PTEN (Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-) variants and mutations
PTEN (also known as Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-) is a human protein-coding gene encoding a phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase protein. A lipid and protein phosphatase that removes phosphate groups from signaling molecules, especially PIP3. By opposing the PI3K-AKT pathway, it limits cell growth and survival signals, and PTEN variants are associated with Cowden syndrome and multiple cancers. This analysis covers 2,275 PTEN variants and mutations. Of these, 49% have computational variant effect predictions. Disease context includes Cowden syndrome 1, macrocephaly-autism syndrome, and PTEN hamartoma tumor syndrome. Example PTEN variants include M1?, M1L, and T2A.
Variant analysis overview
- Gene: PTEN
- Protein: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual
- UniProt accession: P60484
- Organism: Homo sapiens
- Variants analyzed: 2275
- Variant scope: all variants
- Completed: 2026-08-20
Variant and mutation evidence
- Variant composition: 2,102 unspecified-consequence records; 84 missense variants; 46 synonymous variants; 19 frameshift variants; 3 in-frame insertions; 8 in-frame deletions; 3 stop-gained variants; 1 coding sequence variant; 1 splice acceptor variant; 3 splice donor variant; 5 substitution
- Prediction scores: 1,110 variants have prediction scores (49% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Cowden syndrome 1, macrocephaly-autism syndrome, PTEN hamartoma tumor syndrome, Cowden disease, glioma susceptibility 2, Bannayan-Riley-Ruvalcaba syndrome, glioma, endometrial cancer, melanoma, head and neck squamous cell carcinoma, Familial prostate cancer, familial meningioma.
Protein structure and variant hotspots
- Protein features: 2 domains; 12 post-translational modification sites.
- Structural context: 1,942 variants have structural context.
- PTM context: 51 variants overlap post-translational modification sites.
- Experimental data: 384 protein positions have experimental scores. Source: PTEN VAMP-seq Fill-in, PTEN VAMP-seq Combined.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable PTEN variants
Examples include M1?, M1L, T2A, T2I, T2K, T2R, T2S, A3D. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, rs1858394001, NCI-TCGA Cosmic COSV6429, TOPMed rs1858394001, MutPred 0.93, Pathogenic
- M1L (p.Met1Leu), rs1554890324, ClinGen CA377781753, ClinVar RCV004442426, MutPred 0.94, Pathogenic, Macrocephaly-autism syndrome; Cowden syndrome 1
- T2A (p.Thr2Ala), gnomAD rs1478570799, REVEL 0.21, MetaLR 0.52, Uncertain significance, PTEN hamartoma tumor syndrome
- T2I (p.Thr2Ile), Ensembl rs2132145353
- T2K (p.Thr2Lys), Ensembl rs2132145353
- T2R (p.Thr2Arg), Ensembl rs2132145353
- T2S (p.Thr2Ser), gnomAD rs1478570799
- A3D (p.Ala3Asp), Ensembl rs1564801650, Uncertain significance, Hereditary cancer-predisposing syndrome
- A3G (p.Ala3Gly), Ensembl rs1564801650, Uncertain significance
- A3T (p.Ala3Thr), rs1589596120, ClinGen CA377781777, ClinVar RCV001027042, ClinVar RCV001862394, MutPred 0.17, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome
- A3V (p.Ala3Val), rs1564801650, ClinGen CA377781785, ClinVar RCV000773966, ClinVar RCV001304693, MutPred 0.38, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome
- A3R (p.Ala3Arg), rs1858362139, gnomAD 10-87863962-G-GGA, CADD 19.20
- p.Ala17dup, gnomAD 10-87863967-A-AGC, CADD 18.50
- p.Ala15 Ala17del, rs1237307954, gnomAD 10-87863967-AGCGG, CADD 17.60
- A3S (p.Ala3Ser), gnomAD 10-87863968-G-T, CADD 16.80, SIFT 0.00
- A3E (p.Ala3Glu), gnomAD 10-87863969-C-A, CADD 16.40, SIFT 0.00
- A3A (p.Ala3Ala), gnomAD 10-87863970-G-A, CADD 16.20
- A3H (p.Ala3His), gnomAD 10-87863978-C-CAC, CADD 16.20
- A3P (p.Ala3Pro), rs1858364365, gnomAD 10-87863983-G-GCC, CADD 16.50
- p.Ala12 Ala13insVal, gnomAD 10-87863984-C-CGG, CADD 15.80
- I4F (p.Ile4Phe), Ensembl rs1647701808, Likely pathogenic
- I4M (p.Ile4Met), Ensembl rs2132145422, Likely benign
- I4N (p.Ile4Asn), Ensembl rs1858394571, Uncertain significance
- I4S (p.Ile4Ser), rs1858394571, ClinGen CA377781793, ClinVar RCV001182925, Ensembl rs1858394571, Uncertain significance, Hereditary cancer-predisposing syndrome
- I4T (p.Ile4Thr), rs1858394571, ClinGen CA377781795, ClinVar RCV001914392, ClinVar RCV004044069, MutPred 0.53, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome
- I4V (p.Ile4Val), rs1647701808, ClinGen CA377781789, ClinVar RCV002281488, ClinVar RCV002295377, MutPred 0.34, Uncertain significance, PTEN hamartoma tumor syndrome
- I5F (p.Ile5Phe), rs1060500109, ClinGen CA377781801, ClinVar RCV002021517, Ensembl rs1060500109, Uncertain significance, PTEN hamartoma tumor syndrome
- I5M (p.Ile5Met), Ensembl rs2132145458, REVEL 0.53, MetaLR 0.77, Likely benign
- I5N (p.Ile5Asn), rs2132145451, ClinGen CA377781803, ClinVar RCV001979931, ClinVar RCV003303484, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome
- I5R (p.Ile5Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- I5T (p.Ile5Thr), rs2132145451, ClinVar RCV004595062, ClinVar RCV006489036, Ensembl rs2132145451, MutPred 0.65, Likely pathogenic, Macrocephaly-autism syndrome; PTEN hamartoma tumor syndrome
- I5V (p.Ile5Val), rs1060500109, ClinGen CA16612998, NCI-TCGA Cosmic COSV6429, ClinVar RCV000473204, MutPred 0.47, Uncertain significance, PTEN hamartoma tumor syndrome
- K6* (p.Lys6Ter), Ensembl rs1589596143, Pathogenic
- K6E (p.Lys6Glu), rs1589596143, ClinGen CA377781810, NCI-TCGA Cosmic COSV6429, ClinVar RCV000798296, MutPred 0.71, Pathogenic, PTEN hamartoma tumor syndrome
- K6N (p.Lys6Asn), rs876660391, ClinGen CA377781828, NCI-TCGA Cosmic COSV6429, Uncertain significance, Hereditary cancer-predisposing syndrome
- K6R (p.Lys6Arg), rs2493591646, ClinGen CA377781821, ClinVar RCV002407865, ClinVar RCV006471017, Uncertain significance, Hereditary cancer-predisposing syndrome; PTEN hamartoma tumor syndrome
- K6T (p.Lys6Thr), NCI-TCGA Cosmic COSV6428, NCI-TCGA Cosmic COSV6429, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome
- E7* (p.Glu7Ter), rs1554890335, ClinGen CA377781832, NCI-TCGA Cosmic COSV6428, NCI-TCGA Cosmic COSV6429, MutPred 0.35, Pathogenic
- E7D (p.Glu7Asp), rs1554890337, NCI-TCGA TCGA novel, ClinGen CA377781840, ClinVar RCV000645071, REVEL 0.27, MetaLR 0.72, Uncertain significance, Hereditary cancer-predisposing syndrome; PTEN hamartoma tumor syndrome
- E7K (p.Glu7Lys), Ensembl rs1554890335, Pathogenic
- E7Q (p.Glu7Gln), Ensembl rs1554890335, Pathogenic
- E7R (p.Glu7Arg), NCI-TCGA Cosmic COSV6429, Variant assessed as somatic; high impact.
- E7G (p.Glu7Gly), rs2132142216, gnomAD 10-87863954-A-G, CADD 21.30, SIFT 0.00
- E7V (p.Glu7Val), gnomAD 10-87863954-A-T, CADD 20.90, SIFT 0.00
- E7A (p.Glu7Ala), gnomAD 10-87863954-A-C, CADD 21.00, SIFT 0.00
- E7E (p.Glu7Glu), gnomAD 10-87863955-G-A, CADD 20.80
- I8D (p.Ile8Asp), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- I8F (p.Ile8Phe), rs2132145527, ClinGen CA377781844, ClinVar RCV004525219, Ensembl rs2132145527, MutPred 0.33, Uncertain significance, Hereditary cancer-predisposing syndrome
- I8M (p.Ile8Met), Ensembl rs1589596177, Likely benign
- I8N (p.Ile8Asn), Ensembl rs2132145532
- I8S (p.Ile8Ser), Ensembl rs2132145532
- I8T (p.Ile8Thr), NCI-TCGA Cosmic COSV1044, NCI-TCGA Cosmic COSV6429, NCI-TCGA Cosmic COSV6430, Ensembl rs2132145532, Variant assessed as somatic; moderate impact.
- I8V (p.Ile8Val), Ensembl rs2132145527, Uncertain significance, not provided
- V9D (p.Val9Asp), Ensembl rs2132145566, REVEL 0.96, MetaLR 0.96
- V9F (p.Val9Phe), Ensembl rs1564801672, Uncertain significance
- V9G (p.Val9Gly), Ensembl rs2132145566
- V9I (p.Val9Ile), rs1564801672, ClinGen CA377781860, ClinVar RCV000777519, Ensembl rs1564801672, MutPred 0.77, Uncertain significance, Hereditary cancer-predisposing syndrome
- V9L (p.Val9Leu), Ensembl rs1564801672, Uncertain significance, PTEN hamartoma tumor syndrome
- V9A (p.Val9Ala), gnomAD 10-87864026-T-C, CADD 20.70, SIFT 0.03
- V9V (p.Val9Val), gnomAD 10-87864027-C-A, CADD 19.20
- S10A (p.Ser10Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- S10C (p.Ser10Cys), NCI-TCGA Cosmic COSV6429, Uncertain significance, Hereditary cancer-predisposing syndrome
- S10G (p.Ser10Gly), rs572685299, ClinGen CA059806, ClinVar RCV000490915, 1000Genomes rs572685299, REVEL 0.80, MetaLR 0.86, Uncertain significance, Hereditary cancer-predisposing syndrome
- S10N (p.Ser10Asn), NCI-TCGA Cosmic COSV6428, NCI-TCGA Cosmic COSV6429, UniProt VAR 026248, Uncertain significance, Hereditary cancer-predisposing syndrome
- S10R (p.Ser10Arg), rs1564801689, NCI-TCGA Cosmic COSV6429, Ensembl rs1564801689, MutPred 0.61, Uncertain significance, Hereditary cancer-predisposing syndrome
- S10T (p.Ser10Thr), rs2132145601, ClinGen CA377781872, ClinVar RCV004555824, Ensembl rs2132145601, MutPred 0.63, Uncertain significance, PTEN hamartoma tumor syndrome
- S10V (p.Ser10Val), rs1858366519, gnomAD 10-87864007-A-AG, CADD 15.70
- S10L (p.Ser10Leu), gnomAD 10-87864007-AG-A, CADD 15.10
- S10P (p.Ser10Pro), gnomAD 10-87864013-T-C, CADD 15.00, SIFT 0.23
- S10F (p.Ser10Phe), rs1178630827, gnomAD 10-87864014-C-T, CADD 16.30, SIFT 0.01
- S10S (p.Ser10Ser), gnomAD 10-87864015-T-C, CADD 14.60
- S10* (p.Ser10Ter), gnomAD 10-87864020-C-A, CADD 15.70
- R11* (p.Arg11Ter), rs1858395868, ClinGen CA377781878, ClinVar RCV003452518, Pathogenic
- R11G (p.Arg11Gly), rs1858395868, ClinGen CA377781877, ClinVar RCV001299843, Ensembl rs1858395868, MutPred 0.50, Uncertain significance, PTEN hamartoma tumor syndrome
- R11I (p.Arg11Ile), NCI-TCGA Cosmic COSV6429, NCI-TCGA Cosmic COSV6430, Variant assessed as somatic; moderate impact.
- R11K (p.Arg11Lys), rs2132145621, ClinGen CA377781879, NCI-TCGA Cosmic COSV6429, NCI-TCGA Cosmic COSV6430, MutPred 0.42, Uncertain significance, PTEN hamartoma tumor syndrome
- R11T (p.Arg11Thr), Ensembl rs2132145621, Uncertain significance, not provided
- R11L (p.Arg11Leu), gnomAD 10-87863956-C-CT, CADD 19.80
- R11R (p.Arg11Arg), gnomAD 10-87863956-C-A, CADD 19.80
- R11W (p.Arg11Trp), rs528340982, gnomAD 10-87863956-C-T, CADD 20.30, SIFT 0.00
- R11Q (p.Arg11Gln), rs546504608, gnomAD 10-87863957-G-A, CADD 20.50, SIFT 0.00
- R11P (p.Arg11Pro), rs546504608, gnomAD 10-87863957-G-C, CADD 20.20, SIFT 0.00
- N12D (p.Asn12Asp), rs1554890340, ClinGen CA377781890, ClinVar RCV000563465, ClinVar RCV002528943, Uncertain significance, Hereditary cancer-predisposing syndrome; PTEN hamartoma tumor syndrome
- N12G (p.Asn12Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- N12H (p.Asn12His), rs1554890340, ClinGen CA377781889, ClinVar RCV002005308, ClinVar RCV004538698, MutPred 0.39, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome
- N12I (p.Asn12Ile), rs1085308044, ClinGen CA377781896, ClinVar RCV001214844, Ensembl rs1085308044, Likely pathogenic, PTEN hamartoma tumor syndrome
- N12K (p.Asn12Lys), rs587781957, ClinGen CA000420, ClinVar RCV000130333, Ensembl rs587781957, MutPred 0.47, Uncertain significance, Hereditary cancer-predisposing syndrome
- N12S (p.Asn12Ser), rs1085308044, ClinGen CA377781898, ClinVar RCV001776955, ClinVar RCV001868818, Uncertain significance, PTEN hamartoma tumor syndrome
- N12T (p.Asn12Thr), rs1085308044, ClinGen CA377781897, ClinVar RCV000490596, Ensembl rs1085308044, MutPred 0.38, Pathogenic, PTEN hamartoma tumor syndrome
- K13* (p.Lys13Ter), rs1554890348, ClinGen CA377781906, ClinVar RCV000548728, ClinVar RCV001809480, Pathogenic
- K13E (p.Lys13Glu), rs1554890348, ClinGen CA377781904, NCI-TCGA Cosmic COSV6428, NCI-TCGA Cosmic COSV6429, Pathogenic/Likely pathogenic, Cowden syndrome; Hereditary cancer-predisposing syndrome; not provided
- K13N (p.Lys13Asn), rs2132145687, Ensembl rs2132145687, ClinGen CA377781912, ClinVar RCV002357791, MutPred 0.67, Uncertain significance, Hereditary cancer-predisposing syndrome
- K13Q (p.Lys13Gln), rs1554890348, ClinGen CA377781903, ClinVar RCV001049877, Ensembl rs1554890348, MutPred 0.62, Likely pathogenic, PTEN hamartoma tumor syndrome
- K13R (p.Lys13Arg), rs1414611362, ClinGen CA377781909, ClinVar RCV003585765, MutPred 0.63, Uncertain significance, Hereditary cancer-predisposing syndrome
- K13T (p.Lys13Thr), gnomAD rs1414611362
- R14G (p.Arg14Gly), rs1085308047, ClinGen CA377781914, ClinVar RCV000490585, ClinVar RCV000492940, Uncertain significance, PTEN hamartoma tumor syndrome
- R14K (p.Arg14Lys), rs1589596246, ClinGen CA377781918, ClinVar RCV001022037, ClinVar RCV001729779, Uncertain significance, Hereditary cancer-predisposing syndrome
- R14M (p.Arg14Met), NCI-TCGA Cosmic COSV6428, Ensembl rs1589596246, Uncertain significance
- R14S (p.Arg14Ser), Ensembl rs1064794513, NCI-TCGA Cosmic COSV6429, Likely benign
- R14T (p.Arg14Thr), rs1589596246, ClinGen CA377781920, ClinVar RCV001057417, ClinVar RCV002327323, MutPred 0.47, Uncertain significance, Hereditary cancer-predisposing syndrome; PTEN hamartoma tumor syndrome
- R14W (p.Arg14Trp), rs1085308047, ClinGen CA377781916, ClinVar RCV003620824, Ensembl rs1085308047, MutPred 0.54, Uncertain significance, PTEN hamartoma tumor syndrome
- R15* (p.Arg15Ter), rs2132145750, ClinGen CA377781929, NCI-TCGA Cosmic COSV6429, NCI-TCGA Cosmic COSV6430, Pathogenic, in CWS1
- R15G (p.Arg15Gly), rs2132145750, ClinGen CA377781928, ClinVar RCV003300938, Ensembl rs2132145750, MutPred 0.53, Likely pathogenic, Hereditary cancer-predisposing syndrome
- R15I (p.Arg15Ile), rs398123324, NCI-TCGA Cosmic COSV1009, NCI-TCGA Cosmic COSV6429, Likely pathogenic, Hereditary cancer-predisposing syndrome
- R15K (p.Arg15Lys), rs398123324, ClinGen CA16613142, NCI-TCGA Cosmic COSV1009, NCI-TCGA Cosmic COSV6429, Likely pathogenic, PTEN hamartoma tumor syndrome
- R15M (p.Arg15Met), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact., in CWS1
- R15S (p.Arg15Ser), rs1064794096, ClinGen CA377781935, NCI-TCGA Cosmic COSV6429, NCI-TCGA Cosmic COSV6431, MutPred 0.52, Pathogenic/Likely pathogenic, Hereditary cancer-predisposing syndrome; not provided; PTEN hamartoma tumor synd
- R15T (p.Arg15Thr), rs398123324, ClinGen CA377781931, NCI-TCGA Cosmic COSV1009, NCI-TCGA Cosmic COSV6429, MutPred 0.50, Likely pathogenic, PTEN hamartoma tumor syndrome
- R15R (p.Arg15Arg), rs1043104196, gnomAD 10-87864007-A-C, CADD 15.60
- Y16* (p.Tyr16Ter), rs876661009, ClinGen CA10577413, ClinVar RCV000221548, ClinVar RCV003454663, Pathogenic
- Y16C (p.Tyr16Cys), rs2132145799, ClinGen CA377781941, ClinVar RCV003620530, Ensembl rs2132145799, Uncertain significance, PTEN hamartoma tumor syndrome
- Y16D (p.Tyr16Asp), rs1064796078, ClinGen CA16619042, ClinVar RCV000481194, ClinVar RCV006451848, Pathogenic/Likely pathogenic, not provided; PTEN hamartoma tumor syndrome
- Y16H (p.Tyr16His), rs1064796078, ClinGen CA377781939, ClinVar RCV000491437, ClinVar RCV001821414, REVEL 0.87, MetaLR 0.73, Uncertain significance, PTEN hamartoma tumor syndrome
- Y16I (p.Tyr16Ile), NCI-TCGA Cosmic COSV6429, Variant assessed as somatic; high impact.
- Y16L (p.Tyr16Leu), rs786204883, NCI-TCGA Cosmic COSV6429, Pathogenic
- Y16N (p.Tyr16Asn), rs1064796078, ClinGen CA377781937, ClinVar RCV001063300, Ensembl rs1064796078, MutPred 0.56, Uncertain significance, PTEN hamartoma tumor syndrome
- Y16S (p.Tyr16Ser), rs2132145799, ClinGen CA377781942, ClinVar RCV003620722, MutPred 0.49, Uncertain significance, PTEN hamartoma tumor syndrome
- Q17* (p.Gln17Ter), rs786204910, ClinGen CA000485, NCI-TCGA Cosmic COSV6428, ClinVar RCV000169851, CADD 38.00, Pathogenic
- Q17E (p.Gln17Glu), rs786204910, ClinGen CA377781947, ClinVar RCV000563631, ClinVar RCV001556501, MutPred 0.40, Uncertain significance, PTEN hamartoma tumor syndrome
- Q17K (p.Gln17Lys), NCI-TCGA Cosmic COSV6428, NCI-TCGA Cosmic COSV6429, Variant assessed as somatic; high impact.
- Q17R (p.Gln17Arg), rs1858398407, ClinGen CA377781951, ClinVar RCV001219200, Ensembl rs1858398407, MutPred 0.43, Uncertain significance, PTEN hamartoma tumor syndrome
- Q17X, rs951705926, []
- E18* (p.Glu18Ter), Ensembl rs1554890385
- E18D (p.Glu18Asp), rs1554890388, ClinGen CA377781970, ClinVar RCV001054357, ClinVar RCV004671197, MutPred 0.45, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome
- E18K (p.Glu18Lys), Ensembl rs1554890385
- E18Q (p.Glu18Gln), Ensembl rs1554890385
- E18R (p.Glu18Arg), rs2493592237, ClinGen CA2695200937, ClinVar RCV003452595, Pathogenic
- E18V (p.Glu18Val), rs1858367335, gnomAD 10-87864015-TGA-T, CADD 15.60
- E18G (p.Glu18Gly), rs2132142707, gnomAD 10-87864017-A-G, CADD 17.40, SIFT 0.57
- E18E (p.Glu18Glu), gnomAD 10-87864018-G-A, CADD 16.00
- D19E (p.Asp19Glu), 1000Genomes rs540063602, REVEL 0.58, MetaLR 0.79, Likely benign, in malignant melanoma
- D19F (p.Asp19Phe), rs1589596354, ClinGen CA891836079, ClinVar RCV001024195, Ensembl rs1589596354, Uncertain significance, Hereditary cancer-predisposing syndrome
- D19G (p.Asp19Gly), rs1554890392, ClinGen CA377781978, ClinVar RCV000582822, ClinVar RCV001222181, REVEL 0.80, MetaLR 0.72, Uncertain significance, PTEN hamartoma tumor syndrome; Hereditary cancer-predisposing syndrome; not prov
- D19H (p.Asp19His), Ensembl rs121909233, Pathogenic, in malignant melanoma
- D19M (p.Asp19Met), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact., in malignant melanoma
- D19N (p.Asp19Asn), rs121909233, ClinGen CA000517, ClinVar RCV000008285, ClinVar RCV001228979, MutPred 0.50, Uncertain significance, PTEN hamartoma tumor syndrome
- D19V (p.Asp19Val), rs1554890392, ClinGen CA377781983, ClinVar RCV002815672, ClinVar RCV005233024, MutPred 0.47, Pathogenic, PTEN hamartoma tumor syndrome
- D19Y (p.Asp19Tyr), Ensembl rs121909233, Pathogenic, in malignant melanoma
- G20* (p.Gly20Ter), TOPMed rs1554890393
- G20A (p.Gly20Ala), rs1064795967, ClinGen CA377781992, NCI-TCGA Cosmic COSV6428, NCI-TCGA Cosmic COSV6429, Uncertain significance, PTEN hamartoma tumor syndrome
- G20D (p.Gly20Asp), NCI-TCGA Cosmic COSV6429, NCI-TCGA Cosmic COSV6430, Variant assessed as somatic; high impact.
- G20E (p.Gly20Glu), rs1064795967, ClinGen CA16619043, ClinVar RCV000482456, ClinVar RCV004806366, Uncertain significance, not provided; PTEN hamartoma tumor syndrome
- G20R (p.Gly20Arg), TOPMed rs1554890393
- G20V (p.Gly20Val), rs1064795967, ClinGen CA377781994, ClinVar RCV000490850, ClinVar RCV001221711, MutPred 0.64, Likely pathogenic, PTEN hamartoma tumor syndrome
- p.Gly5dup, gnomAD 10-87863956-C-CGG, CADD 19.70
- G20W (p.Gly20Trp), gnomAD 10-87863959-G-T, CADD 20.10, SIFT 0.00
- G20G (p.Gly20Gly), gnomAD 10-87863961-G-T, CADD 19.90
- F21I (p.Phe21Ile), Ensembl rs2132145931
- F21L (p.Phe21Leu), rs1858399493, ClinGen CA377782005, ClinVar RCV001942958, TOPMed rs1858399493, MutPred 0.51, Tier I - Strong, Diffuse pediatric-type high-grade glioma, H3-wildtype and IDH-wildtype
- F21S (p.Phe21Ser), NCI-TCGA TCGA novel, Pathogenic, not provided
- F21V (p.Phe21Val), Ensembl rs2132145931
- F21Y (p.Phe21Tyr), Ensembl rs2132145941
- D22E (p.Asp22Glu), rs786201335, ClinGen CA377782017, ClinVar RCV001807917, ClinVar RCV003326159, MutPred 0.55, Uncertain significance, Macrocephaly-autism syndrome; not provided; Cowden syndrome 1
- D22G (p.Asp22Gly), rs1554890398, ClinGen CA377782015, ClinVar RCV000571172, ClinVar RCV004794415, REVEL 0.87, MetaLR 0.93, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided; PTEN hamartoma tumor synd
- D22H (p.Asp22His), rs876660420, ClinGen CA10578904, ClinVar RCV000221043, ClinVar RCV002515722, MutPred 0.57, Likely pathogenic, PTEN hamartoma tumor syndrome
- D22N (p.Asp22Asn), Ensembl rs876660420, Pathogenic
- D22V (p.Asp22Val), rs1554890398, ClinGen CA377782016, ClinVar RCV004525237, Ensembl rs1554890398, MutPred 0.59, Likely pathogenic, Hereditary cancer-predisposing syndrome
- D22Y (p.Asp22Tyr), rs876660420, ClinGen CA377782011, ClinVar RCV000550017, ClinVar RCV003226941, REVEL 0.96, MetaLR 0.96, Likely pathogenic, PTEN hamartoma tumor syndrome
- L23* (p.Leu23Ter), rs1554890400, NCI-TCGA Cosmic COSV6429, Pathogenic
- L23F (p.Leu23Phe), Ensembl rs2132145999
- L23S (p.Leu23Ser), rs1589596407, ClinGen CA377782023, ClinVar RCV003620926, ClinVar RCV006451861, MutPred 0.78, Conflicting interpretations, PTEN hamartoma tumor syndrome; Hereditary breast ovarian cancer syndrome
- L23V (p.Leu23Val), rs876661244, ClinGen CA10577414, ClinVar RCV000761737, ClinVar RCV001058945, REVEL 0.89, MetaLR 0.97, Uncertain significance, PTEN hamartoma tumor syndrome
- D24E (p.Asp24Glu), rs1320222638, ClinGen CA377782035, ClinVar RCV003619644, ClinGen CA377782036, MutPred 0.86, Uncertain significance, PTEN hamartoma tumor syndrome
- D24A (p.Asp24Ala), rs797044910, ClinGen CA377782033, ClinVar RCV002899003, Uncertain significance, PTEN hamartoma tumor syndrome
- D24G (p.Asp24Gly), rs797044910, ClinGen CA204760, NCI-TCGA Cosmic COSV6429, Pathogenic/Likely pathogenic, Cowden syndrome 1; Hereditary cancer-predisposing syndrome; PTEN hamartoma tumor
- D24H (p.Asp24His), rs786201995, ClinGen CA000187, NCI-TCGA Cosmic COSV6428, REVEL 0.98, MetaLR 0.98, Pathogenic, PTEN hamartoma tumor syndrome
- D24N (p.Asp24Asn), rs786201995, ClinGen CA000185, NCI-TCGA Cosmic COSV6428, Pathogenic, PTEN hamartoma tumor syndrome
- D24V (p.Asp24Val), rs797044910, ClinGen CA377782034, NCI-TCGA Cosmic COSV6429, MutPred 0.85, Pathogenic/Likely pathogenic, Cowden syndrome 1; PTEN hamartoma tumor syndrome
- D24Y (p.Asp24Tyr), rs786201995, NCI-TCGA TCGA novel, ClinGen CA000552, ClinVar RCV000169787, MutPred 0.85, Pathogenic, not provided; Cowden syndrome 1
- L25D (p.Leu25Asp), rs2493592611, ClinGen CA2695200948, ClinVar RCV003452539, Pathogenic
- L25* (p.Leu25Ter), Ensembl rs786204912, Pathogenic
- L25F (p.Leu25Phe), rs786201506, ClinGen CA377782046, ClinVar RCV001379693, ClinVar RCV004728698, REVEL 0.90, MetaLR 0.96, Pathogenic, PTEN hamartoma tumor syndrome; not provided
- L25S (p.Leu25Ser), rs786204912, ClinGen CA000563, ClinVar RCV000169853, ClinVar RCV004943766, MutPred 0.86, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided
- L25V (p.Leu25Val), rs398123326, ClinGen CA000561, ClinVar RCV000078620, ClinVar RCV001221341, MutPred 0.82, Uncertain significance, not provided; PTEN hamartoma tumor syndrome
- T26I (p.Thr26Ile), rs786204853, ClinGen CA000574, ClinVar RCV001065725, ClinVar RCV001263192, REVEL 0.95, MetaLR 0.95, Pathogenic/Likely pathogenic, Hereditary cancer-predisposing syndrome; PTEN hamartoma tumor syndrome; See case
- T26N (p.Thr26Asn), rs786204853, ClinGen CA377782052, ClinVar RCV001220448, ClinVar RCV005262294, MutPred 0.72, Likely pathogenic, Hereditary cancer-predisposing syndrome; PTEN hamartoma tumor syndrome; Cowden s
- T26P (p.Thr26Pro), rs876661010, ClinGen CA10577415, ClinVar RCV000217854, ClinVar RCV002516191, MutPred 0.71, Pathogenic, not provided; PTEN hamartoma tumor syndrome
- T26S (p.Thr26Ser), gnomAD rs786204853, Pathogenic
- T26A (p.Thr26Ala), gnomAD 10-87864028-A-G, CADD 20.70, SIFT 0.31
- T26T (p.Thr26Thr), gnomAD 10-87864030-C-A, CADD 19.00
Public PTEN analysis runs
- PTEN analysis run — PTEN (2,275 variants) — completed 2026-08-20
- PTEN analysis run — PTEN (2,709 variants) — completed 2026-05-27
- PTEN analysis run — PTEN (2,709 variants) — completed 2026-05-15