rs207459999
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The ENST00000361789.2(MT-CYB):c.496G>A(p.Gly166Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Mitomap GenBank:
Absent
Consequence
MT-CYB
ENST00000361789.2 stop_gained
ENST00000361789.2 stop_gained
Scores
Clinical Significance
Mitochondrial-Encephalomyopathy
Conservation
PhyloP100: 7.44
Genes affected
MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.565 CDS is truncated, and there are 3 pathogenic variants in the truncated region.
PM2
No frequency data in Mitomap. Probably very rare.
PP5
Variant M-15242-G-A is Pathogenic according to our data. Variant chrM-15242-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 9680.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYTB | CYTB.1 use as main transcript | c.496G>A | p.Gly166Ter | stop_gained | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CYB | ENST00000361789.2 | c.496G>A | p.Gly166Ter | stop_gained | 1/1 | P1 |
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap
Mitochondrial-Encephalomyopathy
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leigh syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.15242G>A (YP_003024038.1:p.Gly166Ter) variant in MTCYB gene is interpretated to be a Pathogenic variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: PS3, PS6, PM8, PM9 - |
Mitochondrial encephalomyopathy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2000 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at