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
  • The variant label for this record ("m.14596A>T") does not appear to be in HGVS format
  • No CSPEC computer assertion could be determined for this classification!


Variant: m.14596A>T

CA120626

9690 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: f4ab02ef-d4d0-489f-923f-ec539c629d01
Approved on: 2023-08-14
Published on: 2024-08-12

HGVS expressions

NC_012920.1:m.14596A>T
J01415.2:m.14596A>T
ENST00000361681.2:c.78T>A

Uncertain Significance

Met criteria codes 2
PP3 PM2_Supporting
Not Met criteria codes 6
PS2 PS3 PS4 PP1 PP4 PM6

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.14596A>T (p.I26M) variant in MT-ND6 has been reported in one family with primary mitochondrial disease to date (PMID: 8644732). Affected individuals had clinical features consistent with Leber Hereditary Optic Neuropathy (LHON) and/or spastic dystonia. Of note, another variant was seen in this family (m. 11696G>A), however this is present in healthy population databases and likely haplogroup-associated. The m.14596A>T variant was present at homoplasmy in affected individuals. As all tested individuals were homoplasmic for the variant, segregation evidence could not be considered. There are no additional families reported with de novo occurrences to our knowledge. This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). The computation predictor APOGEE predicts this variant to be deleterious (score 0.95 in APOGEE1 and 0.86 in APOGEE2; PP3). There are no cybrids, single fiber studies, or other functional assays reported on this variant. 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 August 14, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PP3.
Met criteria codes
PP3
The computation predictor APOGEE predicts this variant to be deleterious (score 0.95 in APOGEE1 and 0.86 in APOGEE2; PP3).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
Not Met criteria codes
PS2
There are no additional families reported with de novo occurrences to our knowledge.
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
PS4
The m.14596A>T (p.I26M) variant in MT-ND6 has been reported in one family with primary mitochondrial disease to date (PMID: 8644732). Affected individuals had clinical features consistent with Leber Hereditary Optic Neuropathy (LHON) and/or spastic dystonia. The variant was present at homoplasmy in affected individuals.
PP1
As all tested individuals were homoplasmic, segregation evidence could not be considered.
PP4
In DeVries et all 1996 [PMID 8644732] Complex I, II+III, and IV activity of patient muscle were all reduced compared with that of controls, with the Complex I defect being the most pronounced (21%). However, nuclear gene defects were not ruled out.
PM6
There are no additional families reported with de novo occurrences to our knowledge.
Curation History
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