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Gene

PSPH

phosphoserine phosphatase

Summary

Cytogenetic location
7p11.2
Coordinates
Chromosome 7: 56,011,064–56,051,444 (GRCh38)
Exons
8 exons across 40.4 kb
Protein
225 amino acids
Inheritance
Autosomal recessive
Previous symbols
PSP
MANE Select transcript
ENST00000275605.8NM_004577.4
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 moderate
      • 3 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 PSPH is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 7, with a bracket where PSPH sits. PSPH and 11 genes near it on chromosome 7, from 55,531,254 to 56,531,253.Chromosome 77p11.2p22.3p22.2p22.1p21.3p21.2p21.1p15.3p15.2p15.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.21q11.22q11.23q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q31.1q31.2q31.31q31.32q31.33q32.1q32.2q32.3q33q34q35q36.1q36.2q36.355.6 Mb55.8 Mb56 Mb56.2 Mb56.4 MbVOPP1: 55,427,766–55,572,988, reverse strandVOPP1SEPTIN14: 55,793,540–55,862,755, reverse strandSEPTIN14ZNF713: 55,887,260–55,942,530, forward strandZNF713: 55,887,277–55,955,239, forward strandMRPS17: 55,950,705–55,956,500, forward strandMRPS17NIPSNAP2: 55,951,793–56,000,184, forward strandNIPSNAP2PSPH: 56,011,064–56,051,444, reverse strandPSPHCCT6A: 56,051,685–56,063,992, forward strandCCT6ASUMF2: 56,064,002–56,087,955, forward strandSUMF2PHKG1: 56,079,923–56,093,012, reverse strandPHKG1CHCHD2: 56,094,567–56,106,531, reverse strandCHCHD2NUPR2: 56,114,681–56,116,422, reverse strandNUPR2Diagram of PSPH: 8 exons on the reverse strand of chromosome 7Exon 6: 2 known disease-causing sitesExon 8: 56,011,064–56,011,869, 806 basesExon 7: 56,015,023–56,015,171, 149 basesExon 6: 56,017,234–56,017,379, 146 basesExon 5: 56,019,600–56,019,734, 135 basesExon 4: 56,021,073–56,021,231, 159 basesExon 3: 56,031,929–56,032,054, 126 basesExon 2: 56,033,961–56,034,106, 146 basesExon 1: 56,051,138–56,051,444, 307 bases876543215′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 2 kb of the gene's 40.4 kb; 678 of those bases code for the protein.

How a genome test reads PSPH

2

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

2 of them (100%) fall in regions short reads find hard.

  • Low mappability (2 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 40.4 kb of PSPH, introns included, not only the 2 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.). PSPH gene: phosphoserine phosphatase. Retrieved 17 October 2026, from https://dantelabs.com/genes/psph

Vancouver

Dante Labs. PSPH gene: phosphoserine phosphatase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/psph

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