Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000264977
Querying Taster for transcript #2: ENST00000490467
MT speed 0 s - this script 2.937195 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PPP2R3Apolymorphism_automatic7.26974036524553e-13simple_aaeaffectedA171Ssingle base exchangers6779903show file
PPP2R3Apolymorphism_automatic1.91577860020331e-07without_aaeaffectedsingle base exchangers6779903show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999273 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:135720851G>TN/A show variant in all transcripts   IGV
HGNC symbol PPP2R3A
Ensembl transcript ID ENST00000264977
Genbank transcript ID NM_002718
UniProt peptide Q06190
alteration type single base exchange
alteration region CDS
DNA changes c.511G>T
cDNA.1128G>T
g.36337G>T
AA changes A171S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 171
frameshift no
known variant Reference ID: rs6779903
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC57982117126969
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5580.067
0.1060.011
(flanking)0.5080.006
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased36330wt: 0.88 / mu: 0.97wt: AACGATGGGAACGCC
mu: AACGATGGGAACTCC		 CGAT|ggga
distance from splice site 951
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      171LLCGHYNNDGNAPSFGLLRSSSVE
mutated  all conserved    171LLCGHYNNDGNSPSFGLLRSS
Ptroglodytes  all identical  ENSPTRG00000015429  171LLCGHYNNDGNAPSFGLLRSS
Mmulatta  all identical  ENSMMUG00000000932  171LLCGHYNNDGNAPSFGLLRSS
Fcatus  all conserved  ENSFCAG00000010376  171LLCGHYNNDGNSPSFGLLRSS
Mmusculus  all conserved  ENSMUSG00000043154  170LLCGHYNNDGTSPPFGLLRSS
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0038744  n/a
Celegans  no alignment  C06G1.5  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
670695COMPBIASPro-rich.might get lost (downstream of altered splice site)
758793DOMAINEF-hand 1.might get lost (downstream of altered splice site)
9721007DOMAINEF-hand 2.might get lost (downstream of altered splice site)
985996CA_BINDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3453 / 3453
position (AA) of stopcodon in wt / mu AA sequence 1151 / 1151
position of stopcodon in wt / mu cDNA 4070 / 4070
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 618 / 618
chromosome 3
strand 1
last intron/exon boundary 3947
theoretical NMD boundary in CDS 3279
length of CDS 3453
coding sequence (CDS) position 511
cDNA position
(for ins/del: last normal base / first normal base)		 1128
gDNA position
(for ins/del: last normal base / first normal base)		 36337
chromosomal position
(for ins/del: last normal base / first normal base)		 135720851
original gDNA sequence snippet ATTATAACAACGATGGGAACGCCCCATCCTTTGGTTTACTG
altered gDNA sequence snippet ATTATAACAACGATGGGAACTCCCCATCCTTTGGTTTACTG
original cDNA sequence snippet ATTATAACAACGATGGGAACGCCCCATCCTTTGGTTTACTG
altered cDNA sequence snippet ATTATAACAACGATGGGAACTCCCCATCCTTTGGTTTACTG
wildtype AA sequence MAATYRLVVS TVNHYSSVVI DRRFEQAIHY CTGTCHTFTH GIDCIVVHHS VCADLLHIPV
SQFKDADLNS MFLPHENGLS SAEGDYPQQA FTGIPRVKRG STFQNTYNLK DIAGEAISFA
SGKIKEFSFE KLKNSNHAAY RKGRKVKSDS FNRRSVDLDL LCGHYNNDGN APSFGLLRSS
SVEEKPLSHR NSLDTNLTSM FLQNFSEEDL VTQILEKHKI DNFSSGTDIK MCLDILLKCS
EDLKKCTDII KQCIKKKSGS SISEGSGNDT ISSSETVYMN VMTRLASYLK KLPFEFMQSG
NNEALDLTEL ISNMPSLQLT PFSPVFGTEQ PPKYEDVVQL SASDSGRFQT IELQNDKPNS
RKMDTVQSIP NNSTNSLYNL EVNDPRTLKA VQVQSQSLTM NPLENVSSDD LMETLYIEEE
SDGKKALDKG QKTENGPSHE LLKVNEHRAE FPEHATHLKK CPTPMQNEIG KIFEKSFVNL
PKEDCKSKVS KFEEGDQRDF TNSSSQEEID KLLMDLESFS QKMETSLREP LAKGKNSNFL
NSHSQLTGQT LVDLEPKSKV SSPIEKVSPS CLTRIIETNG HKIEEEDRAL LLRILESIED
FAQELVECKS SRGSLSQEKE MMQILQETLT TSSQANLSVC RSPVGDKAKD TTSAVLIQQT
PEVIKIQNKP EKKPGTPLPP PATSPSSPRP LSPVPHVNNV VNAPLSINIP RFYFPEGLPD
TCSNHEQTLS RIETAFMDIE EQKADIYEMG KIAKVCGCPL YWKAPMFRAA GGEKTGFVTA
QSFIAMWRKL LNNHHDDASK FICLLAKPNC SSLEQEDFIP LLQDVVDTHP GLTFLKDAPE
FHSRYITTVI QRIFYTVNRS WSGKITSTEI RKSNFLQTLA LLEEEEDINQ ITDYFSYEHF
YVIYCKFWEL DTDHDLYISQ ADLSRYNDQA SSSRIIERIF SGAVTRGKTI QKEGRMSYAD
FVWFLISEED KRNPTSIEYW FRCMDVDGDG VLSMYELEYF YEEQCERMEA MGIEPLPFHD
LLCQMLDLVK PAVDGKITLR DLKRCRMAHI FYDTFFNLEK YLDHEQRDPF AVQKDVENDG
PEPSDWDRFA AEEYETLVAE ESAQAQFQEG FEDYETDEPA SPSEFGNKSN KILSASLPEK
CGKLQSVDEE *
mutated AA sequence MAATYRLVVS TVNHYSSVVI DRRFEQAIHY CTGTCHTFTH GIDCIVVHHS VCADLLHIPV
SQFKDADLNS MFLPHENGLS SAEGDYPQQA FTGIPRVKRG STFQNTYNLK DIAGEAISFA
SGKIKEFSFE KLKNSNHAAY RKGRKVKSDS FNRRSVDLDL LCGHYNNDGN SPSFGLLRSS
SVEEKPLSHR NSLDTNLTSM FLQNFSEEDL VTQILEKHKI DNFSSGTDIK MCLDILLKCS
EDLKKCTDII KQCIKKKSGS SISEGSGNDT ISSSETVYMN VMTRLASYLK KLPFEFMQSG
NNEALDLTEL ISNMPSLQLT PFSPVFGTEQ PPKYEDVVQL SASDSGRFQT IELQNDKPNS
RKMDTVQSIP NNSTNSLYNL EVNDPRTLKA VQVQSQSLTM NPLENVSSDD LMETLYIEEE
SDGKKALDKG QKTENGPSHE LLKVNEHRAE FPEHATHLKK CPTPMQNEIG KIFEKSFVNL
PKEDCKSKVS KFEEGDQRDF TNSSSQEEID KLLMDLESFS QKMETSLREP LAKGKNSNFL
NSHSQLTGQT LVDLEPKSKV SSPIEKVSPS CLTRIIETNG HKIEEEDRAL LLRILESIED
FAQELVECKS SRGSLSQEKE MMQILQETLT TSSQANLSVC RSPVGDKAKD TTSAVLIQQT
PEVIKIQNKP EKKPGTPLPP PATSPSSPRP LSPVPHVNNV VNAPLSINIP RFYFPEGLPD
TCSNHEQTLS RIETAFMDIE EQKADIYEMG KIAKVCGCPL YWKAPMFRAA GGEKTGFVTA
QSFIAMWRKL LNNHHDDASK FICLLAKPNC SSLEQEDFIP LLQDVVDTHP GLTFLKDAPE
FHSRYITTVI QRIFYTVNRS WSGKITSTEI RKSNFLQTLA LLEEEEDINQ ITDYFSYEHF
YVIYCKFWEL DTDHDLYISQ ADLSRYNDQA SSSRIIERIF SGAVTRGKTI QKEGRMSYAD
FVWFLISEED KRNPTSIEYW FRCMDVDGDG VLSMYELEYF YEEQCERMEA MGIEPLPFHD
LLCQMLDLVK PAVDGKITLR DLKRCRMAHI FYDTFFNLEK YLDHEQRDPF AVQKDVENDG
PEPSDWDRFA AEEYETLVAE ESAQAQFQEG FEDYETDEPA SPSEFGNKSN KILSASLPEK
CGKLQSVDEE *
speed 0.53 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.99999980842214 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:135720851G>TN/A show variant in all transcripts   IGV
HGNC symbol PPP2R3A
Ensembl transcript ID ENST00000490467
Genbank transcript ID NM_001190447
UniProt peptide Q06190
alteration type single base exchange
alteration region intron
DNA changes g.36337G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs6779903
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC57982117126969
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5580.067
0.1060.011
(flanking)0.5080.006
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -70) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased36330wt: 0.88 / mu: 0.97wt: AACGATGGGAACGCC
mu: AACGATGGGAACTCC		 CGAT|ggga
distance from splice site 24823
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
670695COMPBIASPro-rich.might get lost (downstream of altered splice site)
758793DOMAINEF-hand 1.might get lost (downstream of altered splice site)
9721007DOMAINEF-hand 2.might get lost (downstream of altered splice site)
985996CA_BINDPotential.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
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
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 320 / 320
chromosome 3
strand 1
last intron/exon boundary 1441
theoretical NMD boundary in CDS 1071
length of CDS 1245
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 36337
chromosomal position
(for ins/del: last normal base / first normal base)		 135720851
original gDNA sequence snippet ATTATAACAACGATGGGAACGCCCCATCCTTTGGTTTACTG
altered gDNA sequence snippet ATTATAACAACGATGGGAACTCCCCATCCTTTGGTTTACTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDIEEQKADI YEMGKIAKVC GCPLYWKAPM FRAAGGEKTG FVTAQSFIAM WRKLLNNHHD
DASKFICLLA KPNCSSLEQE DFIPLLQDVV DTHPGLTFLK DAPEFHSRYI TTVIQRIFYT
VNRSWSGKIT STEIRKSNFL QTLALLEEEE DINQITDYFS YEHFYVIYCK FWELDTDHDL
YISQADLSRY NDQASSSRII ERIFSGAVTR GKTIQKEGRM SYADFVWFLI SEEDKRNPTS
IEYWFRCMDV DGDGVLSMYE LEYFYEEQCE RMEAMGIEPL PFHDLLCQML DLVKPAVDGK
ITLRDLKRCR MAHIFYDTFF NLEKYLDHEQ RDPFAVQKDV ENDGPEPSDW DRFAAEEYET
LVAEESAQAQ FQEGFEDYET DEPASPSEFG NKSNKILSAS LPEKCGKLQS VDEE*
mutated AA sequence N/A
speed 0.41 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

Problems