chrM-622-G-A

Position:

• chrM-622-G-A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PP5_Strong

The ENST00000387314.1(MT-TF):​n.46G>A variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Uncertain significance (★★★).

• Frequency: Mitomap GenBank: 𝑓 0.0 (AC: 0)
• Consequence: MT-TF ENST00000387314.1 non_coding_transcript_exon
• Scores: Mitotip Uncertain 12
• Clinical Significance: Uncertain significance reviewed by expert panel P:2 U:1 EXIT-&-Deafness
• Conservation: PhyloP100: 5.21

Genes affected

MT-TF (HGNC:7481): (mitochondrially encoded tRNA phenylalanine)

TRNF (HGNC:):

MT-RNR1 (HGNC:7470): (mitochondrially encoded 12S RNA) Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very low frequency in mitomap database: 0.0
• PP5: Variant M-622-G-A is Pathogenic according to our data. Variant chrM-622-G-A is described in ClinVar as [Uncertain_significance]. Clinvar id is 9575.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRNF	TRNF.1	n.46G>A		non_coding_transcript_exon_variant	1/1
RNR1	RNR1.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-TF	ENST00000387314.1	n.46G>A		non_coding_transcript_exon_variant	1/1
MT-RNR1	ENST00000389680.2			upstream_gene_variant

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.0 AC: 0

Gnomad homoplasmic AF: 0.000018 AC: 1 AN: 56417

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56417

Mitomap

EXIT-&-Deafness

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:2 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Mitochondrial disease Pathogenic:1 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Uncertain significance, reviewed by expert panel	curation	ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen	Jun 24, 2024	The m.622G>A variant in MT-TF has been reported in one individual to date, in a woman with adult-onset myopathy and neuropathy. She was healthy until her early 60s when she developed exercise intolerance, fatigue, paresthesia, muscle cramps, and mild hearing impairment. Muscle biopsy showed several atrophic fibers, COX-deficient fibers, subsarcolemmal mitochondrial accumulation, and enlarged mitochondria with paracrystalline inclusions. She had reductions in complex I (50% controls), complex III (68% controls), and complex IV (55% controls) activities. The variant was present at 88% heteroplasmy in muscle, 70% in hair, 66% in urine, 63% in buccal sample, and 36% in blood (PMID: 16769874). Her mother was reported to have similar walking difficulties but did not undergo testing for this variant. Her healthy daughter had the variant present at lower heteroplasmy levels however her daughter was younger than the proband was at symptom onset. This variant is present in population databases (absent in Mitomap's GenBank sequences; one heteroplasmic and one homoplasmic occurrence in gnomAD v3.1.2; eight heteroplasmic occurrences in the Helix dataset). Single fiber testing showed higher levels of the variant in COX-negative fibers (93%±1.0; N = 11) than in COX-positive fibers (82%±8.5; N = 14), p<0.001 (PS3_supporting, PMID: 16769874). Aminoacylation defects and tRNA structural changes were also reported (PMID: 17878308). The computational predictor MitoTIP suggests this variant is neutral (41.5 percentile) and HmtVAR predicts it to be deleterious with a score of 0.7. In summary, this variant 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 June 24, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS3_supporting. -

Myopathy, mitochondrial, late-onset Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 01, 2006

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Uncertain	12
Hmtvar	Pathogenic	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs118203887; hg19: chrM-624;