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: ENST00000355683
Querying Taster for transcript #2: ENST00000357479
MT speed 0 s - this script 2.334223 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
STRN3polymorphism_automatic0.999984212677314simple_aaeaffectedN387Ssingle base exchangers2273171show file
STRN3polymorphism_automatic0.999999997828379simple_aaeaffectedN471Ssingle base exchangers2273171show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1.57873226864233e-05 (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) chr14:31381351T>CN/A show variant in all transcripts   IGV
HGNC symbol STRN3
Ensembl transcript ID ENST00000355683
Genbank transcript ID NM_014574
UniProt peptide Q13033
alteration type single base exchange
alteration region CDS
DNA changes c.1160A>G
cDNA.1376A>G
g.114257A>G
AA changes N387S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 387
frameshift no
known variant Reference ID: rs2273171
databasehomozygous (C/C)heterozygousallele carriers
1000G39111661557
ExAC11818913120949
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2330.906
3.4661
(flanking)5.0711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased114248wt: 0.9975 / mu: 0.9976 (marginal change - not scored)wt: TCGAAAGACATGGAA
mu: TCGAAAGACATGGAG		 GAAA|gaca
Donor marginally increased114258wt: 0.9856 / mu: 0.9873 (marginal change - not scored)wt: TGGAATCCCAAGTAT
mu: TGGAGTCCCAAGTAT		 GAAT|ccca
Donor increased114251wt: 0.21 / mu: 0.97wt: AAAGACATGGAATCC
mu: AAAGACATGGAGTCC		 AGAC|atgg
distance from splice site 38
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      387PANKDAFRKTWNPKYTLRSHFDGV
mutated  all conserved    387PANKDAFRKTWSPKYTLRSHFDG
Ptroglodytes  not conserved  ENSPTRG00000006238  303GIINQSRSASTRMTDHEG
Mmulatta  all identical  ENSMMUG00000011515  231PANKDAFRKTWNPKYTLRSHFDG
Fcatus  all identical  ENSFCAG00000013708  377PANKDAFRKTWNPKY
Mmusculus  all identical  ENSMUSG00000020954  470PANKDAFRKTWNPKYTLRSHFD
Ggallus  all conserved  ENSGALG00000009930  397GDDEIPHIPSGIINQSRSPSS
Trubripes  all identical  ENSTRUG00000011310  383PSCKDSSFRKTWNPKYTLRSHFDG
Drerio  all identical  ENSDARG00000001729  392PANKDAFRKTWNPKYTLRSHFDG
Dmelanogaster  all identical  FBgn0044323  422SAGGAGYRKTWNAKYTLRSHFDG
Celegans  all identical  K07C5.8  352P---NAQQVKWNIKVTLRSHLDS
Xtropicalis  not conserved  ENSXETG00000014156  382GEEDLSHIPAEILSPARTPSSRITDH-EG
protein features
start (aa)end (aa)featuredetails 
478517REPEATWD 1.might get lost (downstream of altered splice site)
531570REPEATWD 2.might get lost (downstream of altered splice site)
584623REPEATWD 3.might get lost (downstream of altered splice site)
679718REPEATWD 4.might get lost (downstream of altered splice site)
721760REPEATWD 5.might get lost (downstream of altered splice site)
767796REPEATWD 6.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2142 / 2142
position (AA) of stopcodon in wt / mu AA sequence 714 / 714
position of stopcodon in wt / mu cDNA 2358 / 2358
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 217 / 217
chromosome 14
strand -1
last intron/exon boundary 2189
theoretical NMD boundary in CDS 1922
length of CDS 2142
coding sequence (CDS) position 1160
cDNA position
(for ins/del: last normal base / first normal base)		 1376
gDNA position
(for ins/del: last normal base / first normal base)		 114257
chromosomal position
(for ins/del: last normal base / first normal base)		 31381351
original gDNA sequence snippet TGCCTTTCGAAAGACATGGAATCCCAAGTATACACTACGTA
altered gDNA sequence snippet TGCCTTTCGAAAGACATGGAGTCCCAAGTATACACTACGTA
original cDNA sequence snippet TGCCTTTCGAAAGACATGGAATCCCAAGTATACACTACGTA
altered cDNA sequence snippet TGCCTTTCGAAAGACATGGAGTCCCAAGTATACACTACGTA
wildtype AA sequence MDELAGGGGG GPGMAAPPRQ QQGPGGNLGL SPGGNGAAGG GGPPASEGAG PAAGPELSRP
QQYTIPGILH YIQHEWARFE MERAHWEVER AELQARIAFL QGERKGQENL KKDLVRRIKM
LEYALKQERA KYHKLKYGTE LNQGDLKMPT FESEETKDTE APTAPQNSQL TWKQGRQLLR
QYLQEVGYTD TILDVRSQRV RSLLGLSNSE PNGSVETKNL EQILNGGESP KQKGQEIKRS
SGDVLETFNF LENADDSDED EENDMIEGIP EGKDKHRMNK HKIGNEGLAA DLTDDPDTEE
ALKEFDFLVT AEDGEGAGEA RSSGDGTEWA EPITFPSGGG KSFIMGSDDV LLSVLGLGDL
ADLTVTNDAD YSYDLPANKD AFRKTWNPKY TLRSHFDGVR ALAFHPVEPV LVTASEDHTL
KLWNLQKTVP AKKSASLDVE PIYTFRAHIG PVLSLAISSN GEQCFSGGID ATIQWWNMPS
PSVDPYDTYE PNVLAGTLVG HTDAVWGLAY SGIKNQLLSC SADGTVRLWN PQEKLPCICT
YNGDKKHGIP TSVDFIGCDP AHMVTSFNTG SAVIYDLETS QSLVILSSQV DSGLQSNNHI
NRVVSHPTLP VTITAHEDRH IKFFDNKTGK MIHSMVAHLD AVTSLAVDPN GIYLMSGSHD
CSIRLWNLDS KTCVQEITAH RKKLDESIYD VAFHSSKAYI ASAGADALAK VFV*
mutated AA sequence MDELAGGGGG GPGMAAPPRQ QQGPGGNLGL SPGGNGAAGG GGPPASEGAG PAAGPELSRP
QQYTIPGILH YIQHEWARFE MERAHWEVER AELQARIAFL QGERKGQENL KKDLVRRIKM
LEYALKQERA KYHKLKYGTE LNQGDLKMPT FESEETKDTE APTAPQNSQL TWKQGRQLLR
QYLQEVGYTD TILDVRSQRV RSLLGLSNSE PNGSVETKNL EQILNGGESP KQKGQEIKRS
SGDVLETFNF LENADDSDED EENDMIEGIP EGKDKHRMNK HKIGNEGLAA DLTDDPDTEE
ALKEFDFLVT AEDGEGAGEA RSSGDGTEWA EPITFPSGGG KSFIMGSDDV LLSVLGLGDL
ADLTVTNDAD YSYDLPANKD AFRKTWSPKY TLRSHFDGVR ALAFHPVEPV LVTASEDHTL
KLWNLQKTVP AKKSASLDVE PIYTFRAHIG PVLSLAISSN GEQCFSGGID ATIQWWNMPS
PSVDPYDTYE PNVLAGTLVG HTDAVWGLAY SGIKNQLLSC SADGTVRLWN PQEKLPCICT
YNGDKKHGIP TSVDFIGCDP AHMVTSFNTG SAVIYDLETS QSLVILSSQV DSGLQSNNHI
NRVVSHPTLP VTITAHEDRH IKFFDNKTGK MIHSMVAHLD AVTSLAVDPN GIYLMSGSHD
CSIRLWNLDS KTCVQEITAH RKKLDESIYD VAFHSSKAYI ASAGADALAK VFV*
speed 0.29 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: 2.1716206930176e-09 (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) chr14:31381351T>CN/A show variant in all transcripts   IGV
HGNC symbol STRN3
Ensembl transcript ID ENST00000357479
Genbank transcript ID NM_001083893
UniProt peptide Q13033
alteration type single base exchange
alteration region CDS
DNA changes c.1412A>G
cDNA.1609A>G
g.114257A>G
AA changes N471S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 471
frameshift no
known variant Reference ID: rs2273171
databasehomozygous (C/C)heterozygousallele carriers
1000G39111661557
ExAC11818913120949
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2330.906
3.4661
(flanking)5.0711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased114248wt: 0.9975 / mu: 0.9976 (marginal change - not scored)wt: TCGAAAGACATGGAA
mu: TCGAAAGACATGGAG		 GAAA|gaca
Donor marginally increased114258wt: 0.9856 / mu: 0.9873 (marginal change - not scored)wt: TGGAATCCCAAGTAT
mu: TGGAGTCCCAAGTAT		 GAAT|ccca
Donor increased114251wt: 0.21 / mu: 0.97wt: AAAGACATGGAATCC
mu: AAAGACATGGAGTCC		 AGAC|atgg
distance from splice site 38
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      471PANKDAFRKTWNPKYTLRSHFDGV
mutated  all conserved    471PANKDAFRKTWSPKYTLRSHF
Ptroglodytes  all identical  ENSPTRG00000006238  377PANKDAFRKTWNPKYTLRSHFDG
Mmulatta  all identical  ENSMMUG00000011515  231PANKDAFRKTWNPKYTLRSHF
Fcatus  all identical  ENSFCAG00000013708  377PANKDAFRKTWNPKY
Mmusculus  all identical  ENSMUSG00000020954  470PANKDAFRKTWNPKYTLRSHF
Ggallus  all identical  ENSGALG00000009930  485FRKTWNPKYTLRSHFDG
Trubripes  all identical  ENSTRUG00000011310  385RKTWNPKYTLRSHFDG
Drerio  all identical  ENSDARG00000001729  392PANKDAFRKTWNPKYTLRSHF
Dmelanogaster  all identical  FBgn0044323  417SAGGAGYRKTWNAKYTLRSHFDG
Celegans  all identical  K07C5.8  353P---NAQQVKWNIKVTLRSHLDS
Xtropicalis  all identical  ENSXETG00000014156  461PSNKDAFRKTWNPKYTLRSHFDG
protein features
start (aa)end (aa)featuredetails 
478517REPEATWD 1.might get lost (downstream of altered splice site)
531570REPEATWD 2.might get lost (downstream of altered splice site)
584623REPEATWD 3.might get lost (downstream of altered splice site)
679718REPEATWD 4.might get lost (downstream of altered splice site)
721760REPEATWD 5.might get lost (downstream of altered splice site)
767796REPEATWD 6.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2394 / 2394
position (AA) of stopcodon in wt / mu AA sequence 798 / 798
position of stopcodon in wt / mu cDNA 2591 / 2591
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 198 / 198
chromosome 14
strand -1
last intron/exon boundary 2422
theoretical NMD boundary in CDS 2174
length of CDS 2394
coding sequence (CDS) position 1412
cDNA position
(for ins/del: last normal base / first normal base)		 1609
gDNA position
(for ins/del: last normal base / first normal base)		 114257
chromosomal position
(for ins/del: last normal base / first normal base)		 31381351
original gDNA sequence snippet TGCCTTTCGAAAGACATGGAATCCCAAGTATACACTACGTA
altered gDNA sequence snippet TGCCTTTCGAAAGACATGGAGTCCCAAGTATACACTACGTA
original cDNA sequence snippet TGCCTTTCGAAAGACATGGAATCCCAAGTATACACTACGTA
altered cDNA sequence snippet TGCCTTTCGAAAGACATGGAGTCCCAAGTATACACTACGTA
wildtype AA sequence MDELAGGGGG GPGMAAPPRQ QQGPGGNLGL SPGGNGAAGG GGPPASEGAG PAAGPELSRP
QQYTIPGILH YIQHEWARFE MERAHWEVER AELQARIAFL QGERKGQENL KKDLVRRIKM
LEYALKQERA KYHKLKYGTE LNQGDLKMPT FESEETKDTE APTAPQNSQL TWKQGRQLLR
QYLQEVGYTD TILDVRSQRV RSLLGLSNSE PNGSVETKNL EQILNGGESP KQKGQEIKRS
SGDVLETFNF LENADDSDED EENDMIEGIP EGKDKHRMNK HKIGNEGLAA DLTDDPDTEE
ALKEFDFLVT AEDGEGAGEA RSSGDGTEWD KDDLSPTAEV WDVDQGLISK LKEQYKKERK
GKKGVKRANR TKLYDMIADL GDDELPHIPS GIINQSRSAS TRMTDHEGAR AEEAEPITFP
SGGGKSFIMG SDDVLLSVLG LGDLADLTVT NDADYSYDLP ANKDAFRKTW NPKYTLRSHF
DGVRALAFHP VEPVLVTASE DHTLKLWNLQ KTVPAKKSAS LDVEPIYTFR AHIGPVLSLA
ISSNGEQCFS GGIDATIQWW NMPSPSVDPY DTYEPNVLAG TLVGHTDAVW GLAYSGIKNQ
LLSCSADGTV RLWNPQEKLP CICTYNGDKK HGIPTSVDFI GCDPAHMVTS FNTGSAVIYD
LETSQSLVIL SSQVDSGLQS NNHINRVVSH PTLPVTITAH EDRHIKFFDN KTGKMIHSMV
AHLDAVTSLA VDPNGIYLMS GSHDCSIRLW NLDSKTCVQE ITAHRKKLDE SIYDVAFHSS
KAYIASAGAD ALAKVFV*
mutated AA sequence MDELAGGGGG GPGMAAPPRQ QQGPGGNLGL SPGGNGAAGG GGPPASEGAG PAAGPELSRP
QQYTIPGILH YIQHEWARFE MERAHWEVER AELQARIAFL QGERKGQENL KKDLVRRIKM
LEYALKQERA KYHKLKYGTE LNQGDLKMPT FESEETKDTE APTAPQNSQL TWKQGRQLLR
QYLQEVGYTD TILDVRSQRV RSLLGLSNSE PNGSVETKNL EQILNGGESP KQKGQEIKRS
SGDVLETFNF LENADDSDED EENDMIEGIP EGKDKHRMNK HKIGNEGLAA DLTDDPDTEE
ALKEFDFLVT AEDGEGAGEA RSSGDGTEWD KDDLSPTAEV WDVDQGLISK LKEQYKKERK
GKKGVKRANR TKLYDMIADL GDDELPHIPS GIINQSRSAS TRMTDHEGAR AEEAEPITFP
SGGGKSFIMG SDDVLLSVLG LGDLADLTVT NDADYSYDLP ANKDAFRKTW SPKYTLRSHF
DGVRALAFHP VEPVLVTASE DHTLKLWNLQ KTVPAKKSAS LDVEPIYTFR AHIGPVLSLA
ISSNGEQCFS GGIDATIQWW NMPSPSVDPY DTYEPNVLAG TLVGHTDAVW GLAYSGIKNQ
LLSCSADGTV RLWNPQEKLP CICTYNGDKK HGIPTSVDFI GCDPAHMVTS FNTGSAVIYD
LETSQSLVIL SSQVDSGLQS NNHINRVVSH PTLPVTITAH EDRHIKFFDN KTGKMIHSMV
AHLDAVTSLA VDPNGIYLMS GSHDCSIRLW NLDSKTCVQE ITAHRKKLDE SIYDVAFHSS
KAYIASAGAD ALAKVFV*
speed 0.11 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