chrX-19359619-C-CCAAT

Position:

• chrX-19359619-C-CCAAT

Variant summary

Our verdict is Pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1_Moderate PM2 PS2 PP4

This summary comes from the ClinGen Evidence Repository: 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. LINK:https://erepo.genome.network/evrepo/ui/classification/CA121215/MONDO:0019169/014

• Frequency: Genomes: not found (cov: 22)
• Consequence: PDHA1 NM_000284.4 frameshift
• Clinical Significance: Pathogenic reviewed by expert panel P:12
• Conservation: PhyloP100: -0.539

Genes affected

PDHA1 (HGNC:8806): (pyruvate dehydrogenase E1 subunit alpha 1) The pyruvate dehydrogenase (PDH) complex is a nuclear-encoded mitochondrial multienzyme complex that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle. The PDH complex is composed of multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). The E1 enzyme is a heterotetramer of two alpha and two beta subunits. This gene encodes the E1 alpha 1 subunit containing the E1 active site, and plays a key role in the function of the PDH complex. Mutations in this gene are associated with pyruvate dehydrogenase E1-alpha deficiency and X-linked Leigh syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Pathogenic. Variant got 9 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PS2: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDHA1	NM_000284.4	c.1142_1145dup	p.Trp383SerfsTer6	frameshift_variant	11/11	ENST00000422285.7	NP_000275.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDHA1	ENST00000422285.7	c.1142_1145dup	p.Trp383SerfsTer6	frameshift_variant	11/11	1	NM_000284.4	ENSP00000394382	P1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: reviewed by expert panel

Submissions by phenotype

Pyruvate dehydrogenase E1-alpha deficiency Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 01, 2022	For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the PDHA1 protein in which other variant(s) (p.Ser388*) have been determined to be pathogenic (PMID: 7981697, 21846590, 21914562, 29756269). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 10880). This variant is also known as c.1256_1259dup, p.Try421Serfs*6. This premature translational stop signal has been observed in individual(s) with clinical features of pyruvate dehydrogenase E1-alpha deficiency (PMID: 1779625, 24718837, 26865159). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp383Serfs*6) in the PDHA1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 8 amino acid(s) of the PDHA1 protein. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 01, 1993	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Feb 04, 2020	The PDHA1 c.1142_1145dupATCA (p.Trp383SerfsTer6) variant results in a frameshift and is predicted to result in premature termination of the protein. Across a selection of the available literature, the p.Trp383SerfsTer6 variant has been identified in at least 10 individuals in a heterozygous state with variable phenotypes related to pyruvate dehydrogenase deficiency. Phenotypes include brain abnormalities (thin corpus callosum, cerebral atrophy, or cerebellar malformations), microcephaly, intellectual disability, hypotonia, elevated lactate and pyruvate levels, and epilepsy (Endo et al. 1991; Lissens et al. 2000; Quintata et al. 2010; DeBrosse et al. 2012). At least four of these individuals carried the p.Trp383SerfsTer6 variant in a de novo state (Lissens et al. 2000; Quintata et al. 2010). Evaluation of patient fibroblasts showed significantly decreased pyruvate dehydrogenase complex and pyruvate dehydrogenase E1 activity levels compared to controls (Endo et al. 1991; Lissens et al. 2000; Quintata et al. 2010). The p.Trp383SerfsTer6 variant is not found in the Genome Aggregation Database and is in a region of good sequencing coverage, so the variant is presumed to be rare. This variant occurs in the last exon and may escape nonsense mediated decay. Based on the collective evidence, the p.Trp383SerfsTer6 variant is classified as pathogenic for pyruvate dehydrogenase deficiency. -
Likely pathogenic, no assertion criteria provided	clinical testing	Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	Sep 26, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)	Apr 01, 2023	- -
Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	May 15, 2020	ACMG codes: PVS1, PS2, PS4M, PM2, PP5 -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 04, 2013	c.1142_1145dupATCA: p.Trp383SerfsX6 (W383SfsX6) in exon 11 of the PDHA1 gene (NM_000284.3). The normal sequence with the bases that are duplicated in braces is: GCCA{ATCA}GTGG. The c.1142_1145dupATCA mutation in the PDHA1 gene has been reported previously in association with pyruvate dehydrogenase complex (PDHc) deficiency (Endo et al., 1991). The duplication causes a frameshift starting with codon Tryptophan 383, changes this amino acid to a Serine residue and creates a premature Stop codon at position 6 of the new reading frame, denoted p.Trp383SerfsX6. This mutation is predicted to cause loss of normal protein function through protein truncation. The variant is found in MITONUC-MITOP panel(s). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Jun 17, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	Dec 17, 2022	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 11, 2017

- -

Pyruvate dehydrogenase complex deficiency Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen

May 06, 2021

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. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs606231189; hg19: chrX-19377737;