The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • The variant label for this record ("m.5532G>A") does not appear to be in HGVS format
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-TW CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.5532G>A

CA120542

9557 (ClinVar)

Gene: MT-TW
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 6de6a969-de2d-4767-8eb0-72d1e06e1674
Approved on: 2024-05-13
Published on: 2024-12-06

HGVS expressions

NC_012920.1:m.5532G>A
J01415.2:m.5532G>A

Uncertain Significance

Met criteria codes 3
PS3_Supporting PM2_Supporting PP1
Not Met criteria codes 2
PS4 PP3

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.5532G>A variant in MT-TW has been reported in one individual with primary mitochondrial disease to date (PMID: 15054399), in a 16-year-old girl with failure to thrive, short stature, recurrent vomiting, developmental delay and regression, ophthalmoplegia, ptosis, pigmentary retinopathy, sensorineural hearing loss, and myopathy. Brain imaging showed generalized atrophy and periventricular white matter changes. Elevated lactate was seen in blood and cerebrospinal fluid. Muscle biopsy showed ragged red fibers and mitochondrial respiratory chain complex I and IV deficiency. The variant was present at 92% heteroplasmy in muscle, 37% in fibroblasts, and 21% in blood. The variant was present at lower heteroplasmy levels in blood from her healthy mother (7%) and brother (9%; PP1; PMID: 15054399). There are no other individuals or families reported in the medical literature. Although there is one occurrence of this variant in population databases (1/61,134 in MITOMAP, absent in Helix and gnomad v3.1.2), the frequency is still low (PM2_supporting). In silico predictors are conflicting as the computational predictor MitoTIP suggests this variant is likely benign (19.4 percentile) but HmtVAR predicts it to be deleterious with a score of 0.7. Single fiber testing showed higher levels of the variant in COX-negative fibers (>90%) than in COX-positive fibers (6-85%, p<0.0001, PS3_supporting, PMID: 15054399). 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 May 13, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PP1, PS3_supporting, PM2_supporting.
Met criteria codes
PS3_Supporting
Single fiber testing showed higher levels of the variant in COX-negative fibers (>90%) than in COX-positive fibers (6-85%), p<0.0001 (PS3_supporting, PMID: 15054399).

PM2_Supporting
Although there is one occurrence of this variant in population databases (1/61,134 in MITOMAP, absent in Helix and gnomad v3.1.2), the frequency is still low (PM2_supporting).
PP1
The variant was present at 92% heteroplasmy in muscle, 37% in fibroblasts, and 21% in blood. The variant was present at lower heteroplasmy levels in blood from her healthy mother (7%) and brother (9%; PP1; PMID: 15054399).
Not Met criteria codes
PS4
The m.5532G>A variant in MT-TW has been reported in one individual with primary mitochondrial disease to date (PMID: 15054399), in a 16-year-old girl with failure to thrive, short stature, recurrent vomiting, developmental delay and regression, ophthalmoplegia, ptosis, pigmentary retinopathy, sensorineural hearing loss, and myopathy. Brain imaging showed generalized atrophy and periventricular white matter changes. Elevated lactate was seen in blood and cerebrospinal fluid. Muscle biopsy showed ragged red fibers and mitochondrial respiratory chain complex I and IV deficiency. The variant was present at 92% heteroplasmy in muscle, 37% in fibroblasts, and 21% in blood.
PP3
In-silico predictors were conflicting: MitoTip, 0.194 “Likely Benign” (<0.5); HmtVar 0.7 “Pathogenic” (>0.35). Nucleotide conservation was 93.3% in Mitomap.
Curation History
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