--- title: "PTEN K6E (c.16A>G, rs1589596143) | Dante Labs" description: "ClinVar classifies PTEN K6E as Pathogenic (reviewed by expert panel). Where it sits in the genome, its predicted effect, and the Genome Test reports that look at it." url: "https://dantelabs.com/genes/pten/variants/k6e" --- 1. [Genes](https://dantelabs.com/genes) 2. [PTEN](https://dantelabs.com/genes/pten) 3. PTEN K6E Variant # PTEN K6E NM_000314.8(PTEN):c.16A>G (p.Lys6Glu) Also known as - p.Lys6Glu - p.K6E - rs1589596143 * ClinVar classification Pathogenic * Review status 3 stars out of 4 reviewed by expert panel * Last evaluated 4 June 2021 * Expert panel Clingen PTEN Variant Curation Expert Panel, Clingen Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bf Facts last changed 16 October 2026 ## Summary K6E is a missense variant in PTEN: it changes a single amino acid in the protein the gene encodes. ClinVar classifies it as pathogenic for PTEN hamartoma tumour syndrome (reviewed by expert panel). ## ClinVar classifications | Condition | Classification | Review status | Submissions | Last evaluated | | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | ----------------------------------------- | ------------ | -------------- | | [PTEN hamartoma tumour syndrome](https://dantelabs.com/conditions/cowden-syndrome-pten-hamartoma-tumour-syndrome) [ClinVar VCV000644390 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/644390/) | Pathogenic | 3 stars out of 4 reviewed by expert panel | 1 submission | 4 June 2021 | Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed. ## Where it lies in PTEN K6E lies in exon 1 of the 9 in PTEN's MANE Select transcript, NM_000314.8. [PTEN variants in exon 1 →](https://dantelabs.com/genes/pten/variants?exon=1) [PTEN's gene diagram →](https://dantelabs.com/genes/pten#gene-structure) ## Molecular details | Gene | [PTEN](https://dantelabs.com/genes/pten) | | --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------- | | Transcript | NM_000314.8 MANE Select | | Coding DNA change (HGVS c.) | c.16A>G | | Protein change (HGVS p.) | p.Lys6Glu p.K6E | | Predicted consequence | Missense [missense_variant (opens in a new tab)](https://purl.obolibrary.org/obo/SO_0001583) | | Predicted impact | Moderate | | Position (GRCh38) | chr10:87864485 A>G | | Position (GRCh37) | chr10:89624242 A>G | | dbSNP ID | [rs1589596143 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs1589596143) | | ClinVar Variation ID | [VCV000644390 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/644390/) | | ClinVar Allele ID | 639262 | | ClinGen Allele Registry ID | [CA377781810 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA377781810) | | ClinVar name | NM_000314.8(PTEN):c.16A>G (p.Lys6Glu) | ## PTEN K6E in other databases - [ClinVar VCV000644390 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/644390/) - [dbSNP rs1589596143 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs1589596143) - [ClinGen Allele Registry CA377781810 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA377781810) - [gnomAD 10-87864485-A-G (opens in a new tab)](https://gnomad.broadinstitute.org/variant/10-87864485-A-G?dataset=gnomad_r4) - [Ensembl rs1589596143 (opens in a new tab)](https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs1589596143) ## Reports that look at this variant (1) These Genome Test condition reports include K6E among the variants they look at. | Report | Conditions | Inheritance | | ----------------------------------------------------------------------------------------------------------------------------------- | ------------------------------ | ------------------ | | [Cowden Syndrome (PTEN hamartoma tumour syndrome)](https://dantelabs.com/conditions/cowden-syndrome-pten-hamartoma-tumour-syndrome) | PTEN hamartoma tumour syndrome | Autosomal dominant | ## Other variants in PTEN - [A34P Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/a34p) - [A39T Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/a39t) - [A39V Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/a39v) - [A148Hfs\*5 Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/a148hfs5) - [c.1A>G Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/c-1a-g) - [c.80-1G>C Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/c-80-1g-c) - [c.106G>A Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/c-106g-a) - [c.165-1G>A Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/c-165-1g-a) - [c.165-1G>C Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/c-165-1g-c) - [c.209+1_209+4del Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pten/variants/c-209plus1to209plus4del) [All PTEN variants](https://dantelabs.com/genes/pten/variants) ## Limitations This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant. Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports. Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements. If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor. ## Sources & credits - Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information. - Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0. - Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16). - Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54). - Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information. - Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16). - Difficult regions from the Genome in a Bottle Consortium (release v3.6). - Transcripts from MANE (release v1.5), NCBI and EMBL-EBI. - Predicted consequences from mehari (release 0.11.0), with transcript models from cdot. - Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026. ## Cite this page APA > Dante Labs. (16 October 2026). PTEN K6E (c.16A>G, rs1589596143) (Version 2026.10.16-c6eea6bf). Retrieved 17 October 2026, from https\://dantelabs.com/genes/pten/variants/k6e Vancouver > Dante Labs. PTEN K6E (c.16A>G, rs1589596143) \[Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 \[cited 17 October 2026]. Available from: https\://dantelabs.com/genes/pten/variants/k6e Download citation [RIS](https://dantelabs.com/genes/pten/variants/k6e/cite.ris) [BibTeX](https://dantelabs.com/genes/pten/variants/k6e/cite.bib) [CSL-JSON](https://dantelabs.com/genes/pten/variants/k6e/cite.json) ## Read your whole genome From $449 Free shipping · Results in 6–8 weeks [Explore the Genome Test](https://dantelabs.com/whole-genome-sequencing)