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 5.129836 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCKdisease_causing_automatic0.999995436528521simple_aaeaffected0Y215Csingle base exchangers104894015show file
GCKdisease_causing_automatic0.999995436528521simple_aaeaffected0Y197Csingle base exchangers104894015show file
GCKdisease_causing_automatic0.999999251212193simple_aaeaffected0Y214Csingle base exchangers104894015show file
GCKdisease_causing_automatic0.999999251212193simple_aaeaffected0Y213Csingle base exchangers104894015show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999995436528521 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032913)
  • known disease mutation: rs16144 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44189397T>CN/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.644A>G
cDNA.806A>G
g.48373A>G
AA changes Y215C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 215
frameshift no
known variant Reference ID: rs104894015
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16144 (pathogenic for Hyperinsulinism due to glucokinase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.6731
3.7021
(flanking)3.5261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased48377wt: 0.24 / mu: 0.32wt: ACGATGATCTCCTGCTACTACGAAGACCATCAGTGCGAGGT
mu: ACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCGAGGT		 ctac|GAAG
Donor gained483720.94mu: CCTGCTGCTACGAAG TGCT|gcta
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      215VNDTVATMISCYYEDHQCEVGMIV
mutated  not conserved    215VNDTVATMISCCYEDHQCEVGMI
Ptroglodytes  all identical  ENSPTRG00000019140  213VNDTVATMISCYYEDHQCEVGMI
Mmulatta  all identical  ENSMMUG00000002427  215VNDTVATMISCYYEDHQCEVGMI
Fcatus  all identical  ENSFCAG00000014361  199VNDTVATMISCYYEDRRCEVGMI
Mmusculus  all identical  ENSMUSG00000041798  214VNDTVATMISCYYEDRQCEVGMI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  224VNDTVATMISCYYEDRSCEVGMI
Dmelanogaster  not conserved  FBgn0001186  289LNDTTGTLMSCAWKNHNCKIGLI
Celegans  not conserved  F14B4.2  232LNDTVGTLMACAFQENSCQIGVI
Xtropicalis  all identical  ENSXETG00000019003  214VNDTVATMISCYYEDHHCEVGLI
protein features
start (aa)end (aa)featuredetails 
220237STRANDmight get lost (downstream of altered splice site)
228228BINDINGATP (By similarity).might get lost (downstream of altered splice site)
231231BINDINGSubstrate.might get lost (downstream of altered splice site)
238240HELIXmight get lost (downstream of altered splice site)
248254STRANDmight get lost (downstream of altered splice site)
256256BINDINGSubstrate.might get lost (downstream of altered splice site)
256256MUTAGENE->A: Inactive enzyme.might get lost (downstream of altered splice site)
257259HELIXmight get lost (downstream of altered splice site)
260263TURNmight get lost (downstream of altered splice site)
267269HELIXmight get lost (downstream of altered splice site)
272280HELIXmight get lost (downstream of altered splice site)
281283STRANDmight get lost (downstream of altered splice site)
288291HELIXmight get lost (downstream of altered splice site)
290290BINDINGSubstrate.might get lost (downstream of altered splice site)
295296NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
295311HELIXmight get lost (downstream of altered splice site)
316318HELIXmight get lost (downstream of altered splice site)
322325TURNmight get lost (downstream of altered splice site)
332336NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
332339HELIXmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
343345STRANDmight get lost (downstream of altered splice site)
346354HELIXmight get lost (downstream of altered splice site)
361396HELIXmight get lost (downstream of altered splice site)
400409STRANDmight get lost (downstream of altered splice site)
411415NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
411415HELIXmight get lost (downstream of altered splice site)
414414MUTAGENK->A: Small change in activity.might get lost (downstream of altered splice site)
416418STRANDmight get lost (downstream of altered splice site)
419430HELIXmight get lost (downstream of altered splice site)
434440STRANDmight get lost (downstream of altered splice site)
444456HELIXmight get lost (downstream of altered splice site)
457459TURNmight get lost (downstream of altered splice site)
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 644
cDNA position
(for ins/del: last normal base / first normal base)		 806
gDNA position
(for ins/del: last normal base / first normal base)		 48373
chromosomal position
(for ins/del: last normal base / first normal base)		 44189397
original gDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered gDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
original cDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered cDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
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 MISCCYEDHQ 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*
speed 0.64 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: 0.999995436528521 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032913)
  • known disease mutation: rs16144 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44189397T>CN/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.590A>G
cDNA.624A>G
g.48373A>G
AA changes Y197C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 197
frameshift no
known variant Reference ID: rs104894015
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16144 (pathogenic for Hyperinsulinism due to glucokinase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.6731
3.7021
(flanking)3.5261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased48377wt: 0.24 / mu: 0.32wt: ACGATGATCTCCTGCTACTACGAAGACCATCAGTGCGAGGT
mu: ACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCGAGGT		 ctac|GAAG
Donor gained483720.94mu: CCTGCTGCTACGAAG TGCT|gcta
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      197VNDTVATMISCYYEDHQCEVGMIV
mutated  not conserved    197VNDTVATMISCCYEDHQCEVGMI
Ptroglodytes  all identical  ENSPTRG00000019140  213VNDTVATMISCYYEDHQCEVGMI
Mmulatta  all identical  ENSMMUG00000002427  215VNDTVATMISCYYEDHQCEVGMI
Fcatus  all identical  ENSFCAG00000014361  199VNDTVATMISCYYEDRRCEVGMI
Mmusculus  all identical  ENSMUSG00000041798  214VNDTVATMISCYYEDRQCEVGMI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  224VNDTVATMISCYYEDRSCEVGMI
Dmelanogaster  not conserved  FBgn0001186  289LNDTTGTLMSCAWKNHNCKIGLI
Celegans  not conserved  F14B4.2  232LNDTVGTLMACAFQENSCQIGVI
Xtropicalis  all identical  ENSXETG00000019003  214VNDTVATMISCYYEDHHCEVGLI
protein features
start (aa)end (aa)featuredetails 
198203STRANDmight get lost (downstream of altered splice site)
204205REGIONSubstrate binding.might get lost (downstream of altered splice site)
205214HELIXmight get lost (downstream of altered splice site)
220237STRANDmight get lost (downstream of altered splice site)
228228BINDINGATP (By similarity).might get lost (downstream of altered splice site)
231231BINDINGSubstrate.might get lost (downstream of altered splice site)
238240HELIXmight get lost (downstream of altered splice site)
248254STRANDmight get lost (downstream of altered splice site)
256256MUTAGENE->A: Inactive enzyme.might get lost (downstream of altered splice site)
256256BINDINGSubstrate.might get lost (downstream of altered splice site)
257259HELIXmight get lost (downstream of altered splice site)
260263TURNmight get lost (downstream of altered splice site)
267269HELIXmight get lost (downstream of altered splice site)
272280HELIXmight get lost (downstream of altered splice site)
281283STRANDmight get lost (downstream of altered splice site)
288291HELIXmight get lost (downstream of altered splice site)
290290BINDINGSubstrate.might get lost (downstream of altered splice site)
295296NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
295311HELIXmight get lost (downstream of altered splice site)
316318HELIXmight get lost (downstream of altered splice site)
322325TURNmight get lost (downstream of altered splice site)
332336NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
332339HELIXmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
343345STRANDmight get lost (downstream of altered splice site)
346354HELIXmight get lost (downstream of altered splice site)
361396HELIXmight get lost (downstream of altered splice site)
400409STRANDmight get lost (downstream of altered splice site)
411415NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
411415HELIXmight get lost (downstream of altered splice site)
414414MUTAGENK->A: Small change in activity.might get lost (downstream of altered splice site)
416418STRANDmight get lost (downstream of altered splice site)
419430HELIXmight get lost (downstream of altered splice site)
434440STRANDmight get lost (downstream of altered splice site)
444456HELIXmight get lost (downstream of altered splice site)
457459TURNmight get lost (downstream of altered splice site)
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 590
cDNA position
(for ins/del: last normal base / first normal base)		 624
gDNA position
(for ins/del: last normal base / first normal base)		 48373
chromosomal position
(for ins/del: last normal base / first normal base)		 44189397
original gDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered gDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
original cDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered cDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
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 ATMISCCYED 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*
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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999251212193 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032913)
  • known disease mutation: rs16144 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44189397T>CN/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.641A>G
cDNA.1111A>G
g.48373A>G
AA changes Y214C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 214
frameshift no
known variant Reference ID: rs104894015
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16144 (pathogenic for Hyperinsulinism due to glucokinase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.6731
3.7021
(flanking)3.5261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased48377wt: 0.24 / mu: 0.32wt: ACGATGATCTCCTGCTACTACGAAGACCATCAGTGCGAGGT
mu: ACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCGAGGT		 ctac|GAAG
Donor gained483720.94mu: CCTGCTGCTACGAAG TGCT|gcta
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      214VNDTVATMISCYYEDHQCEVGMIV
mutated  not conserved    214VNDTVATMISCCYEDHQCEVGMI
Ptroglodytes  all identical  ENSPTRG00000019140  213VNDTVATMISCYYEDHQCEVGMI
Mmulatta  all identical  ENSMMUG00000002427  215VNDTVATMISCYYEDHQCEVGMI
Fcatus  all identical  ENSFCAG00000014361  199VNDTVATMISCYYEDRRCEVGMI
Mmusculus  all identical  ENSMUSG00000041798  214VNDTVATMISCYYEDRQCEVGMI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  224VNDTVATMISCYYEDRSCEVGMI
Dmelanogaster  not conserved  FBgn0001186  289LNDTTGTLMSCAWKNHNCKIGLI
Celegans  not conserved  F14B4.2  232LNDTVGTLMACAFQENSCQIGVI
Xtropicalis  all identical  ENSXETG00000019003  214VNDTVATMISCYYEDHHCEVGLI
protein features
start (aa)end (aa)featuredetails 
205214HELIXlost
220237STRANDmight get lost (downstream of altered splice site)
228228BINDINGATP (By similarity).might get lost (downstream of altered splice site)
231231BINDINGSubstrate.might get lost (downstream of altered splice site)
238240HELIXmight get lost (downstream of altered splice site)
248254STRANDmight get lost (downstream of altered splice site)
256256BINDINGSubstrate.might get lost (downstream of altered splice site)
256256MUTAGENE->A: Inactive enzyme.might get lost (downstream of altered splice site)
257259HELIXmight get lost (downstream of altered splice site)
260263TURNmight get lost (downstream of altered splice site)
267269HELIXmight get lost (downstream of altered splice site)
272280HELIXmight get lost (downstream of altered splice site)
281283STRANDmight get lost (downstream of altered splice site)
288291HELIXmight get lost (downstream of altered splice site)
290290BINDINGSubstrate.might get lost (downstream of altered splice site)
295296NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
295311HELIXmight get lost (downstream of altered splice site)
316318HELIXmight get lost (downstream of altered splice site)
322325TURNmight get lost (downstream of altered splice site)
332336NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
332339HELIXmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
343345STRANDmight get lost (downstream of altered splice site)
346354HELIXmight get lost (downstream of altered splice site)
361396HELIXmight get lost (downstream of altered splice site)
400409STRANDmight get lost (downstream of altered splice site)
411415NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
411415HELIXmight get lost (downstream of altered splice site)
414414MUTAGENK->A: Small change in activity.might get lost (downstream of altered splice site)
416418STRANDmight get lost (downstream of altered splice site)
419430HELIXmight get lost (downstream of altered splice site)
434440STRANDmight get lost (downstream of altered splice site)
444456HELIXmight get lost (downstream of altered splice site)
457459TURNmight get lost (downstream of altered splice site)
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 641
cDNA position
(for ins/del: last normal base / first normal base)		 1111
gDNA position
(for ins/del: last normal base / first normal base)		 48373
chromosomal position
(for ins/del: last normal base / first normal base)		 44189397
original gDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered gDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
original cDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered cDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
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 ISCCYEDHQC 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*
speed 0.62 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: 0.999999251212193 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032913)
  • known disease mutation: rs16144 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44189397T>CN/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.638A>G
cDNA.923A>G
g.48373A>G
AA changes Y213C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 213
frameshift no
known variant Reference ID: rs104894015
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16144 (pathogenic for Hyperinsulinism due to glucokinase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032913)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.6731
3.7021
(flanking)3.5261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased48377wt: 0.24 / mu: 0.32wt: ACGATGATCTCCTGCTACTACGAAGACCATCAGTGCGAGGT
mu: ACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCGAGGT		 ctac|GAAG
Donor gained483720.94mu: CCTGCTGCTACGAAG TGCT|gcta
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      213VNDTVATMISCYYEDHQCEVGMIV
mutated  not conserved    213VNDTVATMISCCYEDHQCEVGMI
Ptroglodytes  all identical  ENSPTRG00000019140  213VNDTVATMISCYYEDHQCEVGMI
Mmulatta  all identical  ENSMMUG00000002427  215VNDTVATMISCYYEDHQCEVGMI
Fcatus  all identical  ENSFCAG00000014361  199VNDTVATMISCYYEDRRCEVGMI
Mmusculus  all identical  ENSMUSG00000041798  214VNDTVATMISCYYEDRQCEVGMI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  224VNDTVATMISCYYEDRSCEVGMI
Dmelanogaster  not conserved  FBgn0001186  289LNDTTGTLMSCAWKNHNCKIGLI
Celegans  not conserved  F14B4.2  232LNDTVGTLMACAFQENSCQIGVI
Xtropicalis  all identical  ENSXETG00000019003  214VNDTVATMISCYYEDHHCEVGLI
protein features
start (aa)end (aa)featuredetails 
205214HELIXlost
220237STRANDmight get lost (downstream of altered splice site)
228228BINDINGATP (By similarity).might get lost (downstream of altered splice site)
231231BINDINGSubstrate.might get lost (downstream of altered splice site)
238240HELIXmight get lost (downstream of altered splice site)
248254STRANDmight get lost (downstream of altered splice site)
256256BINDINGSubstrate.might get lost (downstream of altered splice site)
256256MUTAGENE->A: Inactive enzyme.might get lost (downstream of altered splice site)
257259HELIXmight get lost (downstream of altered splice site)
260263TURNmight get lost (downstream of altered splice site)
267269HELIXmight get lost (downstream of altered splice site)
272280HELIXmight get lost (downstream of altered splice site)
281283STRANDmight get lost (downstream of altered splice site)
288291HELIXmight get lost (downstream of altered splice site)
290290BINDINGSubstrate.might get lost (downstream of altered splice site)
295296NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
295311HELIXmight get lost (downstream of altered splice site)
316318HELIXmight get lost (downstream of altered splice site)
322325TURNmight get lost (downstream of altered splice site)
332336NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
332339HELIXmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
343345STRANDmight get lost (downstream of altered splice site)
346354HELIXmight get lost (downstream of altered splice site)
361396HELIXmight get lost (downstream of altered splice site)
400409STRANDmight get lost (downstream of altered splice site)
411415NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
411415HELIXmight get lost (downstream of altered splice site)
414414MUTAGENK->A: Small change in activity.might get lost (downstream of altered splice site)
416418STRANDmight get lost (downstream of altered splice site)
419430HELIXmight get lost (downstream of altered splice site)
434440STRANDmight get lost (downstream of altered splice site)
444456HELIXmight get lost (downstream of altered splice site)
457459TURNmight get lost (downstream of altered splice site)
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 638
cDNA position
(for ins/del: last normal base / first normal base)		 923
gDNA position
(for ins/del: last normal base / first normal base)		 48373
chromosomal position
(for ins/del: last normal base / first normal base)		 44189397
original gDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered gDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
original cDNA sequence snippet GGCCACGATGATCTCCTGCTACTACGAAGACCATCAGTGCG
altered cDNA sequence snippet GGCCACGATGATCTCCTGCTGCTACGAAGACCATCAGTGCG
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 SCCYEDHQCE 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*
speed 1.28 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

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