rs1057516068
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000361381.2(MT-ND4):āc.1259C>Gā(p.Thr420Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Mitomap GenBank:
š 0.0 ( AC: 0 )
Consequence
MT-ND4
ENST00000361381.2 missense
ENST00000361381.2 missense
Scores
Apogee2
Benign
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 2.32
Genes affected
MT-ND4 (HGNC:7459): (mitochondrially encoded NADH dehydrogenase 4) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Parkinson's disease; macular degeneration; and schizophrenia. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very low frequency in mitomap database: 0.0
BP4
?
Apogee2 supports a benign effect, 0.02378963 < 0.5 .
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-ND4 | ENST00000361381.2 | c.1259C>G | p.Thr420Ser | missense_variant | 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 GenBank
AF:
AC:
0
Mitomap
No disease associated.
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:4
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Developmental delay;C1384666:Hearing impairment;C1391997:Congenital cardiomyopathy;C4551563:Microcephaly Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Center for Neuroscience and Cell Biology, University of Coimbra, Portugal | Nov 21, 2016 | - - |
Developmental delay;C1384666:Hearing impairment;C2243051:Macrocephaly Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Center for Neuroscience and Cell Biology, University of Coimbra, Portugal | Nov 21, 2016 | - - |
Leigh syndrome Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Center for Neuroscience and Cell Biology, University of Coimbra, Portugal | Nov 21, 2016 | - - |
Epilepsy;C0026827:Hypotonia;C0085584:Encephalopathy;C0424605:Developmental delay;C0497327:Dementia;CN239811:Calcification of extrapyramidal basal ganglia Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Center for Neuroscience and Cell Biology, University of Coimbra, Portugal | Nov 21, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Benign
AlphaMissense
Benign
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PROVEAN
Benign
N
Sift
Uncertain
D
Sift4G
Benign
T
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at