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.3273del

CA2573320431

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 275a4c67-01de-4564-b6f5-02e1b9495c29
Approved on: 2023-05-23
Published on: 2024-07-23

HGVS expressions

NC_012920.1:m.3273del
J01415.2:m.3273del

Uncertain Significance

Met criteria codes 3
PP3 PM2_Supporting PS4_Supporting
Not Met criteria codes 3
PP1 PS3 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.3273del variant in MT-TL1 has been reported in two unrelated individuals (PS4_supporting; PMIDs: 7854527, 30701423). The first reported case (PMID: 7854527) was a man with encephalomyopathy and cerebral and basal ganglia calcifications. He also had seizures, hearing loss, cataracts, glaucoma, retinitis pigmentosa, hyperactivity, hypogonadism, renal failure, and neurologic decline in adulthood. He had elevated cerebrospinal fluid (CSF) protein and serum lactate, and muscle biopsy showed ragged red fibers and paracrystalline inclusions. The variant was present at 65% heteroplasmy in muscle. The second reported case (PMID: 30701423) was a woman who was generally healthy until age 20 years when she developed diabetes. She then went on to have hearing loss, cognitive impairment, bilateral cataracts, and retinal dystrophy. She also had basal ganglia calcifications and cerebellar atrophy. She had elevated CSF lactate. Muscle biopsy was unrevealing. The variant as described as present in muscle but the heteroplasmy level was not provided. The variant was reported to be absent in blood from the mother in the first reported case however heteroplasmy level in blood was not determined for the proband, precluding consideration for de novo status. There are no other reports of large families with this variant segregating with disease manifestations. This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). The computational predictor MitoTIP suggests this variant is pathogenic (85.7 percentile; 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 of 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 May 23, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PM2_supporting, PP3.
Met criteria codes
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (85.7 percentile; PP3).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PS4_Supporting
The m.3273del variant in MT-TL1 has been reported in two unrelated individuals (PS4_supporting; PMIDs: 7854527, 30701423). The first reported case (PMID: 7854527) was a man with encephalomyopathy and cerebral and basal ganglia calcifications. He had seizures, hearing loss, cataracts, glaucoma, retinitis pigmentosa, hyperactivity, hypogonadism, renal failure, and neurologic decline in adulthood. He had elevated cerebrospinal fluid (CSF) protein and serum lactate, and muscle biopsy showed ragged red fibers and paracrystalline inclusions. The variant was present at 65% heteroplasmy in muscle. The second reported case (PMID: 30701423) was a woman who was generally healthy until age 20 years when she developed diabetes. She then went on to have hearing loss, cognitive impairment, bilateral cataracts, and retinal dystrophy. She also had basal ganglia calcifications and cerebellar atrophy. She had elevated CSF lactate. Muscle biopsy was unrevealing. The variant as described as present in muscle but the heteroplasmy level was not provided.
Not Met criteria codes
PP1
There are no other reports of large families with this variant segregating with disease manifestations.
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
PM6
The variant was reported to be absent in blood from the mother in the first reported case however heteroplasmy level in blood was not determined for the proband, precluding consideration for de novo status
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