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Gene

PTEN

phosphatase and tensin homolog

Summary

Cytogenetic location
10q23.31
Coordinates
Chromosome 10: 87,863,625–87,971,930 (GRCh38)
Exons
9 exons across 108.3 kb
Protein
403 amino acids
Also known as
MMAC1, TEP1, PTEN1
Previous symbols
BZS, MHAM
MANE Select transcript
ENST00000371953.8NM_000314.8
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Cowden Syndrome (PTEN hamartoma tumour syndrome)

    • Cowden Syndrome 1Autosomal dominant

      Any Cowden disease in which the cause of the disease is a mutation in the PTEN gene.

      • 4 GenCC submitters rate it definitive or strong
      • On the ACMG secondary findings list
    • Lhermitte-Duclos diseaseAutosomal dominant

      A benign overgrowth of the cerebellum (dysplastic gangliocytoma) that in adults is strongly associated with PTEN variants.

      • 1 GenCC submitter rates it definitive or strong
      Actionability

      Its finding prompts PTEN testing and cancer surveillance for PTEN hamartoma tumour syndrome.

    • Macrocephaly-autism syndromeAutosomal dominant

      PTEN variants presenting with a large head size and autism spectrum disorder or developmental delay.

      • 2 GenCC submitters rate it definitive or strong
      Actionability

      Children and adults with a PTEN variant need the same cancer surveillance as in Cowden syndrome.

    • PTEN hamartoma tumour syndromeAutosomal dominant

      The spectrum of PTEN-related conditions, including Cowden and Bannayan-Riley-Ruvalcaba syndromes, with hamartomas and raised risks of breast, thyroid, endometrial, kidney and other cancers.

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

      Regular breast, thyroid, endometrial, kidney, bowel and skin surveillance, and testing of relatives.

How PTEN 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 10, with a bracket where PTEN sits. PTEN and 6 genes near it on chromosome 10, from 87,417,778 to 88,417,777.Chromosome 1010q23.31p15.3p15.2p15.1p14p13p12.33p12.32p12.31p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.31q23.32q23.33q24.1q24.2q24.31q24.32q24.33q25.1q25.2q25.3q26.11q26.12q26.13q26.2q26.387.6 Mb87.8 Mb88 Mb88.2 Mb88.4 MbMINPP1: 87,504,859–87,555,094, forward strandMINPP1PAPSS2: 87,659,613–87,747,708, forward strandPAPSS2ATAD1: 87,744,644–87,842,355, reverse strandATAD1KLLN: 87,859,158–87,863,533, reverse strandKLLNMLDHR: 87,863,559–87,863,654, forward strandMLDHRPTEN: 87,863,625–87,971,930, forward strandPTENRNLS: 88,273,551–88,584,530, reverse strandRNLSDiagram of PTEN: 9 exons on the forward strand of chromosome 10Exon 1: 53 known disease-causing sitesExon 2: 51 known disease-causing sitesExon 3: 25 known disease-causing sitesExon 4: 25 known disease-causing sitesExon 5: 157 known disease-causing sitesExon 6: 92 known disease-causing sitesExon 7: 106 known disease-causing sitesExon 8: 127 known disease-causing sitesExon 9: 21 known disease-causing sitesExon 1: 87,863,625–87,864,548, 924 bases. 21 variants with a page in exon 1. List themExon 2: 87,894,025–87,894,109, 85 bases. 22 variants with a page in exon 2. List themExon 3: 87,925,513–87,925,557, 45 bases. 12 variants with a page in exon 3. List themExon 4: 87,931,046–87,931,089, 44 bases. 5 variants with a page in exon 4. List themExon 5: 87,933,013–87,933,251, 239 bases. 61 variants with a page in exon 5. List themExon 6: 87,952,118–87,952,259, 142 bases. 30 variants with a page in exon 6. List themExon 7: 87,957,853–87,958,019, 167 bases. 23 variants with a page in exon 7. List themExon 8: 87,960,894–87,961,118, 225 bases. 24 variants with a page in exon 8. List themExon 9: 87,965,287–87,971,930, 6,644 bases. 3 variants with a page in exon 9. List them1234567895′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 8.5 kb of the gene's 108.3 kb; 1,212 of those bases code for the protein.

Sequencing PTEN

743

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

128 of them (17%) fall in regions short reads find hard.

  • Low mappability (125 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (23 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 108.3 kb of PTEN, introns included, not only the 8.5 kb of exons.

Variants with a page (238)

The PTEN 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
A34Pc.100G>CExon 287,894,045Pathogenic3 stars out of 4 reviewed by expert panel
A39Tc.115G>AExon 287,894,060Likely pathogenic3 stars out of 4 reviewed by expert panel
A39Vc.116C>TExon 287,894,061Likely pathogenic3 stars out of 4 reviewed by expert panel
A148Hfs*5c.441_442delinsAExon 587,933,200Likely pathogenic3 stars out of 4 reviewed by expert panel
c.1A>GExon 187,864,470Pathogenic3 stars out of 4 reviewed by expert panel
c.80-1G>CIntron 187,894,024Pathogenic3 stars out of 4 reviewed by expert panel
c.106G>AExon 287,894,051Likely pathogenic3 stars out of 4 reviewed by expert panel
c.165-1G>AIntron 287,925,512Likely pathogenic3 stars out of 4 reviewed by expert panel
c.165-1G>CIntron 287,925,512Pathogenic3 stars out of 4 reviewed by expert panel
c.209+1_209+4delExon 387,925,557Pathogenic3 stars out of 4 reviewed by expert panel

See all 238 PTEN variants →

Genes linked to the same conditions

Traits linked to PTEN

The Human Phenotype Ontology lists these as features of the rare conditions PTEN can cause. Each trait's page lists the other genes linked to it.

External links

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.). PTEN gene: phosphatase and tensin homolog. Retrieved 17 October 2026, from https://dantelabs.com/genes/pten

Vancouver

Dante Labs. PTEN gene: phosphatase and tensin homolog [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pten

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