The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene listed was thus derived from ClinVar and/or CAR
  • The variant label for this record ("NC_012920.1(MT-CYB"):m.1630A>G) does not appear to be in HGVS format
  • No CSPEC related information was provided by the message!

  • See Evidence submitted by expert panel for details.

Variant: NC_012920.1(MT-CYB):m.1630A>G

CA913163293

689840 (ClinVar)

Gene: MT-TV
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance (primarily or exclusively heteroplasmic)
UUID: c628946d-40dd-4a8d-8a70-c03fbea12865
Approved on: 2022-11-14
Published on: 2023-03-13

HGVS expressions

NC_012920.1:m.1630A>G
J01415.2:m.1630A>G

Uncertain Significance

Met criteria codes 5
PS3_Supporting PP4 PP3 PM2_Supporting PS4_Supporting
Not Met criteria codes 2
PP1 PM6

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.1630A>G variant in MT-TV has been reported in two unrelated individuals. One individual had features consistent with mitochondrial neurogastrointestinal encephalopathy (MNGIE) with additional features of hearing loss, mild psychomotor delay, headache, and small stature (PMID: 19252805). Another individual had features consistent with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) in addition to bilateral sensorineural hearing loss, myopia, short stature requiring growth hormone supplementation, and delayed onset of puberty (PMID: 21540128; PS4_supporting). The variant was heteroplasmic in the individual with MNGIE-like features at 90% in muscle and 70% in blood, with 60% heteroplasmy being seen in the asymptomatic mother’s blood (PMID: 19252805). In the individual with MELAS, the variant was present at 75% heteroplasmy in blood, 95% in urine, and 90% in fibroblasts; the variant was present in the mother at 93% in blood, 98% in urine, and 95% in fibroblasts (PMIDs: 21540128, 30709774). No correlating segregations or de novo occurrences of this variant were found in our review of the literature. The computational predictor MitoTIP suggests this variant is pathogenic (65th percentile) and HmtVAR predicts it to be pathogenic score of 0.85 (PP3). The m.1630A>G variant is absent in the GenBank dataset, the Helix dataset (although there are four heteroplasmic occurrences), and gnomAD3.1.2 (PM2_supporting). Single-fiber testing (PMID: 19252805) showed 90% heteroplasmy in COX-negative fibers and 50% in COX-positive fibers. Cybrids showed marked decrease in cytochrome-c oxidase activity. Oxygen consumption/respiration activity was also greatly reduced in both homoplasmic and heteroplasmic cybrid lines. Northern blotting showed a pronounced loss of MTTV in mutant cybrids when compared to controls (PMID: 21540128; PS3_supporting). Electron transport enzyme activities were assessed in one of the individuals and her healthy mother, and showed a significant difference between the proband and the mother and a healthy control individual. Exome sequencing was performed in the proband and her mother, ruling out other known genetic etiologies (PMID: 30709774; PP4). 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 November 14, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PP3, PM2_supporting, PS3_supporting, PP4.
Met criteria codes
PS3_Supporting
Single-fiber testing (PMID: 19252805) showed 90% heteroplasmy in COX-negative fibers and 50% in COX-positive fibers. Cybrids showed marked decrease in cytochrome-c oxidase activity. Oxygen consumption/respiration activity was also greatly reduced in both homoplasmic and heteroplasmic cybrid lines. Northern blotting showed a pronounced loss of MT-TV in mutant cybrids when compared to controls. (PMID: 21540128; PS3_supporting).

PP4
Electron transport enzyme activities were assessed in one of the individuals and her healthy mother, and showed a significant difference between the proband and the mother and a healthy control individual. Exome sequencing was performed in the proband and her mother ruling out other known genetic etiologies (PMID: 30709774; PP4). Fibroblast study of proband + mom showed marked difference - the affected daughter showed significantly lower oxygen consumption rate (OCR) and higher glycolytic rate than mom; both had mutant in near homoplasmy in the fibroblasts. Exome sequencing was performed on both individuals. Pathogenic nuclear mutation in VARS2, which interacts with tRNA Val, was found only in mother and was proposed to ameliorate effect of mtDNA mutant vs that of her affected daughter who lacked the nuclear mutation.
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (65th percentile) and HmtVAR predicts it to be pathogenic score of 0.85 (PP3).
PM2_Supporting
The m.1630A>G variant is absent in the GenBank dataset, the Helix dataset (although there are four heteroplasmic occurrences), and gnomAD3.1.2 (PM2_supporting). Absent in Mitomap,(0/ 56910) gnomAD v3.1 (0/56434), and Helix (0/195983) databases (a total of 309,327 sequences).
PS4_Supporting
The m.1630A>G variant in MT-TV has been reported in two unrelated individuals. One individual had features consistent with mitochondrial neurogastrointestinal encephalopathy (MNGIE) with additional features of hearing loss, mild psychomotor delay, headache, and small stature (PMID: 19252805). Another individual had features consistent with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) in addition to bilateral sensorineural hearing loss, myopia, short stature requiring growth hormone supplementation, and delayed onset of puberty (PMID: 21540128; PS4_supporting). The variant was heteroplasmic in the individual with MNGIE-like features at 90% in muscle and 70% in blood, with 60% heteroplasmy being seen in the asymptomatic mother’s blood (PMID: 19252805). In the individual with MELAS, the variant was present at 75% heteroplasmy in blood, 95% in urine, and 90% in fibroblasts; the variant was present in the mother at 93% in blood, 98% in urine, and 95% in fibroblasts (PMIDs: 21540128, 30709774).
Not Met criteria codes
PP1
The unaffected mothers of both probands had relatively high heteroplasmy levels in blood (60%) or blood + urine (93-98%). There are no other large families reported to be considered for evidence of segregation.
PM6
There are no de novo occurrences of this variant reported to our knowledge.
Curation History
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