Yum, tasty mutations...

MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000688308
Querying Taster for transcript #2: ENST00000700029
Querying Taster for transcript #3: ENST00000371953
Querying Taster for transcript #4: ENST00000713839
Querying Taster for transcript #5: ENST00000700021
Querying Taster for transcript #6: ENST00000472832
MT speed 0.07 s - this script 2.495036 s

Transcript summary:

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Yum, tasty mutations...

MutationT@ster 2025

Variant:

10:87960892A>G_1_ENST00000688308

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Prediction:

DeleteriousPermalink

Summary:

  • Model: without_aae
  • Tree vote: 200|0 (del | benign) ?
  • Automatic classification due to ClinVar
Analysed issue Analysis result
Variant Chr10:87960892A>G (GRCh38)
Gene symbol PTEN
Gene constraints LOEUF: 0.68, LOF (oe): 0.46, misssense (oe): 0.46, synonymous (oe): 0.80 ? (gnomAD)
Ensembl transcript ID ENST00000688308.1
Genbank transcript ID
UniProt / AlphaMissense peptide PTEN_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region intron
DNA changes c.802-2A>G
g.98255A>G
AA changes N/A
Frameshift No
Length of protein N/A
Pathogenic variant (ClinVar)
Cowden syndrome 1
PTEN hamartoma tumor syndrome
Hereditary cancer-predisposing syndrome
pathogenicClinVar OMIM
Variant DBs
dbSNP IDrs587782455
gnomADhomozygous (G/G)heterozygousallele carriers
022
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.3640.044
8.8071
(flanking)9.4511
?
Splice sites alteration within used splice site, likely to disturb normal splicing

MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor lost98256wt: 0.00 / mu: 0.00- wt: ttttttttag|GACAAAATGT
 mu: ttttttttgg|GACAAAATGT
Distance from splice site 2
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 10
Strand 1
Original gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTT
Altered gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTGGGACAAAATGTTTCACTTTT
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYYYSY
LLKNHLDYRP VALLFHKMMF ETIPMFSGGT CNPQFVVCQL KVKIYSSNSG PTRREDKFMY
FEFPQPLPVC GDIKVEFFHK QNKMLKKDKM FHFWVNTFFI PGPEETSEKV ENGSLCDQEI
DSICSIERAD NDKEYLVLTL TKNDLDKANK DKANRYFSPN FKVKLYFTKT VEEPSNPEAS
SSTSVTPDVS DNEPDHYRYS DTTDSDPENE PFDEDQHTQI TKV*
Mutated AA sequence
Position of stopcodon in wt / mu CDS N/A
Position (AA) of stopcodon in wt / mu AA sequence N/A
Position of stopcodon in wt / mu cDNA N/A
Position of start ATG in wt / mu cDNA 493 / 493
Last intron/exon boundary 1518
Theoretical NMD boundary in CDS 975
Length of CDS 1212
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 98255
Chromosomal position 87960892
Speed 0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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Yum, tasty mutations...

MutationT@ster 2025

Variant:

10:87960892A>G_2_ENST00000700029

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: without_aae
  • Tree vote: 200|0 (del | benign) ?
  • Automatic classification due to ClinVar
Analysed issue Analysis result
Variant Chr10:87960892A>G (GRCh38)
Gene symbol PTEN
Gene constraints no data
Ensembl transcript ID ENST00000700029.2
Genbank transcript ID
UniProt / AlphaMissense peptide N/A
Variant type Single base exchange
Gene region intron
DNA changes c.895-2A>G
g.98255A>G
AA changes N/A
Frameshift No
Length of protein N/A
Pathogenic variant (ClinVar)
Cowden syndrome 1
PTEN hamartoma tumor syndrome
Hereditary cancer-predisposing syndrome
pathogenicClinVar OMIM
Variant DBs
dbSNP IDrs587782455
gnomADhomozygous (G/G)heterozygousallele carriers
022
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.3640.044
8.8071
(flanking)9.4511
?
Splice sites alteration within used splice site, likely to disturb normal splicing

MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor lost98256wt: 0.00 / mu: 0.00- wt: ttttttttag|GACAAAATGT
 mu: ttttttttgg|GACAAAATGT
Distance from splice site 2
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 10
Strand 1
Original gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTT
Altered gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTGGGACAAAATGTTTCACTTTT
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYYYSY
LLKNHLDYRP VALLFHKMMF ETIPMFSGGT CNPQFVVCQL KVKIYSSNSG PTRREDKFMY
FEFPQPLPVC GDIKVEFFHK QNKMLKKGQG LTMLPRLVSN SWAQAVLTLW HPKELELQDK
MFHFWVNTFF IPGPEETSEK VENGSLCDQE IDSICSIERA DNDKEYLVLT LTKNDLDKAN
KDKANRYFSP NFKVKLYFTK TVEEPSNPEA SSSTSVTPDV SDNEPDHYRY SDTTDSDPEN
EPFDEDQHTQ ITKV*
Mutated AA sequence
Position of stopcodon in wt / mu CDS N/A
Position (AA) of stopcodon in wt / mu AA sequence N/A
Position of stopcodon in wt / mu cDNA N/A
Position of start ATG in wt / mu cDNA 846 / 846
Last intron/exon boundary 1964
Theoretical NMD boundary in CDS 1068
Length of CDS 1305
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 98255
Chromosomal position 87960892
Speed 0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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Yum, tasty mutations...

MutationT@ster 2025

Variant:

10:87960892A>G_3_ENST00000371953

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: without_aae
  • Tree vote: 200|0 (del | benign) ?
  • Automatic classification due to ClinVar
Analysed issue Analysis result
Variant Chr10:87960892A>G (GRCh38)
Gene symbol PTEN
Gene constraints LOEUF: 0.68, LOF (oe): 0.46, misssense (oe): 0.46, synonymous (oe): 0.80 ? (gnomAD)
Ensembl transcript ID ENST00000371953.8
Genbank transcript ID NM_000314 (exact from MANE)
UniProt / AlphaMissense peptide PTEN_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region intron
DNA changes c.802-2A>G
g.98255A>G
AA changes N/A
Frameshift No
Length of protein N/A
Pathogenic variant (ClinVar)
Cowden syndrome 1
PTEN hamartoma tumor syndrome
Hereditary cancer-predisposing syndrome
pathogenicClinVar OMIM
Variant DBs
dbSNP IDrs587782455
gnomADhomozygous (G/G)heterozygousallele carriers
022
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.3640.044
8.8071
(flanking)9.4511
?
Splice sites alteration within used splice site, likely to disturb normal splicing

MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor lost98256wt: 0.00 / mu: 0.00- wt: ttttttttag|GACAAAATGT
 mu: ttttttttgg|GACAAAATGT
Distance from splice site 2
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 10
Strand 1
Original gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTT
Altered gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTGGGACAAAATGTTTCACTTTT
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYYYSY
LLKNHLDYRP VALLFHKMMF ETIPMFSGGT CNPQFVVCQL KVKIYSSNSG PTRREDKFMY
FEFPQPLPVC GDIKVEFFHK QNKMLKKDKM FHFWVNTFFI PGPEETSEKV ENGSLCDQEI
DSICSIERAD NDKEYLVLTL TKNDLDKANK DKANRYFSPN FKVKLYFTKT VEEPSNPEAS
SSTSVTPDVS DNEPDHYRYS DTTDSDPENE PFDEDQHTQI TKV*
Mutated AA sequence
Position of stopcodon in wt / mu CDS N/A
Position (AA) of stopcodon in wt / mu AA sequence N/A
Position of stopcodon in wt / mu cDNA N/A
Position of start ATG in wt / mu cDNA 846 / 846
Last intron/exon boundary 1871
Theoretical NMD boundary in CDS 975
Length of CDS 1212
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 98255
Chromosomal position 87960892
Speed 0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

Yum, tasty mutations...

MutationT@ster 2025

Variant:

10:87960892A>G_4_ENST00000713839

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: without_aae
  • Tree vote: 200|0 (del | benign) ?
  • Automatic classification due to ClinVar
Analysed issue Analysis result
Variant Chr10:87960892A>G (GRCh38)
Gene symbol PTEN
Gene constraints no data
Ensembl transcript ID ENST00000713839.1
Genbank transcript ID
UniProt / AlphaMissense peptide N/A
Variant type Single base exchange
Gene region intron
DNA changes c.895-2A>G
g.98255A>G
AA changes N/A
Frameshift No
Length of protein N/A
Pathogenic variant (ClinVar)
Cowden syndrome 1
PTEN hamartoma tumor syndrome
Hereditary cancer-predisposing syndrome
pathogenicClinVar OMIM
Variant DBs
dbSNP IDrs587782455
gnomADhomozygous (G/G)heterozygousallele carriers
022
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.3640.044
8.8071
(flanking)9.4511
?
Splice sites alteration within used splice site, likely to disturb normal splicing

MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor lost98256wt: 0.00 / mu: 0.00- wt: ttttttttag|GACAAAATGT
 mu: ttttttttgg|GACAAAATGT
Distance from splice site 2
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 10
Strand 1
Original gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTT
Altered gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTGGGACAAAATGTTTCACTTTT
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRDRVLP
YCPGGSRTPE PKQSALLSVP KCCDYRFLDS KHKNHYKIYN LCAERHYDTA KFNCRVAQYP
FEDHNPPQLE LIKPFCEDLD QWLSEDDNHV AAIHCKAGKG RTGVMICAYL LHRGKFLKAQ
EALDFYGEVR TRDKKGVTIP SQRRYVYYYS YLLKNHLDYR PVALLFHKMM FETIPMFSGG
TCNPQFVVCQ LKVKIYSSNS GPTRREDKFM YFEFPQPLPV CGDIKVEFFH KQNKMLKKDK
MFHFWVNTFF IPGPEETSEK VENGSLCDQE IDSICSIERA DNDKEYLVLT LTKNDLDKAN
KDKANRYFSP NFKVKLYFTK TVEEPSNPEA SSSTSVTPDV SDNEPDHYRY SDTTDSDPEN
EPFDEDQHTQ ITKV*
Mutated AA sequence
Position of stopcodon in wt / mu CDS N/A
Position (AA) of stopcodon in wt / mu AA sequence N/A
Position of stopcodon in wt / mu cDNA N/A
Position of start ATG in wt / mu cDNA 838 / 838
Last intron/exon boundary 1956
Theoretical NMD boundary in CDS 1068
Length of CDS 1305
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 98255
Chromosomal position 87960892
Speed 0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

Yum, tasty mutations...

MutationT@ster 2025

Variant:

10:87960892A>G_5_ENST00000700021

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: without_aae
  • Tree vote: 200|0 (del | benign) ?
  • Automatic classification due to ClinVar
Analysed issue Analysis result
Variant Chr10:87960892A>G (GRCh38)
Gene symbol PTEN
Gene constraints no data
Ensembl transcript ID ENST00000700021.1
Genbank transcript ID NM_001304718 (by similarity)
UniProt / AlphaMissense peptide N/A
Variant type Single base exchange
Gene region intron
DNA changes c.757-2A>G
g.98255A>G
AA changes N/A
Frameshift No
Length of protein N/A
Pathogenic variant (ClinVar)
Cowden syndrome 1
PTEN hamartoma tumor syndrome
Hereditary cancer-predisposing syndrome
pathogenicClinVar OMIM
Variant DBs
dbSNP IDrs587782455
gnomADhomozygous (G/G)heterozygousallele carriers
022
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.3640.044
8.8071
(flanking)9.4511
?
Splice sites alteration within used splice site, likely to disturb normal splicing

MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor lost98256wt: 0.00 / mu: 0.00- wt: ttttttttag|GACAAAATGT
 mu: ttttttttgg|GACAAAATGT
Distance from splice site 2
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 10
Strand 1
Original gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTT
Altered gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTGGGACAAAATGTTTCACTTTT
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVSCAERH
YDTAKFNCRV AQYPFEDHNP PQLELIKPFC EDLDQWLSED DNHVAAIHCK AGKGRTGVMI
CAYLLHRGKF LKAQEALDFY GEVRTRDKKG VTIPSQRRYV YYYSYLLKNH LDYRPVALLF
HKMMFETIPM FSGGTCNPQF VVCQLKVKIY SSNSGPTRRE DKFMYFEFPQ PLPVCGDIKV
EFFHKQNKML KKDKMFHFWV NTFFIPGPEE TSEKVENGSL CDQEIDSICS IERADNDKEY
LVLTLTKNDL DKANKDKANR YFSPNFKVKL YFTKTVEEPS NPEASSSTSV TPDVSDNEPD
HYRYSDTTDS DPENEPFDED QHTQITKV*
Mutated AA sequence
Position of stopcodon in wt / mu CDS N/A
Position (AA) of stopcodon in wt / mu AA sequence N/A
Position of stopcodon in wt / mu cDNA N/A
Position of start ATG in wt / mu cDNA 676 / 676
Last intron/exon boundary 1656
Theoretical NMD boundary in CDS 930
Length of CDS 1167
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 98255
Chromosomal position 87960892
Speed 0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

Yum, tasty mutations...

MutationT@ster 2025

Variant:

10:87960892A>G_6_ENST00000472832

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: without_aae
  • Tree vote: 200|0 (del | benign) ?
  • Automatic classification due to ClinVar
Analysed issue Analysis result
Variant Chr10:87960892A>G (GRCh38)
Gene symbol PTEN
Gene constraints LOEUF: 0.78, LOF (oe): 0.40, misssense (oe): 0.54, synonymous (oe): 0.80 ? (gnomAD)
Ensembl transcript ID ENST00000472832.3
Genbank transcript ID
UniProt / AlphaMissense peptide N/A
Variant type Single base exchange
Gene region intron
DNA changes c.802-2A>G
g.98255A>G
AA changes N/A
Frameshift No
Length of protein N/A
Pathogenic variant (ClinVar)
Cowden syndrome 1
PTEN hamartoma tumor syndrome
Hereditary cancer-predisposing syndrome
pathogenicClinVar OMIM
Variant DBs
dbSNP IDrs587782455
gnomADhomozygous (G/G)heterozygousallele carriers
022
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.3640.044
8.8071
(flanking)9.4511
?
Splice sites alteration within used splice site, likely to disturb normal splicing

MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor lost98256wt: 0.00 / mu: 0.00- wt: ttttttttag|GACAAAATGT
 mu: ttttttttgg|GACAAAATGT
Distance from splice site 2
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 10
Strand 1
Original gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTT
Altered gDNA sequence snippet TTTTCTTTTTTTTTTTTTTTGGGACAAAATGTTTCACTTTT
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYYYSY
LLKNHLDYRP VALLFHKMMF ETIPMFSGGT CNPQFVVCQL KVKIYSSNSG PTRREDKFMY
FEFPQPLPVC GDIKVEFFHK QNKMLKKDKM FHFWVNTFFI PGPEETSEKV ENGSLCDQEI
DSICSIERAD NDKEYLVLTL TKNDLDKANK DKANRYFSPN FKVS*
Mutated AA sequence
Position of stopcodon in wt / mu CDS N/A
Position (AA) of stopcodon in wt / mu AA sequence N/A
Position of stopcodon in wt / mu cDNA N/A
Position of start ATG in wt / mu cDNA 142 / 142
Last intron/exon boundary 942
Theoretical NMD boundary in CDS 750
Length of CDS 1035
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 98255
Chromosomal position 87960892
Speed 0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table