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Gene

PDHA1

pyruvate dehydrogenase E1 subunit alpha 1

Summary

Cytogenetic location
Xp22.12
Coordinates
Chromosome X: 19,343,927–19,361,718 (GRCh38)
Exons
11 exons across 17.8 kb
Protein
390 amino acids
Inheritance
Autosomal recessive
Also known as
E1alpha
Previous symbols
PDHA
MANE Select transcript
ENST00000422285.7NM_000284.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Pyruvate Dehydrogenase & Pyruvate Carboxylase Deficiency

    • Pyruvate Dehydrogenase DeficiencyAutosomal recessive

      Caused by variants in PDHA1 (X-linked, often new in the child) or in PDHB, DLAT, PDHX, DLD, PDP1 or LIAS, which can cause lactic acidosis, developmental delay, seizures and movement problems.

      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing allows a ketogenic diet, avoidance of high-carbohydrate loads, and thiamine for responsive forms.

Broader groupings

  • Leigh Syndrome

    • One of 69 genes linked to it

      A progressive neurological disease defined by specific neuropathological features associating brainstem and basal ganglia lesions.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How PDHA1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome X, with a bracket where PDHA1 sits. PDHA1 and 4 genes near it on chromosome X, from 18,852,823 to 19,852,822.Chromosome XXp22.12p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2819 Mb19.2 Mb19.4 Mb19.6 Mb19.8 MbPHKA2: 18,889,806–18,984,998, reverse strandPHKA2ADGRG2: 18,989,307–19,122,962, reverse strandADGRG2PDHA1: 19,343,927–19,361,718, forward strandPDHA1MAP3K15: 19,360,056–19,515,513, reverse strandMAP3K15SH3KBP1: 19,533,966–19,887,650, reverse strandSH3KBP1Diagram of PDHA1: 11 exons on the forward strand of chromosome XExon 1: 1 known disease-causing siteExon 2: 1 known disease-causing siteExon 3: 7 known disease-causing sitesExon 4: 5 known disease-causing sitesExon 5: 11 known disease-causing sitesExon 6: 6 known disease-causing sitesExon 7: 18 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 9: 7 known disease-causing sitesExon 10: 16 known disease-causing sitesExon 11: 21 known disease-causing sitesExon 1: 19,343,927–19,344,094, 168 basesExon 2: 19,349,312–19,349,371, 60 basesExon 3: 19,349,937–19,350,110, 174 bases. 1 variant with a page in exon 3. List themExon 4: 19,351,281–19,351,407, 127 basesExon 5: 19,353,082–19,353,173, 92 bases. 1 variant with a page in exon 5. List themExon 6: 19,354,491–19,354,583, 93 basesExon 7: 19,355,349–19,355,504, 156 basesExon 8: 19,355,686–19,355,757, 72 basesExon 9: 19,357,652–19,357,719, 68 basesExon 10: 19,358,916–19,359,024, 109 bases. 1 variant with a page in exon 10. List themExon 11: 19,359,489–19,361,718, 2,230 bases. 2 variants with a page in exon 11. List them12345678910115′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.3 kb of the gene's 17.8 kb; 1,173 of those bases code for the protein.

How a genome test reads PDHA1

102

positions in PDHA1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 17.8 kb of PDHA1, introns included, not only the 3.3 kb of exons.

Variants with a page (5)

The PDHA1 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A169Vc.506C>TExon 519,353,169Pathogenic3 stars out of 4 reviewed by expert panel
R72Cc.214C>TExon 319,350,033Likely pathogenic3 stars out of 4 reviewed by expert panel
R304Xc.910C>TExon 1019,358,926Pathogenic3 stars out of 4 reviewed by expert panel
R378Cc.1132C>TExon 1119,359,612Pathogenic3 stars out of 4 reviewed by expert panel
W383Sfs*6c.1142_1145dupExon 1119,359,619Pathogenic3 stars out of 4 reviewed by expert panel

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). PDHA1 gene: pyruvate dehydrogenase E1 subunit alpha 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/pdha1

Vancouver

Dante Labs. PDHA1 gene: pyruvate dehydrogenase E1 subunit alpha 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pdha1

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