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: ENST00000403799
Querying Taster for transcript #2: ENST00000395796
Querying Taster for transcript #3: ENST00000345378
Querying Taster for transcript #4: ENST00000437084
MT speed 0 s - this script 4.881732 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCKdisease_causing_automatic0.999999999953351simple_aae0T227Msingle base exchangers80356655show file
GCKdisease_causing_automatic0.999999999953351simple_aae0T229Msingle base exchangers80356655show file
GCKdisease_causing_automatic0.999999999965333simple_aae0T211Msingle base exchangers80356655show file
GCKdisease_causing_automatic0.99999999999911simple_aae0T228Msingle base exchangers80356655show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999953351 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032577)
  • known disease mutation at this position (HGMD CM096860)
  • known disease mutation at this position (HGMD CM920305)
  • known disease mutation: rs16134 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44187429G>AN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000395796
Genbank transcript ID NM_033508
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.680C>T
cDNA.965C>T
g.50341C>T
AA changes T227M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 227
frameshift no
known variant Reference ID: rs80356655
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16134 (pathogenic for Maturity-onset diabetes of the young, type 2|Permanent neonatal diabetes mellitus 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5550.006
5.9151
(flanking)4.8821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased50337wt: 0.8603 / mu: 0.8819 (marginal change - not scored)wt: TCCCCCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGC
mu: TCCCCCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGC		 ccag|GCAC
Donor marginally increased50346wt: 0.8839 / mu: 0.9031 (marginal change - not scored)wt: CGGGCTGCAATGCCT
mu: TGGGCTGCAATGCCT		 GGCT|gcaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      227DHQCEVGMIVGTGCNACYMEEMQN
mutated  not conserved    227DHQCEVGMIVGMGCNACYMEEMQ
Ptroglodytes  all identical  ENSPTRG00000019140  227DHQCEVGMIVGTGCNACYMEEMQ
Mmulatta  all identical  ENSMMUG00000002427  229DHQCEVGMIVGTGCNACYMEEMQ
Fcatus  all identical  ENSFCAG00000014361  213DRRCEVGMIVGTGCNACYMEEMH
Mmusculus  all identical  ENSMUSG00000041798  228DRQCEVGMIVGTGCNACYMEEMQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  238DRSCEVGMIVGTGCNACYMEEMR
Dmelanogaster  all identical  FBgn0001186  303NHNCKIGLIVGTGANACYMERVE
Celegans  all identical  F14B4.2  246ENSCQIGVIVGTGTNACYMERLD
Xtropicalis  all identical  ENSXETG00000019003  228DHHCEVGLIVGTGCNACYMEEMS
protein features
start (aa)end (aa)featuredetails 
220237STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1395 / 1395
position (AA) of stopcodon in wt / mu AA sequence 465 / 465
position of stopcodon in wt / mu cDNA 1680 / 1680
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 286 / 286
chromosome 7
strand -1
last intron/exon boundary 1536
theoretical NMD boundary in CDS 1200
length of CDS 1395
coding sequence (CDS) position 680
cDNA position
(for ins/del: last normal base / first normal base)		 965
gDNA position
(for ins/del: last normal base / first normal base)		 50341
chromosomal position
(for ins/del: last normal base / first normal base)		 44187429
original gDNA sequence snippet CCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGCTACA
altered gDNA sequence snippet CCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGCTACA
original cDNA sequence snippet GGTCGGCATGATCGTGGGCACGGGCTGCAATGCCTGCTACA
altered cDNA sequence snippet GGTCGGCATGATCGTGGGCATGGGCTGCAATGCCTGCTACA
wildtype AA sequence MPRPRSQLPQ PNSQVEQILA EFQLQEEDLK KVMRRMQKEM DRGLRLETHE EASVKMLPTY
VRSTPEGSEV GDFLSLDLGG TNFRVMLVKV GEGEEGQWSV KTKHQMYSIP EDAMTGTAEM
LFDYISECIS DFLDKHQMKH KKLPLGFTFS FPVRHEDIDK GILLNWTKGF KASGAEGNNV
VGLLRDAIKR RGDFEMDVVA MVNDTVATMI SCYYEDHQCE VGMIVGTGCN ACYMEEMQNV
ELVEGDEGRM CVNTEWGAFG DSGELDEFLL EYDRLVDESS ANPGQQLYEK LIGGKYMGEL
VRLVLLRLVD ENLLFHGEAS EQLRTRGAFE TRFVSQVESD TGDRKQIYNI LSTLGLRPST
TDCDIVRRAC ESVSTRAAHM CSAGLAGVIN RMRESRSEDV MRITVGVDGS VYKLHPSFKE
RFHASVRRLT PSCEITFIES EEGSGRGAAL VSAVACKKAC MLGQ*
mutated AA sequence MPRPRSQLPQ PNSQVEQILA EFQLQEEDLK KVMRRMQKEM DRGLRLETHE EASVKMLPTY
VRSTPEGSEV GDFLSLDLGG TNFRVMLVKV GEGEEGQWSV KTKHQMYSIP EDAMTGTAEM
LFDYISECIS DFLDKHQMKH KKLPLGFTFS FPVRHEDIDK GILLNWTKGF KASGAEGNNV
VGLLRDAIKR RGDFEMDVVA MVNDTVATMI SCYYEDHQCE VGMIVGMGCN ACYMEEMQNV
ELVEGDEGRM CVNTEWGAFG DSGELDEFLL EYDRLVDESS ANPGQQLYEK LIGGKYMGEL
VRLVLLRLVD ENLLFHGEAS EQLRTRGAFE TRFVSQVESD TGDRKQIYNI LSTLGLRPST
TDCDIVRRAC ESVSTRAAHM CSAGLAGVIN RMRESRSEDV MRITVGVDGS VYKLHPSFKE
RFHASVRRLT PSCEITFIES EEGSGRGAAL VSAVACKKAC MLGQ*
speed 0.89 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

disease causing

 Model: simple_aae, prob: 0.999999999953351 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032577)
  • known disease mutation at this position (HGMD CM096860)
  • known disease mutation at this position (HGMD CM920305)
  • known disease mutation: rs16134 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44187429G>AN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000345378
Genbank transcript ID NM_033507
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.686C>T
cDNA.848C>T
g.50341C>T
AA changes T229M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 229
frameshift no
known variant Reference ID: rs80356655
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16134 (pathogenic for Maturity-onset diabetes of the young, type 2|Permanent neonatal diabetes mellitus 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5550.006
5.9151
(flanking)4.8821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased50337wt: 0.8603 / mu: 0.8819 (marginal change - not scored)wt: TCCCCCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGC
mu: TCCCCCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGC		 ccag|GCAC
Donor marginally increased50346wt: 0.8839 / mu: 0.9031 (marginal change - not scored)wt: CGGGCTGCAATGCCT
mu: TGGGCTGCAATGCCT		 GGCT|gcaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      229DHQCEVGMIVGTGCNACYMEEMQN
mutated  not conserved    229DHQCEVGMIVGMGCNACYMEEMQ
Ptroglodytes  all identical  ENSPTRG00000019140  227DHQCEVGMIVGTGCNACYMEEMQ
Mmulatta  all identical  ENSMMUG00000002427  229DHQCEVGMIVGTGCNACYMEEMQ
Fcatus  all identical  ENSFCAG00000014361  213DRRCEVGMIVGTGCNACYMEEMH
Mmusculus  all identical  ENSMUSG00000041798  228DRQCEVGMIVGTGCNACYMEEMQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  238DRSCEVGMIVGTGCNACYMEEMR
Dmelanogaster  all identical  FBgn0001186  303NHNCKIGLIVGTGANACYMERVE
Celegans  all identical  F14B4.2  246ENSCQIGVIVGTGTNACYMERLD
Xtropicalis  all identical  ENSXETG00000019003  228DHHCEVGLIVGTGCNACYMEEMS
protein features
start (aa)end (aa)featuredetails 
220237STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1401 / 1401
position (AA) of stopcodon in wt / mu AA sequence 467 / 467
position of stopcodon in wt / mu cDNA 1563 / 1563
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 163 / 163
chromosome 7
strand -1
last intron/exon boundary 1419
theoretical NMD boundary in CDS 1206
length of CDS 1401
coding sequence (CDS) position 686
cDNA position
(for ins/del: last normal base / first normal base)		 848
gDNA position
(for ins/del: last normal base / first normal base)		 50341
chromosomal position
(for ins/del: last normal base / first normal base)		 44187429
original gDNA sequence snippet CCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGCTACA
altered gDNA sequence snippet CCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGCTACA
original cDNA sequence snippet GGTCGGCATGATCGTGGGCACGGGCTGCAATGCCTGCTACA
altered cDNA sequence snippet GGTCGGCATGATCGTGGGCATGGGCTGCAATGCCTGCTACA
wildtype AA sequence MAMDVTRSQA QTALTLVEQI LAEFQLQEED LKKVMRRMQK EMDRGLRLET HEEASVKMLP
TYVRSTPEGS EVGDFLSLDL GGTNFRVMLV KVGEGEEGQW SVKTKHQMYS IPEDAMTGTA
EMLFDYISEC ISDFLDKHQM KHKKLPLGFT FSFPVRHEDI DKGILLNWTK GFKASGAEGN
NVVGLLRDAI KRRGDFEMDV VAMVNDTVAT MISCYYEDHQ CEVGMIVGTG CNACYMEEMQ
NVELVEGDEG RMCVNTEWGA FGDSGELDEF LLEYDRLVDE SSANPGQQLY EKLIGGKYMG
ELVRLVLLRL VDENLLFHGE ASEQLRTRGA FETRFVSQVE SDTGDRKQIY NILSTLGLRP
STTDCDIVRR ACESVSTRAA HMCSAGLAGV INRMRESRSE DVMRITVGVD GSVYKLHPSF
KERFHASVRR LTPSCEITFI ESEEGSGRGA ALVSAVACKK ACMLGQ*
mutated AA sequence MAMDVTRSQA QTALTLVEQI LAEFQLQEED LKKVMRRMQK EMDRGLRLET HEEASVKMLP
TYVRSTPEGS EVGDFLSLDL GGTNFRVMLV KVGEGEEGQW SVKTKHQMYS IPEDAMTGTA
EMLFDYISEC ISDFLDKHQM KHKKLPLGFT FSFPVRHEDI DKGILLNWTK GFKASGAEGN
NVVGLLRDAI KRRGDFEMDV VAMVNDTVAT MISCYYEDHQ CEVGMIVGMG CNACYMEEMQ
NVELVEGDEG RMCVNTEWGA FGDSGELDEF LLEYDRLVDE SSANPGQQLY EKLIGGKYMG
ELVRLVLLRL VDENLLFHGE ASEQLRTRGA FETRFVSQVE SDTGDRKQIY NILSTLGLRP
STTDCDIVRR ACESVSTRAA HMCSAGLAGV INRMRESRSE DVMRITVGVD GSVYKLHPSF
KERFHASVRR LTPSCEITFI ESEEGSGRGA ALVSAVACKK ACMLGQ*
speed 1.00 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

disease causing

 Model: simple_aae, prob: 0.999999999965333 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032577)
  • known disease mutation at this position (HGMD CM096860)
  • known disease mutation at this position (HGMD CM920305)
  • known disease mutation: rs16134 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44187429G>AN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000437084
Genbank transcript ID N/A
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.632C>T
cDNA.666C>T
g.50341C>T
AA changes T211M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 211
frameshift no
known variant Reference ID: rs80356655
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16134 (pathogenic for Maturity-onset diabetes of the young, type 2|Permanent neonatal diabetes mellitus 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5550.006
5.9151
(flanking)4.8821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased50337wt: 0.8603 / mu: 0.8819 (marginal change - not scored)wt: TCCCCCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGC
mu: TCCCCCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGC		 ccag|GCAC
Donor marginally increased50346wt: 0.8839 / mu: 0.9031 (marginal change - not scored)wt: CGGGCTGCAATGCCT
mu: TGGGCTGCAATGCCT		 GGCT|gcaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      211DHQCEVGMIVGTGCNACYMEEMQN
mutated  not conserved    211DHQCEVGMIVGMGCNACYMEEMQ
Ptroglodytes  all identical  ENSPTRG00000019140  227DHQCEVGMIVGTGCNACYMEEMQ
Mmulatta  all identical  ENSMMUG00000002427  229DHQCEVGMIVGTGCNACYMEEMQ
Fcatus  all identical  ENSFCAG00000014361  213DRRCEVGMIVGTGCNACYMEEMH
Mmusculus  all identical  ENSMUSG00000041798  228DRQCEVGMIVGTGCNACYMEEMQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  238DRSCEVGMIVGTGCNACYMEEMR
Dmelanogaster  all identical  FBgn0001186  303NHNCKIGLIVGTGANACYMERVE
Celegans  all identical  F14B4.2  246ENSCQIGVIVGTGTNACYMERLD
Xtropicalis  all identical  ENSXETG00000019003  228DHHCEVGLIVGTGCNACYMEEMS
protein features
start (aa)end (aa)featuredetails 
205214HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1347 / 1347
position (AA) of stopcodon in wt / mu AA sequence 449 / 449
position of stopcodon in wt / mu cDNA 1381 / 1381
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 35 / 35
chromosome 7
strand -1
last intron/exon boundary 1237
theoretical NMD boundary in CDS 1152
length of CDS 1347
coding sequence (CDS) position 632
cDNA position
(for ins/del: last normal base / first normal base)		 666
gDNA position
(for ins/del: last normal base / first normal base)		 50341
chromosomal position
(for ins/del: last normal base / first normal base)		 44187429
original gDNA sequence snippet CCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGCTACA
altered gDNA sequence snippet CCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGCTACA
original cDNA sequence snippet GGTCGGCATGATCGTGGGCACGGGCTGCAATGCCTGCTACA
altered cDNA sequence snippet GGTCGGCATGATCGTGGGCATGGGCTGCAATGCCTGCTACA
wildtype AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MMKHKKLPLG FTFSFPVRHE DIDKGILLNW TKGFKASGAE GNNVVGLLRD AIKRRGDFEM
DVVAMVNDTV ATMISCYYED HQCEVGMIVG TGCNACYMEE MQNVELVEGD EGRMCVNTEW
GAFGDSGELD EFLLEYDRLV DESSANPGQQ LYEKLIGGKY MGELVRLVLL RLVDENLLFH
GEASEQLRTR GAFETRFVSQ VESDTGDRKQ IYNILSTLGL RPSTTDCDIV RRACESVSTR
AAHMCSAGLA GVINRMRESR SEDVMRITVG VDGSVYKLHP SFKERFHASV RRLTPSCEIT
FIESEEGSGR GAALVSAVAC KKACMLGQ*
mutated AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MMKHKKLPLG FTFSFPVRHE DIDKGILLNW TKGFKASGAE GNNVVGLLRD AIKRRGDFEM
DVVAMVNDTV ATMISCYYED HQCEVGMIVG MGCNACYMEE MQNVELVEGD EGRMCVNTEW
GAFGDSGELD EFLLEYDRLV DESSANPGQQ LYEKLIGGKY MGELVRLVLL RLVDENLLFH
GEASEQLRTR GAFETRFVSQ VESDTGDRKQ IYNILSTLGL RPSTTDCDIV RRACESVSTR
AAHMCSAGLA GVINRMRESR SEDVMRITVG VDGSVYKLHP SFKERFHASV RRLTPSCEIT
FIESEEGSGR GAALVSAVAC KKACMLGQ*
speed 0.81 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999911 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032577)
  • known disease mutation at this position (HGMD CM096860)
  • known disease mutation at this position (HGMD CM920305)
  • known disease mutation: rs16134 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44187429G>AN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000403799
Genbank transcript ID NM_000162
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.683C>T
cDNA.1153C>T
g.50341C>T
AA changes T228M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 228
frameshift no
known variant Reference ID: rs80356655
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16134 (pathogenic for Maturity-onset diabetes of the young, type 2|Permanent neonatal diabetes mellitus 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032577)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096860)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920305)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5550.006
5.9151
(flanking)4.8821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased50337wt: 0.8603 / mu: 0.8819 (marginal change - not scored)wt: TCCCCCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGC
mu: TCCCCCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGC		 ccag|GCAC
Donor marginally increased50346wt: 0.8839 / mu: 0.9031 (marginal change - not scored)wt: CGGGCTGCAATGCCT
mu: TGGGCTGCAATGCCT		 GGCT|gcaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      228DHQCEVGMIVGTGCNACYMEEMQN
mutated  not conserved    228DHQCEVGMIVGMGCNACYMEEMQ
Ptroglodytes  all identical  ENSPTRG00000019140  227DHQCEVGMIVGTGCNACYMEEMQ
Mmulatta  all identical  ENSMMUG00000002427  229DHQCEVGMIVGTGCNACYMEEMQ
Fcatus  all identical  ENSFCAG00000014361  213DRRCEVGMIVGTGCNACYMEEMH
Mmusculus  all identical  ENSMUSG00000041798  228DRQCEVGMIVGTGCNACYMEEMQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  238DRSCEVGMIVGTGCNACYMEEMR
Dmelanogaster  all identical  FBgn0001186  303NHNCKIGLIVGTGANACYMERVE
Celegans  all identical  F14B4.2  246ENSCQIGVIVGTGTNACYMERLD
Xtropicalis  all identical  ENSXETG00000019003  228DHHCEVGLIVGTGCNACYMEEMS
protein features
start (aa)end (aa)featuredetails 
220237STRANDlost
228228BINDINGATP (By similarity).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1398 / 1398
position (AA) of stopcodon in wt / mu AA sequence 466 / 466
position of stopcodon in wt / mu cDNA 1868 / 1868
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 471 / 471
chromosome 7
strand -1
last intron/exon boundary 1724
theoretical NMD boundary in CDS 1203
length of CDS 1398
coding sequence (CDS) position 683
cDNA position
(for ins/del: last normal base / first normal base)		 1153
gDNA position
(for ins/del: last normal base / first normal base)		 50341
chromosomal position
(for ins/del: last normal base / first normal base)		 44187429
original gDNA sequence snippet CCCGACCTCCACCCCAGGCACGGGCTGCAATGCCTGCTACA
altered gDNA sequence snippet CCCGACCTCCACCCCAGGCATGGGCTGCAATGCCTGCTACA
original cDNA sequence snippet GGTCGGCATGATCGTGGGCACGGGCTGCAATGCCTGCTACA
altered cDNA sequence snippet GGTCGGCATGATCGTGGGCATGGGCTGCAATGCCTGCTACA
wildtype AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN
VVGLLRDAIK RRGDFEMDVV AMVNDTVATM ISCYYEDHQC EVGMIVGTGC NACYMEEMQN
VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES SANPGQQLYE KLIGGKYMGE
LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS
TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK
ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ*
mutated AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN
VVGLLRDAIK RRGDFEMDVV AMVNDTVATM ISCYYEDHQC EVGMIVGMGC NACYMEEMQN
VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES SANPGQQLYE KLIGGKYMGE
LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS
TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK
ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ*
speed 0.88 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
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Problems