M-5131-TAA-T

Position:

• chrM-5131-TAA-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

Variant has been reported in ClinVar as Uncertain significance (★★★).

• Frequency: Mitomap GenBank: Absent
• Consequence: ND2 frameshift
• Clinical Significance: Uncertain significance reviewed by expert panel P:1 U:1 Exercise-intolerance-(EXIT)
• Conservation: PhyloP100: -1.04

Genes affected

ND2 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: No frequency data in Mitomap. Probably very rare.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ND2	unassigned_transcript_4794	c.664_665delAA	p.Asn222fs	frameshift_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap

Exercise-intolerance-(EXIT)

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Mitochondrial complex I deficiency Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Aug 22, 2002

- -

Mitochondrial disease Uncertain:1

Uncertain significance, reviewed by expert panel

curation

ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen

Oct 09, 2023

The m.5133_5134delAA variant in MT-ND2 has been reported in one individual from one family (PMID: 12192017), in a male with exercise intolerance, ragged red fibers, and reduced complex I activity. The variant was present at 93% heteroplasmy (PMID:19273755). This variant was reported to have occurred on the paternal mitochondrial DNA as two haplogroups were reportedly present in the proband, one matching his mother’s haplogroup and the other matching his father’s, although the variant was not present in his mother or father (PS2_supporting, PMID: 12192017). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). There are no in silico predictors for this type of variant in mitochondrial DNA. There are no cybrids, single fiber studies, or other functional assays reported on this variant. This 2 base pair deletion starting at amino acid L221 in the MT-ND2 gene results in a stop codon at position 251 (L251Ter). This results in a truncated MT-ND2 gene product (PM4). Of note, this expert panel considered whether this variant should be reviewed for several reasons: (1) analysis of the mitochondrial genome was limited at the time of this report in 2002, raising concern on whether this variant was truly present in the proband or technical artifact; (2) it is possible the variant was present in the nuclear DNA but erroneously assigned to mitochondrial DNA; (3) nuclear DNA etiologies were not assessed in this proband; and (4) there are no other validated occurrences of paternal inheritance of mitochondrial DNA. However, this expert panel elected to review this variant with the current evidence and it meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on October 9, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS2_supporting, PM2_supporting, PM4. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs199476116; hg19: chrM-5132;