Skip to content
Use your HSA or FSA funds

Gene

PHGDH

phosphoglycerate dehydrogenase

Summary

Cytogenetic location
1p12
Coordinates
Chromosome 1: 119,711,934–119,744,215 (GRCh38)
Exons
12 exons across 32.3 kb
Protein
533 amino acids
Inheritance
Autosomal recessive
Also known as
SERA, PGDH, PDG
MANE Select transcript
ENST00000641023.2NM_006623.4
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 report relevant to this gene

  • Disorders of Glycine & Serine Metabolism

    • Serine Deficiency DisordersAutosomal recessive

      Caused by variants in PHGDH, PSAT1 or PSPH, which block serine production and can cause small head size, seizures and developmental delay.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing allows serine and glycine supplementation, which can prevent or improve symptoms when started early, including before birth.

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 PHGDH is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where PHGDH sits. PHGDH and 9 genes near it on chromosome 1, from 119,228,075 to 120,228,074.Chromosome 11p12p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44119.4 Mb119.6 Mb119.8 Mb120 Mb120.2 MbHAO2: 119,368,727–119,394,258, forward strandHAO2HSD3B2: 119,413,725–119,453,802, forward strandHSD3B2HSD3B1: 119,493,057–119,529,426, forward strandHSD3B1ZNF697: 119,619,377–119,648,454, reverse strandZNF697PHGDH: 119,711,934–119,744,215, forward strandPHGDHHMGCS2: 119,747,979–119,769,092, reverse strandHMGCS2REG4: 119,794,017–119,811,580, reverse strandREG4ADAM30: 119,893,533–119,896,515, reverse strandADAM30NOTCH2: 119,909,256–120,100,779, reverse strandNOTCH2SEC22B: 120,150,898–120,176,533, reverse strandSEC22BDiagram of PHGDH: 12 exons on the forward strand of chromosome 1Exon 1: 12 known disease-causing sitesExon 2: 10 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 4: 8 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 7: 18 known disease-causing sitesExon 8: 20 known disease-causing sitesExon 9: 11 known disease-causing sitesExon 10: 8 known disease-causing sitesExon 11: 12 known disease-causing sitesExon 12: 4 known disease-causing sitesExon 1: 119,711,934–119,712,160, 227 basesExon 2: 119,721,170–119,721,321, 152 basesExon 3: 119,723,376–119,723,441, 66 basesExon 4: 119,726,851–119,726,905, 55 basesExon 5: 119,727,004–119,727,102, 99 basesExon 6: 119,734,634–119,734,766, 133 basesExon 7: 119,735,295–119,735,443, 149 basesExon 8: 119,737,114–119,737,266, 153 basesExon 9: 119,740,386–119,740,518, 133 basesExon 10: 119,741,767–119,741,897, 131 basesExon 11: 119,742,807–119,743,044, 238 basesExon 12: 119,743,886–119,744,215, 330 bases1246810125′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 1.9 kb of the gene's 32.3 kb; 1,602 of those bases code for the protein.

How a genome test reads PHGDH

135

positions in PHGDH 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 32.3 kb of PHGDH, introns included, not only the 1.9 kb of exons.

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.). PHGDH gene: phosphoglycerate dehydrogenase. Retrieved 17 October 2026, from https://dantelabs.com/genes/phgdh

Vancouver

Dante Labs. PHGDH gene: phosphoglycerate dehydrogenase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/phgdh

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test