chr1-155610327-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_018116.4(MSTO1):c.79C>T(p.Gln27Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000471 in 849,286 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 Pathogenic (no stars).
Frequency
Genomes: not found (cov: 26)
Exomes 𝑓: 0.0000047 ( 0 hom. )
Consequence
MSTO1
NM_018116.4 stop_gained
NM_018116.4 stop_gained
Scores
3
2
2
Clinical Significance
Conservation
PhyloP100: 3.05
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 Likely_pathogenic. Variant got 7 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 15 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 1-155610327-C-T is Pathogenic according to our data. Variant chr1-155610327-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 987950.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.79C>T | p.Gln27Ter | stop_gained | 1/14 | ENST00000245564.8 | |
LOC105371452 | XR_922171.2 | n.77-435G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTO1 | ENST00000245564.8 | c.79C>T | p.Gln27Ter | stop_gained | 1/14 | 1 | NM_018116.4 | P1 | |
ENST00000456382.2 | n.54G>A | non_coding_transcript_exon_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 26
GnomAD3 genomes
?
Cov.:
26
GnomAD4 exome AF: 0.00000471 AC: 4AN: 849286Hom.: 0 Cov.: 11 AF XY: 0.00000935 AC XY: 4AN XY: 427730
GnomAD4 exome
AF:
AC:
4
AN:
849286
Hom.:
Cov.:
11
AF XY:
AC XY:
4
AN XY:
427730
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 26
GnomAD4 genome
?
Cov.:
26
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 03, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
MutationTaster
Benign
A;A;A;A
Vest4
0.067, 0.11
GERP RS
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