chrM-8313-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 5 ACMG points: 5P and 0B. PM6_SupportingPS3_SupportingPP3PM2_SupportingPS4_Supporting
This summary comes from the ClinGen Evidence Repository: The m.8313G>A variant in MT-TK has been reported in two unrelated probands with primary mitochondrial disease (PS4_supporting). One of these individuals had a severe gastroenteropathy, peripheral neuropathy, seizures, dementia, ataxia, retinitis pigmentosa, deafness, and died by age 15 years (PMID:9380435). The other individual had onset in her 20s of myopathy, nasal speech and swallowing difficulty, peripheral neuropathy, ptosis, and osteoporosis. Her condition was progressive and after several years she was non-ambulatory, had bulbar failure, and required tracheostomy and tube feeding (PMID:19618438). In both individuals, the variant was heteroplasmic, ranging from 54% in fibroblasts to 74-82% in muscle. In one of the reported cases, the variant was reported de novo as it was absent in blood from the proband’s mother, maternal aunt, and two brothers (PMID:9380435), however no additional tissues were tested (including that blood in the proband was not tested) and technology performed at the time of publication would not detect low heteroplasmy levels of the variant. In the other case, multiple tissues from the mother were tested as was muscle from two healthy brothers and the variant was not detectable (PMID:19618438), confirming de novo occurrence (PM6_supporting). Of note, three additional unrelated probands in a large cohort of individuals with autism spectrum disorder were reported to have this variant (PMID:35778412), however additional clinical details were not provided and there was no evidence these individuals had other features of primary mitochondrial disease. There is one occurrence of this variant in population databases (MITOMAP GenBank sequences, 1/59,389 or 0.002%; absent in Helix dataset and gnomAD v3.1.2). Although there is one occurrence, the frequency is still low (PM2_supporting). The computational predictor MitoTIP suggests this variant is pathogenic (73.6 percentile) and HmtVAR predicts it to be pathogenic score of 0.85 (PP3). Several functional studies reported show the deleterious effects of this variant (PS3_supporting). A single fiber study (PMID:19618438) demonstrated higher levels of variant in COX-negative fibers (96.44%; n =10) than in COX-positive fibers (72.11%; n= 10; P<0.001). A cybrid study (PMID:12737626) showed that cybrids with high levels of the variant had severe respiratory chain defects, diminished O2 consumption, and translational defects. Furthermore, a 7000-fold loss of aminoacylation efficiency was reported (PMIDs: 15477393, 15100439). In summary, this variant meets criteria to be classified as uncertain significance however, after extensive discussion, this Expert Panel elected to modify the classification to likely pathogenic given consistent functional evidence of a severe deleterious effect across multiple assays. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on March 13, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID:32906214): PS4_supporting, PM2_supporting, PP3, PM6_supporting, PS3_supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA254837/MONDO:0044970/014
Frequency
Consequence
ENST00000387421.1 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 5 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TRNK | TRNK.1 use as main transcript | n.19G>A | non_coding_transcript_exon_variant | 1/1 | ||||
| COX2 | COX2.1 use as main transcript | downstream_gene_variant | YP_003024029.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MT-TK | ENST00000387421.1 | n.19G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
| MT-CO2 | ENST00000361739.1 | downstream_gene_variant | ENSP00000354876 | P1 |
Frequencies
GnomAD4 exome Cov.: 0
Mitomap
ClinVar
Submissions by phenotype
Mitochondrial disease Pathogenic:1
| Likely pathogenic, reviewed by expert panel | curation | ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen | Mar 13, 2023 | The m.8313G>A variant in MT-TK has been reported in two unrelated probands with primary mitochondrial disease (PS4_supporting). One of these individuals had a severe gastroenteropathy, peripheral neuropathy, seizures, dementia, ataxia, retinitis pigmentosa, deafness, and died by age 15 years (PMID: 9380435). The other individual had onset in her 20s of myopathy, nasal speech and swallowing difficulty, peripheral neuropathy, ptosis, and osteoporosis. Her condition was progressive and after several years she was non-ambulatory, had bulbar failure, and required tracheostomy and tube feeding (PMID: 19618438). In both individuals, the variant was heteroplasmic, ranging from 54% in fibroblasts to 74-82% in muscle. In one of the reported cases, the variant was reported de novo as it was absent in blood from the proband’s mother, maternal aunt, and two brothers (PMID: 9380435), however no additional tissues were tested (including that blood in the proband was not tested) and technology performed at the time of publication would not detect low heteroplasmy levels of the variant. In the other case, multiple tissues from the mother were tested as was muscle from two healthy brothers and the variant was not detectable (PMID: 19618438), confirming de novo occurrence (PM6_supporting). Of note, three additional unrelated probands in a large cohort of individuals with autism spectrum disorder were reported to have this variant (PMID: 35778412), however additional clinical details were not provided and there was no evidence these individuals had other features of primary mitochondrial disease. There is one occurrence of this variant in population databases (MITOMAP GenBank sequences, 1/59,389 or 0.002%; absent in Helix dataset and gnomAD v3.1.2). Although there is one occurrence, the frequency is still low (PM2_supporting). The computational predictor MitoTIP suggests this variant is pathogenic (73.6 percentile) and HmtVAR predicts it to be pathogenic score of 0.85 (PP3). Several functional studies reported show the deleterious effects of this variant (PS3_supporting). A single fiber study (PMID: 19618438) demonstrated higher levels of variant in COX-negative fibers (96.44%; n =10) than in COX-positive fibers (72.11%; n= 10; P<0.001). A cybrid study (PMID: 12737626) showed that cybrids with high levels of the variant had severe respiratory chain defects, diminished O2 consumption, and translational defects. Furthermore, a 7000-fold loss of aminoacylation efficiency was reported (PMIDs: 15477393, 15100439). In summary, this variant meets criteria to be classified as uncertain significance however, after extensive discussion, this Expert Panel elected to modify the classification to likely pathogenic given consistent functional evidence of a severe deleterious effect across multiple assays. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on March 13, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PM2_supporting, PP3, PM6_supporting, PS3_supporting. - |
Mitochondrial DNA depletion syndrome 1 Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at