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: ENST00000367501
Querying Taster for transcript #2: ENST00000367500
MT speed 0 s - this script 4.225636 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SWT1polymorphism_automatic7.76619879516716e-11simple_aaeaffectedI148Vsingle base exchangers10489579show file
SWT1polymorphism_automatic7.76619879516716e-11simple_aaeaffectedI148Vsingle base exchangers10489579show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999922338 (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) chr1:185143721A>GN/A show variant in all transcripts   IGV
HGNC symbol SWT1
Ensembl transcript ID ENST00000367501
Genbank transcript ID N/A
UniProt peptide Q5T5J6
alteration type single base exchange
alteration region CDS
DNA changes c.442A>G
cDNA.536A>G
g.17510A>G
AA changes I148V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 148
frameshift no
known variant Reference ID: rs10489579
databasehomozygous (G/G)heterozygousallele carriers
1000G55010771627
ExAC90751461723692
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3750
-0.0130
(flanking)0.8890.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained175090.78mu: CATGGAGTTAAAAGC TGGA|gtta
Donor gained175040.88mu: TTGACCATGGAGTTA GACC|atgg
distance from splice site 218
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      148LTNAGSKLDHGIKSLSSPKIASDV
mutated  all conserved    148LTNAGSKLDHGVKSLSSPKIASD
Ptroglodytes  all identical  ENSPTRG00000001777  148LTNAGSKLDHGIKSLSSPKIASD
Mmulatta  all identical  ENSMMUG00000013882  148LTNARSKLDHGIKSLSSPKIASD
Fcatus  all identical  ENSFCAG00000011286  147LTNVRSKADHGIKNFCGPKIAKD
Mmusculus  all identical  ENSMUSG00000052748  161LTNIGSKLNYEIKNHSRIKITKD
Ggallus  no alignment  ENSGALG00000005117  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000094010  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
388515DOMAINPINc.might get lost (downstream of altered splice site)
430430CONFLICTL -> V (in Ref. 1; AAG60612).might get lost (downstream of altered splice site)
571571CONFLICTN -> S (in Ref. 3; AAH30781).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2703 / 2703
position (AA) of stopcodon in wt / mu AA sequence 901 / 901
position of stopcodon in wt / mu cDNA 2797 / 2797
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 95 / 95
chromosome 1
strand 1
last intron/exon boundary 2668
theoretical NMD boundary in CDS 2523
length of CDS 2703
coding sequence (CDS) position 442
cDNA position
(for ins/del: last normal base / first normal base)		 536
gDNA position
(for ins/del: last normal base / first normal base)		 17510
chromosomal position
(for ins/del: last normal base / first normal base)		 185143721
original gDNA sequence snippet GGAGCAAGCTTGACCATGGAATTAAAAGCCTTAGTAGTCCT
altered gDNA sequence snippet GGAGCAAGCTTGACCATGGAGTTAAAAGCCTTAGTAGTCCT
original cDNA sequence snippet GGAGCAAGCTTGACCATGGAATTAAAAGCCTTAGTAGTCCT
altered cDNA sequence snippet GGAGCAAGCTTGACCATGGAGTTAAAAGCCTTAGTAGTCCT
wildtype AA sequence MSSKESCGKK ETSQRKDTTT SSPNFGEKDK KERKTPASST SSSSIRSVSS EKRKLKSDHT
DVLYYNIKRR QGLKRLSVEI DTLRRRPKIG SSSQRPIKLK EASYSNDNQI ILQSPSSNGT
KKDIHKCVDF KPKDIKLTNA GSKLDHGIKS LSSPKIASDV KPKAEGQASE NKWSHLLVQR
EKMKELKKGR NSKFRDNSEK CVLEKWKRNQ FSQDYNSNKI IKEPLGSRRQ KISFKIPIKS
RDTLQKLVEE NVFNIDSNNS KTKQEEREYL ESSQVSLNVT RQKTEHLLSD FTYKRTVHEW
KRKHHYDHQE SNDSHSRENL TQSFEAPCCS VSSESIQDAD QEMQIVEELH AARVGKSVDL
PGELMSMEID LEDDVHSSSA NNTSDRKLLI VIDTNILMNH LKFVRILKTT EVPGFDKLVL
IIPWVVMQEL DRMKEGKLLK RAQHKAIPAV HFINDSLKNQ DRKLWGQSIQ LASQKHYGLS
DENNDDRVLK CCLQHQELFP CSFVILCTDD RNLRNKGLIS GVKSLSKEEL SAELLHLSLN
TDVCHQPCIP KQQLKAETTP LKESYKEEST NSGLSILLES IVSDLEKSLG TGLSSILETE
MKIAFGNLWM EILYLKPPWT LLHLLQCFKK HWLAVFGLVM EKNLLLTIES LYKNLRKANK
AVDFTTVKFL LQDSRSLLHA FSTRSNYDGI LPQTFAQVNN LLQTFAEVKT KLKPNSSENT
VTKKQEGTSL KNSHNQEITV FSSSHLPQPS RHQEIWSILE SVWITIYQNS TDVFQRLGSN
SALTTSNIAS FEEAFICLQK LMAAVRDILE GIQRILAPNS NYQDVETLYN FLIKYEVNKN
VKFTAQEIYD CVSQTEYREK LTIGCRQLVE MEYTMQQCNA SVYMEAKNRG WCEDMLNYRI
*
mutated AA sequence MSSKESCGKK ETSQRKDTTT SSPNFGEKDK KERKTPASST SSSSIRSVSS EKRKLKSDHT
DVLYYNIKRR QGLKRLSVEI DTLRRRPKIG SSSQRPIKLK EASYSNDNQI ILQSPSSNGT
KKDIHKCVDF KPKDIKLTNA GSKLDHGVKS LSSPKIASDV KPKAEGQASE NKWSHLLVQR
EKMKELKKGR NSKFRDNSEK CVLEKWKRNQ FSQDYNSNKI IKEPLGSRRQ KISFKIPIKS
RDTLQKLVEE NVFNIDSNNS KTKQEEREYL ESSQVSLNVT RQKTEHLLSD FTYKRTVHEW
KRKHHYDHQE SNDSHSRENL TQSFEAPCCS VSSESIQDAD QEMQIVEELH AARVGKSVDL
PGELMSMEID LEDDVHSSSA NNTSDRKLLI VIDTNILMNH LKFVRILKTT EVPGFDKLVL
IIPWVVMQEL DRMKEGKLLK RAQHKAIPAV HFINDSLKNQ DRKLWGQSIQ LASQKHYGLS
DENNDDRVLK CCLQHQELFP CSFVILCTDD RNLRNKGLIS GVKSLSKEEL SAELLHLSLN
TDVCHQPCIP KQQLKAETTP LKESYKEEST NSGLSILLES IVSDLEKSLG TGLSSILETE
MKIAFGNLWM EILYLKPPWT LLHLLQCFKK HWLAVFGLVM EKNLLLTIES LYKNLRKANK
AVDFTTVKFL LQDSRSLLHA FSTRSNYDGI LPQTFAQVNN LLQTFAEVKT KLKPNSSENT
VTKKQEGTSL KNSHNQEITV FSSSHLPQPS RHQEIWSILE SVWITIYQNS TDVFQRLGSN
SALTTSNIAS FEEAFICLQK LMAAVRDILE GIQRILAPNS NYQDVETLYN FLIKYEVNKN
VKFTAQEIYD CVSQTEYREK LTIGCRQLVE MEYTMQQCNA SVYMEAKNRG WCEDMLNYRI
*
speed 1.13 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: simple_aae, prob: 0.999999999922338 (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) chr1:185143721A>GN/A show variant in all transcripts   IGV
HGNC symbol SWT1
Ensembl transcript ID ENST00000367500
Genbank transcript ID NM_001105518
UniProt peptide Q5T5J6
alteration type single base exchange
alteration region CDS
DNA changes c.442A>G
cDNA.607A>G
g.17510A>G
AA changes I148V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 148
frameshift no
known variant Reference ID: rs10489579
databasehomozygous (G/G)heterozygousallele carriers
1000G55010771627
ExAC90751461723692
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3750
-0.0130
(flanking)0.8890.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained175090.78mu: CATGGAGTTAAAAGC TGGA|gtta
Donor gained175040.88mu: TTGACCATGGAGTTA GACC|atgg
distance from splice site 218
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      148LTNAGSKLDHGIKSLSSPKIASDV
mutated  all conserved    148LTNAGSKLDHGVKSLSSPKIASD
Ptroglodytes  all identical  ENSPTRG00000001777  148LTNAGSKLDHGIKSLSSPKIASD
Mmulatta  all identical  ENSMMUG00000013882  148LTNARSKLDHGIKSLSSPKIASD
Fcatus  all identical  ENSFCAG00000011286  147LTNVRSKADHGIKNFCGPKIAKD
Mmusculus  all identical  ENSMUSG00000052748  161LTNIGSKLNYEIKNHSRIKITKD
Ggallus  no alignment  ENSGALG00000005117  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000094010  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
388515DOMAINPINc.might get lost (downstream of altered splice site)
430430CONFLICTL -> V (in Ref. 1; AAG60612).might get lost (downstream of altered splice site)
571571CONFLICTN -> S (in Ref. 3; AAH30781).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2703 / 2703
position (AA) of stopcodon in wt / mu AA sequence 901 / 901
position of stopcodon in wt / mu cDNA 2868 / 2868
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 166 / 166
chromosome 1
strand 1
last intron/exon boundary 2739
theoretical NMD boundary in CDS 2523
length of CDS 2703
coding sequence (CDS) position 442
cDNA position
(for ins/del: last normal base / first normal base)		 607
gDNA position
(for ins/del: last normal base / first normal base)		 17510
chromosomal position
(for ins/del: last normal base / first normal base)		 185143721
original gDNA sequence snippet GGAGCAAGCTTGACCATGGAATTAAAAGCCTTAGTAGTCCT
altered gDNA sequence snippet GGAGCAAGCTTGACCATGGAGTTAAAAGCCTTAGTAGTCCT
original cDNA sequence snippet GGAGCAAGCTTGACCATGGAATTAAAAGCCTTAGTAGTCCT
altered cDNA sequence snippet GGAGCAAGCTTGACCATGGAGTTAAAAGCCTTAGTAGTCCT
wildtype AA sequence MSSKESCGKK ETSQRKDTTT SSPNFGEKDK KERKTPASST SSSSIRSVSS EKRKLKSDHT
DVLYYNIKRR QGLKRLSVEI DTLRRRPKIG SSSQRPIKLK EASYSNDNQI ILQSPSSNGT
KKDIHKCVDF KPKDIKLTNA GSKLDHGIKS LSSPKIASDV KPKAEGQASE NKWSHLLVQR
EKMKELKKGR NSKFRDNSEK CVLEKWKRNQ FSQDYNSNKI IKEPLGSRRQ KISFKIPIKS
RDTLQKLVEE NVFNIDSNNS KTKQEEREYL ESSQVSLNVT RQKTEHLLSD FTYKRTVHEW
KRKHHYDHQE SNDSHSRENL TQSFEAPCCS VSSESIQDAD QEMQIVEELH AARVGKSVDL
PGELMSMEID LEDDVHSSSA NNTSDRKLLI VIDTNILMNH LKFVRILKTT EVPGFDKLVL
IIPWVVMQEL DRMKEGKLLK RAQHKAIPAV HFINDSLKNQ DRKLWGQSIQ LASQKHYGLS
DENNDDRVLK CCLQHQELFP CSFVILCTDD RNLRNKGLIS GVKSLSKEEL SAELLHLSLN
TDVCHQPCIP KQQLKAETTP LKESYKEEST NSGLSILLES IVSDLEKSLG TGLSSILETE
MKIAFGNLWM EILYLKPPWT LLHLLQCFKK HWLAVFGLVM EKNLLLTIES LYKNLRKANK
AVDFTTVKFL LQDSRSLLHA FSTRSNYDGI LPQTFAQVNN LLQTFAEVKT KLKPNSSENT
VTKKQEGTSL KNSHNQEITV FSSSHLPQPS RHQEIWSILE SVWITIYQNS TDVFQRLGSN
SALTTSNIAS FEEAFICLQK LMAAVRDILE GIQRILAPNS NYQDVETLYN FLIKYEVNKN
VKFTAQEIYD CVSQTEYREK LTIGCRQLVE MEYTMQQCNA SVYMEAKNRG WCEDMLNYRI
*
mutated AA sequence MSSKESCGKK ETSQRKDTTT SSPNFGEKDK KERKTPASST SSSSIRSVSS EKRKLKSDHT
DVLYYNIKRR QGLKRLSVEI DTLRRRPKIG SSSQRPIKLK EASYSNDNQI ILQSPSSNGT
KKDIHKCVDF KPKDIKLTNA GSKLDHGVKS LSSPKIASDV KPKAEGQASE NKWSHLLVQR
EKMKELKKGR NSKFRDNSEK CVLEKWKRNQ FSQDYNSNKI IKEPLGSRRQ KISFKIPIKS
RDTLQKLVEE NVFNIDSNNS KTKQEEREYL ESSQVSLNVT RQKTEHLLSD FTYKRTVHEW
KRKHHYDHQE SNDSHSRENL TQSFEAPCCS VSSESIQDAD QEMQIVEELH AARVGKSVDL
PGELMSMEID LEDDVHSSSA NNTSDRKLLI VIDTNILMNH LKFVRILKTT EVPGFDKLVL
IIPWVVMQEL DRMKEGKLLK RAQHKAIPAV HFINDSLKNQ DRKLWGQSIQ LASQKHYGLS
DENNDDRVLK CCLQHQELFP CSFVILCTDD RNLRNKGLIS GVKSLSKEEL SAELLHLSLN
TDVCHQPCIP KQQLKAETTP LKESYKEEST NSGLSILLES IVSDLEKSLG TGLSSILETE
MKIAFGNLWM EILYLKPPWT LLHLLQCFKK HWLAVFGLVM EKNLLLTIES LYKNLRKANK
AVDFTTVKFL LQDSRSLLHA FSTRSNYDGI LPQTFAQVNN LLQTFAEVKT KLKPNSSENT
VTKKQEGTSL KNSHNQEITV FSSSHLPQPS RHQEIWSILE SVWITIYQNS TDVFQRLGSN
SALTTSNIAS FEEAFICLQK LMAAVRDILE GIQRILAPNS NYQDVETLYN FLIKYEVNKN
VKFTAQEIYD CVSQTEYREK LTIGCRQLVE MEYTMQQCNA SVYMEAKNRG WCEDMLNYRI
*
speed 0.85 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