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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000314742
Querying Taster for transcript #2: ENST00000561308
Querying Taster for transcript #3: ENST00000560133
Querying Taster for transcript #4: ENST00000560941
MT speed 0 s - this script 4.230124 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
LINS1polymorphism_automatic6.25699492218246e-12simple_aaeaffectedI29Vsingle base exchangers11247226show file
LINS1polymorphism_automatic6.25699492218246e-12simple_aaeaffectedI29Vsingle base exchangers11247226show file
LINS1polymorphism_automatic1.40514719970675e-07without_aaeaffectedsingle base exchangers11247226show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999993743 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:101120963T>CN/A show variant in all transcripts   IGV
HGNC symbol LINS1
Ensembl transcript ID ENST00000314742
Genbank transcript ID NM_001040616
UniProt peptide Q8NG48
alteration type single base exchange
alteration region CDS
DNA changes c.85A>G
cDNA.308A>G
g.22473A>G
AA changes I29V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs11247226
databasehomozygous (C/C)heterozygousallele carriers
1000G2579811238
ExAC94891378923278
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1850.004
-0.8720
(flanking)-0.2920.003
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22481wt: 0.69 / mu: 0.76wt: AGCCATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGA
mu: AGCCATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGA		 ttat|CTCA
Acc marginally increased22484wt: 0.8675 / mu: 0.8883 (marginal change - not scored)wt: CATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGATCA
mu: CATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGATCA		 tctc|AACC
Donor gained224670.64mu: GCCATGATTACGTCT CATG|atta
distance from splice site 188
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29GATLENDSHDYIFYLNPAVSDQDC
mutated  all conserved    29GATLENDSHDYVFYLNPAVSDQD
Ptroglodytes  all identical  ENSPTRG00000023792  29GATLENDSHDYIFYLNPAVSDQD
Mmulatta  all identical  ENSMMUG00000016503  29GVTLENDSHDYIFYLNPGVSDQD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000053091  37GTTLEDDVHGYIFYLNPDLSEQD
Ggallus  not conserved  ENSGALG00000007112  27GTLLPKESYYYTSFLNLCVGQ--
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2274 / 2274
position (AA) of stopcodon in wt / mu AA sequence 758 / 758
position of stopcodon in wt / mu cDNA 2497 / 2497
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 224 / 224
chromosome 15
strand -1
last intron/exon boundary 1618
theoretical NMD boundary in CDS 1344
length of CDS 2274
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 308
gDNA position
(for ins/del: last normal base / first normal base)		 22473
chromosomal position
(for ins/del: last normal base / first normal base)		 101120963
original gDNA sequence snippet AAAATGACAGCCATGATTACATCTTTTATCTCAACCCAGCA
altered gDNA sequence snippet AAAATGACAGCCATGATTACGTCTTTTATCTCAACCCAGCA
original cDNA sequence snippet AAAATGACAGCCATGATTACATCTTTTATCTCAACCCAGCA
altered cDNA sequence snippet AAAATGACAGCCATGATTACGTCTTTTATCTCAACCCAGCA
wildtype AA sequence MKVFCEVLEE LYKKVLLGAT LENDSHDYIF YLNPAVSDQD CSTATSLEWA NTCGIQGRHQ
PISVGVAPIA VAPVCLKTNS QMSGSREVML LQLTVIKVMT TRILSVKTEF HAKEQYRDVI
KILLESAKVD SKLICMFQNS DKLLSHMAAQ CLALLLYFQL REKITLSNSW IAFCQKNLSE
YSESNKAIYC LWTLTAIIKE IFKDSCSQKT EILKQFLTHF DTIFEVFYNS LFSQHFENCR
DTSKIVNILM CFLDLLELLI ASRIHLKLHF TCQRILFLKP SCMLEVITWP IQAFVKRKVI
IFLKKCLLCK VGEDLCRGSV PALMPPDHHV AVDMLALANA VLQAVNSGLL KTLSVYEKHS
FFGGDEVQPE CELITSPDHV ILRAASLVIM KSLEIKFQNY SSASEVKVDL QRFMSELLTF
LKPHLQPSLQ LHNPCKWLSR VFIEQDDDML EAAKASLGIY LTLTRGCEAT ESLTQGKEMW
DHHTHENGYN PHCIFLFFLK NIGFDSTVLL DFLISSETCF LEYFVRYLKL LQKDWDNFFT
ICNNFDATES KYDISICGCV PSLVQDQSSN QTIPHRLTAP HSHRDVCARH SWASDAPSEP
LKAVMSKGAH TMCASSLSSP RASQSLVDYD SSDDSDVEST EQCLANSKQT SLHQQATKEI
QDAAGTSRDK KEFSLEPPSR PLVLKEFDTA FSFDCEVAPN DVVSEVGIFY RIVKCFQELQ
DAICRLQKKN LFPYNPTALL KLLKYIEVIS NKTMNTL*
mutated AA sequence MKVFCEVLEE LYKKVLLGAT LENDSHDYVF YLNPAVSDQD CSTATSLEWA NTCGIQGRHQ
PISVGVAPIA VAPVCLKTNS QMSGSREVML LQLTVIKVMT TRILSVKTEF HAKEQYRDVI
KILLESAKVD SKLICMFQNS DKLLSHMAAQ CLALLLYFQL REKITLSNSW IAFCQKNLSE
YSESNKAIYC LWTLTAIIKE IFKDSCSQKT EILKQFLTHF DTIFEVFYNS LFSQHFENCR
DTSKIVNILM CFLDLLELLI ASRIHLKLHF TCQRILFLKP SCMLEVITWP IQAFVKRKVI
IFLKKCLLCK VGEDLCRGSV PALMPPDHHV AVDMLALANA VLQAVNSGLL KTLSVYEKHS
FFGGDEVQPE CELITSPDHV ILRAASLVIM KSLEIKFQNY SSASEVKVDL QRFMSELLTF
LKPHLQPSLQ LHNPCKWLSR VFIEQDDDML EAAKASLGIY LTLTRGCEAT ESLTQGKEMW
DHHTHENGYN PHCIFLFFLK NIGFDSTVLL DFLISSETCF LEYFVRYLKL LQKDWDNFFT
ICNNFDATES KYDISICGCV PSLVQDQSSN QTIPHRLTAP HSHRDVCARH SWASDAPSEP
LKAVMSKGAH TMCASSLSSP RASQSLVDYD SSDDSDVEST EQCLANSKQT SLHQQATKEI
QDAAGTSRDK KEFSLEPPSR PLVLKEFDTA FSFDCEVAPN DVVSEVGIFY RIVKCFQELQ
DAICRLQKKN LFPYNPTALL KLLKYIEVIS NKTMNTL*
speed 0.70 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: 0.999999999993743 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:101120963T>CN/A show variant in all transcripts   IGV
HGNC symbol LINS1
Ensembl transcript ID ENST00000561308
Genbank transcript ID N/A
UniProt peptide Q8NG48
alteration type single base exchange
alteration region CDS
DNA changes c.85A>G
cDNA.239A>G
g.22473A>G
AA changes I29V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs11247226
databasehomozygous (C/C)heterozygousallele carriers
1000G2579811238
ExAC94891378923278
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1850.004
-0.8720
(flanking)-0.2920.003
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22481wt: 0.69 / mu: 0.76wt: AGCCATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGA
mu: AGCCATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGA		 ttat|CTCA
Acc marginally increased22484wt: 0.8675 / mu: 0.8883 (marginal change - not scored)wt: CATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGATCA
mu: CATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGATCA		 tctc|AACC
Donor gained224670.64mu: GCCATGATTACGTCT CATG|atta
distance from splice site 188
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29GATLENDSHDYIFYLNPAVSDQDC
mutated  all conserved    29GATLENDSHDYVFYLNPAVSDQD
Ptroglodytes  all identical  ENSPTRG00000023792  29GATLENDSHDYIFYLNPAVSDQD
Mmulatta  all identical  ENSMMUG00000016503  29GVTLENDSHDYIFYLNPGVSDQD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000053091  37GTTLEDDVHGYIFYLNPDLSEQD
Ggallus  not conserved  ENSGALG00000007112  27GTLLPKESYYYTSFLNLCVGQ--
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1311 / 1311
position (AA) of stopcodon in wt / mu AA sequence 437 / 437
position of stopcodon in wt / mu cDNA 1465 / 1465
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 155 / 155
chromosome 15
strand -1
last intron/exon boundary 786
theoretical NMD boundary in CDS 581
length of CDS 1311
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 239
gDNA position
(for ins/del: last normal base / first normal base)		 22473
chromosomal position
(for ins/del: last normal base / first normal base)		 101120963
original gDNA sequence snippet AAAATGACAGCCATGATTACATCTTTTATCTCAACCCAGCA
altered gDNA sequence snippet AAAATGACAGCCATGATTACGTCTTTTATCTCAACCCAGCA
original cDNA sequence snippet AAAATGACAGCCATGATTACATCTTTTATCTCAACCCAGCA
altered cDNA sequence snippet AAAATGACAGCCATGATTACGTCTTTTATCTCAACCCAGCA
wildtype AA sequence MKVFCEVLEE LYKKVLLGAT LENDSHDYIF YLNPAVSDQD CSTATSLEWA NTCGIQGRHQ
PISVGVAPIA VAPVCLKTNS QMSGSREVML LQLTVIKVMT TRILSVKTEF HAKEQYRDVI
KILLESAKVD SKLICMFQNS DKLLSHMAAQ CLALLLYFQL REKITLSNSW IAFCQKNLSE
YSESNKAIYC LWTLTAIIKE IFKDSCSQKT EILKQFLTHF DTIFEVFYNS LFSQHFENCR
DTSKIVNILM CFLDLLELLI ASRIHLKLHF TCQRILFLKP SCMLEVITWP IQAFVKRKVI
IFLKKCLLCK VGEDLCRGSV PALMPPDHHV AVDMLALANA VLQAVNSGLL KTLSVYEKHS
FFGGDEVQPE CELITSPDHV ILRAASLVIM KSLEIKFQNY SSASEVKGNS PNSFCMQCVI
IYLSTVIHNY QISGLV*
mutated AA sequence MKVFCEVLEE LYKKVLLGAT LENDSHDYVF YLNPAVSDQD CSTATSLEWA NTCGIQGRHQ
PISVGVAPIA VAPVCLKTNS QMSGSREVML LQLTVIKVMT TRILSVKTEF HAKEQYRDVI
KILLESAKVD SKLICMFQNS DKLLSHMAAQ CLALLLYFQL REKITLSNSW IAFCQKNLSE
YSESNKAIYC LWTLTAIIKE IFKDSCSQKT EILKQFLTHF DTIFEVFYNS LFSQHFENCR
DTSKIVNILM CFLDLLELLI ASRIHLKLHF TCQRILFLKP SCMLEVITWP IQAFVKRKVI
IFLKKCLLCK VGEDLCRGSV PALMPPDHHV AVDMLALANA VLQAVNSGLL KTLSVYEKHS
FFGGDEVQPE CELITSPDHV ILRAASLVIM KSLEIKFQNY SSASEVKGNS PNSFCMQCVI
IYLSTVIHNY QISGLV*
speed 0.75 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: 0.99999985948528 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:101120963T>CN/A show variant in all transcripts   IGV
HGNC symbol LINS1
Ensembl transcript ID ENST00000560133
Genbank transcript ID N/A
UniProt peptide Q8NG48
alteration type single base exchange
alteration region intron
DNA changes g.22473A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs11247226
databasehomozygous (C/C)heterozygousallele carriers
1000G2579811238
ExAC94891378923278
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1850.004
-0.8720
(flanking)-0.2920.003
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22481wt: 0.69 / mu: 0.76wt: AGCCATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGA
mu: AGCCATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGA		 ttat|CTCA
Acc marginally increased22484wt: 0.8675 / mu: 0.8883 (marginal change - not scored)wt: CATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGATCA
mu: CATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGATCA		 tctc|AACC
Donor gained224670.64mu: GCCATGATTACGTCT CATG|atta
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features no protein features affected
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 158 / 158
chromosome 15
strand -1
last intron/exon boundary 432
theoretical NMD boundary in CDS 224
length of CDS 954
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)		 22473
chromosomal position
(for ins/del: last normal base / first normal base)		 101120963
original gDNA sequence snippet AAAATGACAGCCATGATTACATCTTTTATCTCAACCCAGCA
altered gDNA sequence snippet AAAATGACAGCCATGATTACGTCTTTTATCTCAACCCAGCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MKVFCEVLEE LYKKICMFQN SDKLLSHMAA QCLALLLYFQ LREKITLSNS WIAFCQKNLS
EYSESNKAIY CLWTLTAIIK EIFKDSCSQK TEILKQFLTH FDTIFEVFYN SLFSQHFENC
RDTSKIVNIL MCFLDLLELL IASRIHLKLH FTCQRILFLK PSCMLEVITW PIQAFVKRKV
IIFLKKCLLC KVGEDLCRGS VPALMPPDHH VAVDMLALAN AVLQAVNSGL LKTLSVYEKH
SFFGGDEVQP ECELITSPDH VILRAASLVI MKSLEIKFQN YSSASEVKGN SPNSFCMQCV
IIYLSTVIHN YQISGLV*
mutated AA sequence N/A
speed 0.54 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

annotation problem

back to results table