The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NC_012920.1:m.14598T>C

CA16043602

374080 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: eb945fb4-8ad8-470b-bbff-4a9d8e06a79d
Approved on: 2023-08-14
Published on: 2024-08-12

HGVS expressions

NC_012920.1:m.14598T>C
J01415.2:m.14598T>C
ENST00000361681.2:c.76A>G

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 5
BS1 PS3 PS4 PP1 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_mtDNA

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.14598T>C (p.I26V) variant in MT-ND6 was reviewed by the Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel on August 14, 2023. There are no individuals with this variant reported in the medical literature to our knowledge. There are two prior reports in ClinVar for this variant, however details are not provided precluding consideration of these cases for this curation. As such, there are no reported de novo occurrences or large families to consider for evidence of variant segregation. This variant is present in population databases including in Mitomap GenBank sequences (7/61,168 (0.012%) and seen across five top level (single letter) haplogroups with European, Asian, and African ancestry), Helix database (26/195,983 sequences (0.013%), in addition to three heteroplasmic occurrences and seen across six top level haplogroups with European, Asian, and African ancestry), and gnomAD v3.1.2 (9/56,416 sequences (0.016%) in addition to three heteroplasmic occurrences and seen across seven top level haplogroups with European, Asian, and African ancestry). The computational predictor APOGEE gives a consensus rating of neutral with a score of 0.31 (Min=0, Max=1; APOGEE2 scores on 0.0499), which predicts no damaging effect on gene function (BP4). There are no cybrids, single fiber studies, or other key functional assays reported for this variant to date. In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. We note that two expert panel members felt likely benign was the more appropriate classification (compared to five who agreed with uncertain significance). This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on August 14, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied: BP4.
Met criteria codes
BP4
The computational predictor APOGEE gives a consensus rating of neutral with a score of 0.31 (Min=0, Max=1; APOGEE2 scores on 0.0499), which predicts no damaging effect on gene function (BP4).
Not Met criteria codes
BS1
Population frequencies for this variant do not reach the criteria to meet BS1 (>0.5%) in either Mitomap, gnomAD, or Helix. Mitomap has 7/59,389 FL Seq (0.012%) spread over 8 top level haplogroups (single letter) with European, and Asian ancestry; gnomAD v3.1.2 has 9 homoplasmic/56,416 (0.016%) plus 3 heteroplasmic spread over 7 top level haplogroups with European, Asian, and African ancestry; Helix has 75 homoplasmic/195,983 sequences (0.013%) plus 13 heteroplasmic spread over 6 top level haplogroups with European, Asian, and African ancestry.
PS3
There are no cybrids, single fiber studies, or other key functional assays reported for this variant to date.
PS4
The m.14598T>C (p.I26V) variant in MT-ND6 was reviewed by the Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel on August 14, 2023. There are no individuals with this variant reported in the medical literature to our knowledge. There are two prior reports in ClinVar for this variant, however details are not provided precluding consideration of these cases for this curation
PP1
As such, there are no reported de novo occurrences or large families to consider for evidence of variant segregation.
PM2
. This variant is present in population databases including in Mitomap GenBank sequences (7/61,168 (0.012%) and seen across five top level (single letter) haplogroups with European, Asian, and African ancestry), Helix database (26/195,983 sequences (0.013%), in addition to three heteroplasmic occurrences and seen across six top level haplogroups with European, Asian, and African ancestry), and gnomAD v3.1.2 (9/56,416 sequences (0.016%) in addition to three heteroplasmic occurrences and seen across seven top level haplogroups with European, Asian, and African ancestry).
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