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: ENST00000341809
Querying Taster for transcript #2: ENST00000537195
MT speed 0 s - this script 4.162262 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRT77polymorphism_automatic2.15025997007956e-10simple_aaeaffectedD336Nsingle base exchangers10783528show file
KRT77polymorphism_automatic2.15025997007956e-10simple_aaeaffectedD103Nsingle base exchangers10783528show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999784974 (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) chr12:53088484C>TN/A show variant in all transcripts   IGV
HGNC symbol KRT77
Ensembl transcript ID ENST00000341809
Genbank transcript ID NM_175078
UniProt peptide Q7Z794
alteration type single base exchange
alteration region CDS
DNA changes c.1006G>A
cDNA.1035G>A
g.8764G>A
AA changes D336N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 336
frameshift no
known variant Reference ID: rs10783528
databasehomozygous (T/T)heterozygousallele carriers
1000G3049861290
ExAC74841779925283
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3250.004
1.1040.017
(flanking)-0.2590.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased8764wt: 0.46 / mu: 0.93wt: TCATCGATGCAGTGC
mu: TCATCAATGCAGTGC		 ATCG|atgc
Donor increased8766wt: 0.31 / mu: 0.62wt: ATCGATGCAGTGCGG
mu: ATCAATGCAGTGCGG		 CGAT|gcag
Donor increased8755wt: 0.50 / mu: 0.63wt: TGGACAGCATCATCG
mu: TGGACAGCATCATCA		 GACA|gcat
Donor marginally increased8761wt: 0.8883 / mu: 0.9042 (marginal change - not scored)wt: GCATCATCGATGCAG
mu: GCATCATCAATGCAG		 ATCA|tcga
Donor increased8769wt: 0.54 / mu: 0.80wt: GATGCAGTGCGGACC
mu: AATGCAGTGCGGACC		 TGCA|gtgc
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      336NNRSLDLDSIIDAVRTQYELIAQR
mutated  all conserved    336NNRSLDLDSIINAVRTQYELIAQ
Ptroglodytes  all identical  ENSPTRG00000004988  341NNRSLDLDSIIDAVRTQYELIAQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000067594  339NNRSLDLDSIIDAVRAQYEIIAQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
164474REGIONRod.lost
312335REGIONLinker 12.might get lost (downstream of altered splice site)
336336CONFLICTD -> N (in Ref. 1; CAD91892).lost
336474REGIONCoil 2.lost
418418SITEStutter.might get lost (downstream of altered splice site)
475578REGIONTail.might get lost (downstream of altered splice site)
533533CONFLICTR -> G (in Ref. 1; CAD91892).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1737 / 1737
position (AA) of stopcodon in wt / mu AA sequence 579 / 579
position of stopcodon in wt / mu cDNA 1766 / 1766
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 30 / 30
chromosome 12
strand -1
last intron/exon boundary 1492
theoretical NMD boundary in CDS 1412
length of CDS 1737
coding sequence (CDS) position 1006
cDNA position
(for ins/del: last normal base / first normal base)		 1035
gDNA position
(for ins/del: last normal base / first normal base)		 8764
chromosomal position
(for ins/del: last normal base / first normal base)		 53088484
original gDNA sequence snippet TGGACCTGGACAGCATCATCGATGCAGTGCGGACCCAGTAT
altered gDNA sequence snippet TGGACCTGGACAGCATCATCAATGCAGTGCGGACCCAGTAT
original cDNA sequence snippet TGGACCTGGACAGCATCATCGATGCAGTGCGGACCCAGTAT
altered cDNA sequence snippet TGGACCTGGACAGCATCATCAATGCAGTGCGGACCCAGTAT
wildtype AA sequence MSHQFSSQSA FSSMSRRVYS TSSSAGSGGG SPAVGSVCYA RGRCGGGGYG IHGRGFGSRS
LYNLGGSRSI SINLMGRSTS GFCQGGGVGG FGGGRGFGVG STGAGGFGGG GFGGAGFGTS
NFGLGGFGPY CPPGGIQEVT INQSLLEPLH LEVDPEIQRI KTQEREQIMV LNNKFASFID
KVRFLEQQNQ VLQTKWELLQ QVNTSTGTNN LEPLLENYIG DLRRQVDLLS AEQMRQNAEV
RSMQDVVEDY KSKYEDEINK RTGSENDFVV LKKDVDAAYV SKVDLESRVD TLTGEVNFLK
YLFLTELSQV QTHISDTNVI LSMDNNRSLD LDSIIDAVRT QYELIAQRSK DEAEALYQTK
YQELQITAGR HGDDLKNSKM EIAELNRTVQ RLQAEISNVK KQIEQMQSLI SDAEERGEQA
LQDAWQKLQD LEEALQQSKE ELARLLRDYQ AMLGVKLSLD VEIATYRQLL EGEESRMSGE
LQSHVSISVQ NSQVSVNGGA GGGGSYGSGG YGGGSGGGYG GGRSYRGGGA RGRSGGGYGS
GCGGGGGSYG GSGRSGRGSS RVQIIQTSTN TSHRRILE*
mutated AA sequence MSHQFSSQSA FSSMSRRVYS TSSSAGSGGG SPAVGSVCYA RGRCGGGGYG IHGRGFGSRS
LYNLGGSRSI SINLMGRSTS GFCQGGGVGG FGGGRGFGVG STGAGGFGGG GFGGAGFGTS
NFGLGGFGPY CPPGGIQEVT INQSLLEPLH LEVDPEIQRI KTQEREQIMV LNNKFASFID
KVRFLEQQNQ VLQTKWELLQ QVNTSTGTNN LEPLLENYIG DLRRQVDLLS AEQMRQNAEV
RSMQDVVEDY KSKYEDEINK RTGSENDFVV LKKDVDAAYV SKVDLESRVD TLTGEVNFLK
YLFLTELSQV QTHISDTNVI LSMDNNRSLD LDSIINAVRT QYELIAQRSK DEAEALYQTK
YQELQITAGR HGDDLKNSKM EIAELNRTVQ RLQAEISNVK KQIEQMQSLI SDAEERGEQA
LQDAWQKLQD LEEALQQSKE ELARLLRDYQ AMLGVKLSLD VEIATYRQLL EGEESRMSGE
LQSHVSISVQ NSQVSVNGGA GGGGSYGSGG YGGGSGGGYG GGRSYRGGGA RGRSGGGYGS
GCGGGGGSYG GSGRSGRGSS RVQIIQTSTN TSHRRILE*
speed 0.93 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: 0.999999999784974 (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) chr12:53088484C>TN/A show variant in all transcripts   IGV
HGNC symbol KRT77
Ensembl transcript ID ENST00000537195
Genbank transcript ID N/A
UniProt peptide Q7Z794
alteration type single base exchange
alteration region CDS
DNA changes c.307G>A
cDNA.1120G>A
g.8764G>A
AA changes D103N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 103
frameshift no
known variant Reference ID: rs10783528
databasehomozygous (T/T)heterozygousallele carriers
1000G3049861290
ExAC74841779925283
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3250.004
1.1040.017
(flanking)-0.2590.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased8764wt: 0.46 / mu: 0.93wt: TCATCGATGCAGTGC
mu: TCATCAATGCAGTGC		 ATCG|atgc
Donor increased8766wt: 0.31 / mu: 0.62wt: ATCGATGCAGTGCGG
mu: ATCAATGCAGTGCGG		 CGAT|gcag
Donor increased8755wt: 0.50 / mu: 0.63wt: TGGACAGCATCATCG
mu: TGGACAGCATCATCA		 GACA|gcat
Donor marginally increased8761wt: 0.8883 / mu: 0.9042 (marginal change - not scored)wt: GCATCATCGATGCAG
mu: GCATCATCAATGCAG		 ATCA|tcga
Donor increased8769wt: 0.54 / mu: 0.80wt: GATGCAGTGCGGACC
mu: AATGCAGTGCGGACC		 TGCA|gtgc
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      103NNRSLDLDSIIDAVRTQYELIAQR
mutated  all conserved    103NNRSLDLDSIINAVRTQYELIAQ
Ptroglodytes  all identical  ENSPTRG00000004988  341NNRSLDLDSIIDAVRTQYELIAQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000067594  339NNRSLDLDSIIDAVRAQYEIIAQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1163REGIONHead.lost
164200REGIONCoil 1A.might get lost (downstream of altered splice site)
164474REGIONRod.might get lost (downstream of altered splice site)
201219REGIONLinker 1.might get lost (downstream of altered splice site)
220311REGIONCoil 1B.might get lost (downstream of altered splice site)
250250MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
312335REGIONLinker 12.might get lost (downstream of altered splice site)
336336CONFLICTD -> N (in Ref. 1; CAD91892).might get lost (downstream of altered splice site)
336474REGIONCoil 2.might get lost (downstream of altered splice site)
418418SITEStutter.might get lost (downstream of altered splice site)
475578REGIONTail.might get lost (downstream of altered splice site)
533533CONFLICTR -> G (in Ref. 1; CAD91892).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1038 / 1038
position (AA) of stopcodon in wt / mu AA sequence 346 / 346
position of stopcodon in wt / mu cDNA 1851 / 1851
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 814 / 814
chromosome 12
strand -1
last intron/exon boundary 1577
theoretical NMD boundary in CDS 713
length of CDS 1038
coding sequence (CDS) position 307
cDNA position
(for ins/del: last normal base / first normal base)		 1120
gDNA position
(for ins/del: last normal base / first normal base)		 8764
chromosomal position
(for ins/del: last normal base / first normal base)		 53088484
original gDNA sequence snippet TGGACCTGGACAGCATCATCGATGCAGTGCGGACCCAGTAT
altered gDNA sequence snippet TGGACCTGGACAGCATCATCAATGCAGTGCGGACCCAGTAT
original cDNA sequence snippet TGGACCTGGACAGCATCATCGATGCAGTGCGGACCCAGTAT
altered cDNA sequence snippet TGGACCTGGACAGCATCATCAATGCAGTGCGGACCCAGTAT
wildtype AA sequence MRQNAEVRSM QDVVEDYKSK YEDEINKRTG SENDFVVLKK DVDAAYVSKV DLESRVDTLT
GEVNFLKYLF LTELSQVQTH ISDTNVILSM DNNRSLDLDS IIDAVRTQYE LIAQRSKDEA
EALYQTKYQE LQITAGRHGD DLKNSKMEIA ELNRTVQRLQ AEISNVKKQI EQMQSLISDA
EERGEQALQD AWQKLQDLEE ALQQSKEELA RLLRDYQAML GVKLSLDVEI ATYRQLLEGE
ESRMSGELQS HVSISVQNSQ VSVNGGAGGG GSYGSGGYGG GSGGGYGGGR SYRGGGARGR
SGGGYGSGCG GGGGSYGGSG RSGRGSSRVQ IIQTSTNTSH RRILE*
mutated AA sequence MRQNAEVRSM QDVVEDYKSK YEDEINKRTG SENDFVVLKK DVDAAYVSKV DLESRVDTLT
GEVNFLKYLF LTELSQVQTH ISDTNVILSM DNNRSLDLDS IINAVRTQYE LIAQRSKDEA
EALYQTKYQE LQITAGRHGD DLKNSKMEIA ELNRTVQRLQ AEISNVKKQI EQMQSLISDA
EERGEQALQD AWQKLQDLEE ALQQSKEELA RLLRDYQAML GVKLSLDVEI ATYRQLLEGE
ESRMSGELQS HVSISVQNSQ VSVNGGAGGG GSYGSGGYGG GSGGGYGGGR SYRGGGARGR
SGGGYGSGCG GGGGSYGGSG RSGRGSSRVQ IIQTSTNTSH RRILE*
speed 1.14 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