chrM-616-T-G

Position:

• chrM-616-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The ENST00000387314.1(MT-TF):​n.40T>G variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Mitomap GenBank: 𝑓 0.0 (AC: 1)
• Consequence: MT-TF ENST00000387314.1 non_coding_transcript_exon
• Scores: Mitotip Pathogenic 20
• Clinical Significance: Pathogenic no assertion criteria provided P:1 Maternally-inherited-epilepsy-/-mito-tubulointerstitial-kidney-disease-(MITKD)-/-Gitelman-like-syndrome,Maternally-inherited-epilepsy
• Conservation: PhyloP100: 3.71

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 Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very low frequency in mitomap database: 0.0
• PP5: Variant M-616-T-G is Pathogenic according to our data. Variant chrM-616-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 9577.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRNF	TRNF.1	n.40T>G		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.40T>G		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: 1

Mitomap

Maternally-inherited-epilepsy-/-mito-tubulointerstitial-kidney-disease-(MITKD)-/-Gitelman-like-syndrome,Maternally-inherited-epilepsy

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Epilepsy, mitochondrial Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Feb 09, 2010

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Pathogenic	20
Hmtvar	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs387906420; hg19: chrM-618;