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.4160T>C") does not appear to be in HGVS format
  • No CSPEC computer assertion could be determined for this classification!


Variant: m.4160T>C

CA340942

9723 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 004e4dea-3fe7-4853-8e41-f62a3911f151

HGVS expressions

NC_012920.1:m.4160T>C
J01415.2:m.4160T>C
ENST00000361390.2:c.854T>C

Uncertain Significance

Met criteria codes 3
PP3 PM6_Supporting PM2_Supporting
Not Met criteria codes 2
PS3 PS4

Evidence Links 1

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.4160T>C (p.L285P) variant in MT-ND1 has been reported in three unrelated individuals to date (PMIDs: 2018041, 22258525, 35699829), however only one case was included in this curation (PMID: 35699829). This individual had Leber Hereditary Optic Neuropathy (LHON) and dystonia, and the variant was present at 80.2% in blood, 90.8% in urine, and 81.7% in buccal. This variant occurred de novo in this individual as it was absent in blood, buccal, and urine samples from his mother and sister (PM6_supporting, PMID: 35699829). One of the other reported families with this variant had LHON however they also had the m.14484T>C variant, one of the three most common variants associated with LHON (PMIDs: 2018041, 29249004), and therefore was not included in this curation. Another individual was reported to have developmental delay, vision involvement, peripheral nervous system involvement, and muscle involvement however the m.4160T>C variant was only present at 11% heteroplasmy (PMID: 22258525). Given the low heteroplasmy, this case was also excluded from this curation. The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.89 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). There are single occurrences in population databases, however these are from reported affected individuals (PM2_supporting). Cybrid studies were performed however were not considered in this curation given the presence of other mitochondrial DNA variants (PMIDs: 35699829, 28455970). 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 January 8, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PP3, PM6_supporting.
Met criteria codes
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.89 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
PM6_Supporting
This variant occurred de novo in one individual (absent in blood, buccal, and urine from mother and sister; PM6_supporting, PMID: 35699829).
PM2_Supporting
There are single occurrences in population databases, however these are from reported affected individuals (PM2_supporting).
Not Met criteria codes
PS3
Cybrid studies supported the functional impact of this variant. However given these patients also harbored the m.14484 T>C, p.M64V therefore it will not be counted (PMID: 35699829).

PS4
The m.4160T>C (p.L285P) variant in MT-ND1 has been reported in three unrelated individuals to date (PMIDs: 2018041, 22258525, 35699829), however only one case was included in this curation (PMID: 35699829). This individual had Leber Hereditary Optic Neuropathy (LHON) and dystonia, and the variant was present at 80.2% in blood, 90.8% in urine, and 81.7% in buccal. This variant occurred de novo in this individual as it was absent in blood, buccal, and urine samples from his mother and sister (PM6_supporting, PMID: 35699829). One of the other reported families with this variant had LHON however they also had the m.14484T>C variant, one of the three most common variants associated with LHON (PMIDs: 2018041, 29249004), and therefore was not included in this curation. Another individual was reported to have developmental delay, vision involvement, peripheral nervous system involvement, and muscle involvement however this variant was only present at 11% heteroplasmy (PMID: 22258525). Given the low heteroplasmy, this case was also excluded from this curation.
Approved on: 2024-01-08
Published on: 2024-04-02
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