M-616-T-G

Position:

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

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
Variant links:
Genes affected
MT-TF (HGNC:7481): (mitochondrially encoded tRNA phenylalanine)
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]

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ACMG classification

Classification made for transcript

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
TRNFTRNF.1 use as main transcriptn.40T>G non_coding_transcript_exon_variant 1/1
RNR1RNR1.1 use as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-TFENST00000387314.1 linkuse as main transcriptn.40T>G non_coding_transcript_exon_variant 1/1
MT-RNR1ENST00000389680.2 linkuse as main transcript 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
LINK: link

Submissions by phenotype

Epilepsy, mitochondrial Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMFeb 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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs387906420; hg19: chrM-618; API