The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000284.4(PDHA1):c.214C>T (p.Arg72Cys)

CA320653

214938 (ClinVar)

Gene: PDHA1
Condition: pyruvate dehydrogenase deficiency
Inheritance Mode: X-linked inheritance
UUID: d5172594-7221-4b8d-a69c-d1e5ea5ad636

HGVS expressions

NM_000284.4:c.214C>T
NM_000284.4(PDHA1):c.214C>T (p.Arg72Cys)
NC_000023.11:g.19350033C>T
CM000685.2:g.19350033C>T
NC_000023.10:g.19368151C>T
CM000685.1:g.19368151C>T
NC_000023.9:g.19278072C>T
NG_016781.1:g.11141C>T
ENST00000422285.7:c.214C>T
ENST00000355808.9:c.214C>T
ENST00000379805.3:c.214C>T
ENST00000379806.9:c.328C>T
ENST00000417819.5:c.298C>T
ENST00000422285.6:c.214C>T
ENST00000423505.5:c.328C>T
ENST00000492364.1:n.316C>T
ENST00000540249.5:c.214C>T
ENST00000545074.5:c.214C>T
NM_000284.3:c.214C>T
NM_001173454.1:c.328C>T
NM_001173455.1:c.214C>T
NM_001173456.1:c.214C>T
NM_001173454.2:c.328C>T
NM_001173455.2:c.214C>T
NM_001173456.2:c.214C>T

Likely Pathogenic

Met criteria codes 4
PM6 PM2 PP4 PP3
Not Met criteria codes 2
BS1 BA1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The c.214C>T (p.R72C) variant in PDHA1 has been reported in multiples males with pyruvate dehydrogenase deficiency with phenotypes ranging from childhood onset Leigh syndrome spectrum (PMID: 8664900) to living into adulthood with ataxia, neuropathy, and dystonia (PMID: 21914562). We did not come across any affected female case reports in this extensive literature review. This variant has been reported to be inherited from a healthy mother (PMID: 10679936; case 3-4) and there have been several de novo case reports, as well. Indeed, this variant has been identified as a de novo occurrence (unconfirmed parental relationships) in at least three unrelated individuals with pyruvate dehydrogenase deficiency [PM6; Utilized ClinGen SVI de novo scoring guidance (phenotype consistent but not highly specific); PMID: 10679936, case 3-2; PMID: 10679936, case 3-3; PMID: 21914562, case AM23]. Additionally, this variant has been seen in at least one other individual with documented decreased pyruvate dehydrogenase activity (PP4; Patient 3 in PMID: 15384102 had Leigh syndrome and decreased total PDH complex activity (in native and DCA-activated states) in fibroblast cell line (<3rd percentile of controls). This variant is absent from gnomAD v2.1.1 (PM2). The computational predictor REVEL gives a score of 0.955, which is above the threshold of 0.75, evidence that correlates with impact to PDHA1 function (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for pyruvate dehydrogenase deficiency inherited in an X-linked manner. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel on May 20, 2020. PDHA1-specific ACMG/AMP criteria applied: PM2, PM6, PP3, PP4.
Met criteria codes
PM6
This variant has been identified as a de novo occurrence (unconfirmed parental relationships) in at least three unrelated individuals with pyruvate dehydrogenase deficiency - Utilized ClinGen SVI de novo scoring guidance (phenotype consistent but not highly specific); TOTAL 1.5 [0.5 (PMID: 10679936, case 3-2) + 0.5 (PMID: 10679936, case 3-3) + (PMID: 21914562, case AM23)]
PM2
This variant is absent from gnomAD v2.1.1.
PP4
This variant has been seen in at least one other individual with documented decreased pyruvate dehydrogenase activity (PP4; Patient 3 in PMID: 15384102 had Leigh syndrome and decreased total PDH complex activity (in native and DCA-activated states) in fibroblast cell line (<3rd percentile of controls) - see Table II.
PP3
The computational predictor REVEL gives a score of 0.955, which is above the threshold of 0.75, evidence that correlates with impact to PDHA1 function.
Not Met criteria codes
BS1
Absent
BA1
Absent
Approved on: 2021-10-25
Published on: 2021-10-25
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