Genetic Variant MT-ND2:p.Ile57Ile (chrM-4640-C-T) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP7

The ENST00000361453.3(MT-ND2):c.171C>T(p.Ile57Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. I57I) has been classified as Benign.

Frequency

Mitomap GenBank:

𝑓 0.00020 ( AC: 11 )

Consequence

MT-ND2
ENST00000361453.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

No linked disesase in Mitomap

Conservation

PhyloP100: -9.19

Publications

0 publications found

Variant links:

Genes affected

MT-ND2 (HGNC:7456): (mitochondrially encoded NADH dehydrogenase 2) 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; multiple sclerosis; myocardial infarction; neurodegenerative disease (multiple); and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

MT-ND2 links:

TRNQ (HGNC:7495): (mitochondrially encoded tRNA glutamine)

TRNQ links:

TRNM (HGNC:7492): (mitochondrially encoded tRNA methionine)

TRNM Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

TRNM links:

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new If you want to explore the variant's impact on the transcript ENST00000361453.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP7

Synonymous conserved (PhyloP=-9.19 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361453.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MT-ND2	ENST00000361453.3	TSL:6	c.171C>T	p.Ile57Ile	synonymous	Exon 1 of 1	ENSP00000355046.4	P03891
MT-TQ	ENST00000387372.1	TSL:6	n.-240G>A		upstream_gene	N/A
MT-TM	ENST00000387377.1	TSL:6	n.*171C>T		downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.00020

AC:

Gnomad homoplasmic

AF:

0.000018

AC:

AN:

56432

Gnomad heteroplasmic

AF:

0.0

AC:

AN:

56432

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-9.2

Mutation Taster

=87/113

disease causing

(source)

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Mitomap

ClinVar

Computational scores

Publications

Other links and lift over