the variant. In summary, the variant meets criteria to be classified as likely pathogenic based upon phenotype, family history, segregation studies, absence from controls and computational predictions. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
Polyphen
1.0
.;D;.
Vest4
0.80, 0.77
MutPred
Gain of catalytic residue at W24 (P = 0.1955);Gain of catalytic residue at W24 (P = 0.1955);Gain of catalytic residue at W24 (P = 0.1955);
MVP
0.76
MPC
3.6
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.