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 0.38 s - this script 2.758189 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Amino acid changes	Variant type	Protein length	Features at a glance
ENST00000700029	PTEN	Deleterious	10\|0	complex_aae	No	Y178*	Single base exchange	NMD	Amino acid sequence changed NMD
ENST00000688308	PTEN	Deleterious	10\|0	complex_aae	No	Y178*	Single base exchange	NMD	Amino acid sequence changed NMD Protein features (might be) affected
ENST00000713839	PTEN	Deleterious	10\|0	complex_aae	No	Y209*	Single base exchange	NMD	Amino acid sequence changed NMD
ENST00000700021	PTEN	Deleterious	10\|0	complex_aae	No	Y163*	Single base exchange	NMD	Amino acid sequence changed NMD
ENST00000472832	PTEN	Deleterious	10\|0	complex_aae	No	Y178*	Single base exchange	NMD	Amino acid sequence changed NMD
ENST00000371953(MANE Select)	PTEN	Deleterious	10\|0	complex_aae	No	Y178*	Single base exchange	NMD	Amino acid sequence changed NMD Protein features (might be) affected

MutationT@ster 2025

Variant:

10:87952159T>A_2_ENST00000700029

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr10:87952159T>A (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

CDS

DNA changes

c.534T>A
g.89522T>A

AA changes

Y178* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		178	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P
mutated	no alignment	n/a
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.82	1
	1.86	1
(flanking)	8.82	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

1

Original gDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered gDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

Original cDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered cDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

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

MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYY*

Position of stopcodon in wt / mu CDS

1305 / 534

Position (AA) of stopcodon in wt / mu AA sequence

435 / 178

Position of stopcodon in wt / mu cDNA

2150 / 1379

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

534

cDNA position

1379

gDNA position

89522

Chromosomal position

87952159

Speed

0.08 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

MutationT@ster 2025

Variant:

10:87952159T>A_1_ENST00000688308

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr10:87952159T>A (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

CDS

DNA changes

c.534T>A
g.89522T>A

AA changes

Y178* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		178	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P
mutated	no alignment	n/a
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
2	403	CHAIN		lost
14	185	DOMAIN	Phosphatase tensin-type	lost
169	184	HELIX		lost
190	350	DOMAIN	C2 tensin-type	lost
192	202	STRAND		lost
206	209	STRAND		lost
213	219	STRAND		lost
222	226	STRAND		lost
232	235	STRAND		lost
238	259	STRAND		lost
262	264	STRAND		lost
268	276	STRAND		lost
277	279	HELIX		lost
280	284	STRAND		lost
289	289	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
294	294	MOD_RES	Phosphoserine	lost
310	312	STRAND		lost
315	321	STRAND		lost
319	319	MOD_RES	Phosphothreonine	lost
321	321	MOD_RES	Phosphothreonine	lost
322	324	HELIX		lost
328	330	HELIX		lost
335	337	STRAND		lost
336	336	MOD_RES	Phosphotyrosine	lost
338	348	REGION	Required	lost
342	349	STRAND		lost
352	403	REGION		lost
353	370	COMPBIAS	Polar residues	lost
366	366	MOD_RES	Phosphothreonine	lost
370	370	MOD_RES	Phosphoserine	lost
371	385	COMPBIAS	Basic and acidic residues	lost
380	380	MOD_RES	Phosphoserine	lost
382	382	MOD_RES	Phosphothreonine	lost
383	383	MOD_RES	Phosphothreonine	lost
385	385	MOD_RES	Phosphoserine	lost
395	403	STRAND		lost
401	401	MOD_RES	Phosphothreonine	lost
401	403	MOTIF	PDZ domain-binding	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.82	1
	1.86	1
(flanking)	8.82	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

1

Original gDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered gDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

Original cDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered cDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

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

MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYY*

Position of stopcodon in wt / mu CDS

1212 / 534

Position (AA) of stopcodon in wt / mu AA sequence

404 / 178

Position of stopcodon in wt / mu cDNA

1704 / 1026

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

534

cDNA position

1026

gDNA position

89522

Chromosomal position

87952159

Speed

0.08 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

MutationT@ster 2025

Variant:

10:87952159T>A_4_ENST00000713839

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr10:87952159T>A (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

CDS

DNA changes

c.627T>A
g.89522T>A

AA changes

Y209* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		209	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P
mutated	no alignment	n/a
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.82	1
	1.86	1
(flanking)	8.82	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

1

Original gDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered gDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

Original cDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered cDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

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

MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRDRVLP
YCPGGSRTPE PKQSALLSVP KCCDYRFLDS KHKNHYKIYN LCAERHYDTA KFNCRVAQYP
FEDHNPPQLE LIKPFCEDLD QWLSEDDNHV AAIHCKAGKG RTGVMICAYL LHRGKFLKAQ
EALDFYGEVR TRDKKGVTIP SQRRYVYY*

Position of stopcodon in wt / mu CDS

1305 / 627

Position (AA) of stopcodon in wt / mu AA sequence

435 / 209

Position of stopcodon in wt / mu cDNA

2142 / 1464

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

627

cDNA position

1464

gDNA position

89522

Chromosomal position

87952159

Speed

0.08 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

MutationT@ster 2025

Variant:

10:87952159T>A_5_ENST00000700021

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr10:87952159T>A (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

CDS

DNA changes

c.489T>A
g.89522T>A

AA changes

Y163* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		163	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P
mutated	no alignment	n/a
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.82	1
	1.86	1
(flanking)	8.82	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

1

Original gDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered gDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

Original cDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered cDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

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

MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVSCAERH
YDTAKFNCRV AQYPFEDHNP PQLELIKPFC EDLDQWLSED DNHVAAIHCK AGKGRTGVMI
CAYLLHRGKF LKAQEALDFY GEVRTRDKKG VTIPSQRRYV YY*

Position of stopcodon in wt / mu CDS

1167 / 489

Position (AA) of stopcodon in wt / mu AA sequence

389 / 163

Position of stopcodon in wt / mu cDNA

1842 / 1164

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

489

cDNA position

1164

gDNA position

89522

Chromosomal position

87952159

Speed

0.04 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

MutationT@ster 2025

Variant:

10:87952159T>A_6_ENST00000472832

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr10:87952159T>A (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

CDS

DNA changes

c.534T>A
g.89522T>A

AA changes

Y178* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		178	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P
mutated	no alignment	n/a
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.82	1
	1.86	1
(flanking)	8.82	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

1

Original gDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered gDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

Original cDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered cDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

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

MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYY*

Position of stopcodon in wt / mu CDS

1035 / 534

Position (AA) of stopcodon in wt / mu AA sequence

345 / 178

Position of stopcodon in wt / mu cDNA

1176 / 675

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

534

cDNA position

675

gDNA position

89522

Chromosomal position

87952159

Speed

0.05 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

MutationT@ster 2025

Variant:

10:87952159T>A_3_ENST00000371953

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr10:87952159T>A (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

CDS

DNA changes

c.534T>A
g.89522T>A

AA changes

Y178* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		178	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P	V	A	L	L	F	H	K	M	M	F	E	T	I	P	M	F	S	G	G	T	C	N	P	Q	F	V	V	C	Q	L	K	V	K	I	Y	S	S	N	S	G	P	T	R	R	E	D	K	F	M	Y	F	E	F	P	Q	P	L	P	V	C	G	D
mutated	no alignment	n/a
Ptroglodytes	all identical	178	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P	V	A	L	L	F	H	K	M	M	F	E	T	I	P	M	F	S	G	G	T	C	N	P	Q	F	V	V	C	Q	L	K	V	K	I	Y	S	S	N	S	G	P	T	R	R	E	D	K	F	M	Y
Mmulatta	no homologue
Fcatus	all identical	178	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P	V	A	L	L	F	H	K	M	M	F	E	T	I	P	M	F	S	G	G	T	C	N	P	Q	F	V	V	C	Q	L	K	V	K	I	Y	S	S	N	S	G	P	T	R	R	E	D	K	F	M	Y
Mmusculus	no homologue
Ggallus	partly conserved	178	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	H	L	D	Y	R	P	V	A	L	L	F	H	K	M	M	F	E	T	I	P	M	F	S	G	G	T	C	N	P	Q	F	V	V	Y	Q	L	K	V	K	I	F	T	S	P	S	G	P	S	R	R	E	D	K	Y	M	Y
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	partly conserved	186	T	I	P	S	Q	R	R	Y	V	Q	Y	F	S	K	L	V	C	S	S	V	P	Y	S	K	V	S	L	N	V	C	E	I	R	F	S	E	-	-	-	-	S	S	C	V	Q	N	L	G	M	V	E	C	S	I	S	V	L	H	D	S	A	T	E	N	A	K	P	D	R	L	K	T	L
Celegans	no homologue
Xtropicalis	partly conserved	177	T	I	P	S	Q	R	R	Y	V	Y	Y	Y	S	Y	L	L	K	N	N	L	E	Y	R	P	V	P	L	L	F	H	K	I	E	F	E	T	I	P	M	F	S	G	S	T	C	N	P	Q	F	V	V	Y	Q	L	K	V	K	I	F	T	S	T	A	G	P	-	K	R	I	E	K	L	M	Y

Protein features

Start (aa)	End (aa)	Feature	Details
2	403	CHAIN		lost
14	185	DOMAIN	Phosphatase tensin-type	lost
169	184	HELIX		lost
190	350	DOMAIN	C2 tensin-type	lost
192	202	STRAND		lost
206	209	STRAND		lost
213	219	STRAND		lost
222	226	STRAND		lost
232	235	STRAND		lost
238	259	STRAND		lost
262	264	STRAND		lost
268	276	STRAND		lost
277	279	HELIX		lost
280	284	STRAND		lost
289	289	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
294	294	MOD_RES	Phosphoserine	lost
310	312	STRAND		lost
315	321	STRAND		lost
319	319	MOD_RES	Phosphothreonine	lost
321	321	MOD_RES	Phosphothreonine	lost
322	324	HELIX		lost
328	330	HELIX		lost
335	337	STRAND		lost
336	336	MOD_RES	Phosphotyrosine	lost
338	348	REGION	Required	lost
342	349	STRAND		lost
352	403	REGION		lost
353	370	COMPBIAS	Polar residues	lost
366	366	MOD_RES	Phosphothreonine	lost
370	370	MOD_RES	Phosphoserine	lost
371	385	COMPBIAS	Basic and acidic residues	lost
380	380	MOD_RES	Phosphoserine	lost
382	382	MOD_RES	Phosphothreonine	lost
383	383	MOD_RES	Phosphothreonine	lost
385	385	MOD_RES	Phosphoserine	lost
395	403	STRAND		lost
401	401	MOD_RES	Phosphothreonine	lost
401	403	MOTIF	PDZ domain-binding	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.82	1
	1.86	1
(flanking)	8.82	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

1

Original gDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered gDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

Original cDNA sequence snippet

AGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCA

Altered cDNA sequence snippet

AGGCGCTATGTGTATTATTAAAGCTACCTGTTAAAGAATCA

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

MTAIIKEIVS RNKRRYQEDG FDLDLTYIYP NIIAMGFPAE RLEGVYRNNI DDVVRFLDSK
HKNHYKIYNL CAERHYDTAK FNCRVAQYPF EDHNPPQLEL IKPFCEDLDQ WLSEDDNHVA
AIHCKAGKGR TGVMICAYLL HRGKFLKAQE ALDFYGEVRT RDKKGVTIPS QRRYVYY*

Position of stopcodon in wt / mu CDS

1212 / 534

Position (AA) of stopcodon in wt / mu AA sequence

404 / 178

Position of stopcodon in wt / mu cDNA

2057 / 1379

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

534

cDNA position

1379

gDNA position

89522

Chromosomal position

87952159

Speed

0.05 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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