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  • See Evidence submitted by expert panel for details.

Variant: NM_000284.4(PDHA1):c.1142_1145dup (p.Trp383fs)

CA121215

10880 (ClinVar)

Gene: PDHA1
Condition: pyruvate dehydrogenase deficiency
Inheritance Mode: X-linked inheritance
UUID: 4e0dd4ad-0ca9-40b8-8164-554f50b09a61

HGVS expressions

NM_000284.4:c.1142_1145dup
NM_000284.4(PDHA1):c.1142_1145dup (p.Trp383fs)
NC_000023.11:g.19359622_19359625dup
CM000685.2:g.19359622_19359625dup
NC_000023.10:g.19377740_19377743dup
CM000685.1:g.19377740_19377743dup
NC_000023.9:g.19287661_19287664dup
NG_016781.1:g.20730_20733dup
NG_021184.1:g.160639_160642dup
ENST00000422285.7:c.1142_1145dup
ENST00000379804.1:c.299_302dup
ENST00000379806.9:c.1256_1259dup
ENST00000422285.6:c.1142_1145dup
ENST00000478795.1:n.581_584dup
ENST00000540249.5:c.1049_1052dup
ENST00000545074.5:c.1163_1166dup
NM_000284.3:c.1142_1145dup
NM_001173454.1:c.1256_1259dup
NM_001173455.1:c.1163_1166dup
NM_001173456.1:c.1049_1052dup
NM_001173454.2:c.1256_1259dup
NM_001173455.2:c.1163_1166dup
NM_001173456.2:c.1049_1052dup

Pathogenic

Met criteria codes 4
PVS1_Moderate PS2_Very Strong PP4 PM2
Not Met criteria codes 2
BS2 PM1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The c.1142_c.1145dup variant in the PDHA1 gene is a frameshift variant in the final exon of PDHA1, which is predicted to escape nonsense mediated decay and result in amino acid truncation that removes less than 10% of the predicted protein product (PVS1_moderate PMID: 30192042). This variant is absent from population databases (PM2). This variant has been reported in several patients with presentations consistent with PDHA1-related disease in the literature. While this variant has been reported several times before, only five cases met criteria for scoring, including four assumed de novo cases in PMID: 10679936 and PMID: 20002461, and one maternity confirmed de novo case in PMID: 26865159. Several commercial testing laboratories (GeneDx, Illumina, and Ambry) have identified this variant was harbored by maternity confirmed de novo probands with presentations consistent with PDHA1-related disease (minimum of 3 and maximum of 6 probands- SCV001251622.1, SCV000252046.3, SCV000742395.2). Upon further review, the expert panel determined that while unable to confirm the identity of these patients, taken together these data in conjunction with the cases reported in the literature were sufficient to support elevating scoring to PS2_Very Strong per SVI de novo variant scoring criteria v1.0. PMID: 1779625 and PMID: 8504309 reported elevated pyruvate in the blood, and blood and CSF of the respective probands. PMID: 23021068 performed PDC activity assays < 3rd percentile in fibroblasts (PP4). In summary, this variant meets criteria to be classified as a pathogenic of PDHA1- related pyruvate dehydrogenase deficiency in an X-linked manner. PDHA1-specific ACMG/AMP criteria applied: (PVS1_moderate, PM2, PS2_Very Strong, PP4). This was reviewed with the PDHA1 expert panel on 4/6/2021 and approved on 4/18/2021.
Met criteria codes
PVS1_Moderate
Located in last exon so predicted to escaped NMD. Frameshift; located in region with several pathogenic duplications and deletions. Expert panel review: Since not one of PM1 locations, should be modified to moderate based on Abou Tayoun et al 2018.
PS2_Very Strong
Utilized ClinGen SVI de novo scoring guidance (phenotype consistent but not highly specific); TOTAL POINT RANGE: (3.0-9.0); 4.0 needed for Very Strong Lab Cases: GeneDx 3.0 unique cases, Ambry 2.0, Illumina 1.0 (Range 3.0-6.0) Lit Review TOTAL = 3.0; (0.5 for case 30-5 in PMID: 10679936+0.5 for case F-9 in PMID: 20002461+0.5 for case F-10 in PMID: 20002461+0.5 for case F-11 in PMID: 20002461; 1.0 Family 1 PMID: 26865159 )
PP4
Elevated pyruvate (blood and CSF) in proband in PMID: 8504309; elevated blood pyruvate in proband in PMID: 1779625; < 3rd percentile for fibroblast PDC activity (nmol/min/mg) in PMID: 23021068
PM2
Absent
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2021-05-06
Published on: 2021-05-06
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