rs762798018
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_018116.4(MSTO1):c.22G>A(p.Val8Met) variant causes a missense change. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 27)
Exomes 𝑓: 0.00022 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MSTO1
NM_018116.4 missense
NM_018116.4 missense
Scores
3
12
4
Clinical Significance
Conservation
PhyloP100: 4.08
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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTO1 | NM_018116.4 | c.22G>A | p.Val8Met | missense_variant | 1/14 | ENST00000245564.8 | |
LOC105371452 | XR_922171.2 | n.77-378C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTO1 | ENST00000245564.8 | c.22G>A | p.Val8Met | missense_variant | 1/14 | 1 | NM_018116.4 | P1 | |
ENST00000456382.2 | n.103+8C>T | splice_region_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 7AN: 150766Hom.: 0 Cov.: 27 FAILED QC
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GnomAD3 exomes AF: 0.000202 AC: 25AN: 123620Hom.: 0 AF XY: 0.000257 AC XY: 17AN XY: 66222
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000219 AC: 152AN: 695628Hom.: 0 Cov.: 9 AF XY: 0.000247 AC XY: 88AN XY: 356964
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000464 AC: 7AN: 150880Hom.: 0 Cov.: 27 AF XY: 0.0000679 AC XY: 5AN XY: 73688
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome Uncertain:2
Uncertain significance, no assertion criteria provided | literature only | OMIM | Aug 28, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | 3billion | Jan 03, 2022 | Same nucleotide change resulting in same amino acid change has been previously reported to be associated with MSTO1 related disorder (ClinVar ID: VCV000438835, PS1_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000175, PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.644, PP3_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2023 | Reported in the heterozygous state in a family with mitochondrial myopathy, ataxia, minor dysmorphisms, endocrine dysfunctions, and psychiatric symptoms (Gal et al., 2017); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34426522, 33672784, 30684668, 29339779, 31604776, 36468072, 33222031, 28554942) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
.;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
.;N;N
REVEL
Uncertain
Sift
Uncertain
.;D;D
Sift4G
Uncertain
.;D;D
Polyphen
1.0
.;D;.
Vest4
0.73, 0.70
MutPred
Gain of disorder (P = 0.0831);Gain of disorder (P = 0.0831);Gain of disorder (P = 0.0831);
MVP
0.78
MPC
3.3
ClinPred
T
GERP RS
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