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GeneBe

rs199476140

chrM-4365-C-CA

Variant summary

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

The ENST00000387372.1(MT-TQ):n.35_36insT variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Mitomap GenBank:
Absent

Consequence

MT-TQ
ENST00000387372.1 non_coding_transcript_exon

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1
Myopathy

Conservation

PhyloP100: 8.87
Variant links:
Genes affected
MT-TQ (HGNC:7495): (mitochondrially encoded tRNA glutamine)
MT-TM (HGNC:7492): (mitochondrially encoded tRNA methionine)
MT-TI (HGNC:7488): (mitochondrially encoded tRNA isoleucine)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
No frequency data in Mitomap. Probably very rare.
PP5
?
    PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
Variant M-4365-C-CA is Pathogenic according to our data. Variant chrM-4365-C-CA is described in ClinVar as [Pathogenic]. Clinvar id is 9614.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRNQTRNQ.1 use as main transcriptn.35_36insT non_coding_transcript_exon_variant 1/1
TRNMTRNM.1 use as main transcript upstream_gene_variant
TRNITRNI.1 use as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-TQENST00000387372.1 linkuse as main transcriptn.35_36insT non_coding_transcript_exon_variant 1/1
MT-TMENST00000387377.1 linkuse as main transcript upstream_gene_variant
MT-TIENST00000387365.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap

Myopathy

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Myopathy Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMOct 01, 2000- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs199476140; hg19: chrM-4366; API