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MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000241256
Querying Taster for transcript #2: ENST00000427970
MT speed 2.89 s - this script 4.916422 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GHSRdisease_causing0.999999999972726simple_aaeaffectedA204Esingle base exchangers121917883show file
GHSRdisease_causing0.999999999972726simple_aaeaffectedA204Esingle base exchangers121917883show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999972726      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs7632 (probable pathogenic)
  • known disease mutation at this position (HGMD CM061011)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:172165593G>TN/A show variant in all transcripts   IGV
HGNC symbol GHSR
Ensembl transcript ID ENST00000241256
Genbank transcript ID NM_198407
UniProt peptide Q92847
alteration type single base exchange
alteration region CDS
DNA changes c.611C>A
cDNA.654C>A
g.654C>A
AA changes A204E Score: 107 explain score(s)
position(s) of altered AA
if AA alteration in CDS
204
frameshift no
known variant Reference ID: rs121917883
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC033

known as potential disease variant: rs7632 (probable pathogenic for Short stature due to growth hormone secretagogue receptor deficiency|Inborn genetic diseases) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM061011)

known disease mutation at this position, please check HGMD for details (HGMD ID CM061011)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061011)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.340.924
6.0971
(flanking)6.0971
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained6540.69mu: GTTTGAGGTGCGCTC TTGA|ggtg
Donor gained6500.31mu: CCGAGTTTGAGGTGC GAGT|ttga
distance from splice site 186
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      204WDTNECRPTEFAVRSGLLTVMVWV
mutated  not conserved    204WDTNECRPTEFEVRSGLLTVMVW
Ptroglodytes  all identical  ENSPTRG00000015630  204WDTNECRPTEFAVRSGLLTVMVW
Mmulatta  all identical  ENSMMUG00000004194  204WDTNECRPTEFAVRSGLLTVMVW
Fcatus  all identical  ENSFCAG00000011266  155RDTNECRATEFAVRSGLLTVMVW
Mmusculus  all identical  ENSMUSG00000051136  203RDTNECRATEFAVRSGLLTVMVW
Ggallus  all identical  ENSGALG00000009187  184EYAIRSGLLTIMVW
Trubripes  all identical  ENSTRUG00000012927  220WPLEAVDTRECRMTQYAV
Drerio  all identical  ENSDARG00000056230  198WDTNECKATEYAIRSGLLT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023610  204LDTNECKATEYAIKSGLLTIMVW
protein features
start (aa)end (aa)featuredetails 
184211TOPO_DOMExtracellular (Potential).lost
212235TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
236263TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
264285TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
286302TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
303326TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
327366TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1101 / 1101
position (AA) of stopcodon in wt / mu AA sequence 367 / 367
position of stopcodon in wt / mu cDNA 1144 / 1144
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 44 / 44
chromosome 3
strand -1
last intron/exon boundary 840
theoretical NMD boundary in CDS 746
length of CDS 1101
coding sequence (CDS) position 611
cDNA position
(for ins/del: last normal base / first normal base)
654
gDNA position
(for ins/del: last normal base / first normal base)
654
chromosomal position
(for ins/del: last normal base / first normal base)
172165593
original gDNA sequence snippet GTGCCGCCCCACCGAGTTTGCGGTGCGCTCTGGACTGCTCA
altered gDNA sequence snippet GTGCCGCCCCACCGAGTTTGAGGTGCGCTCTGGACTGCTCA
original cDNA sequence snippet GTGCCGCCCCACCGAGTTTGCGGTGCGCTCTGGACTGCTCA
altered cDNA sequence snippet GTGCCGCCCCACCGAGTTTGAGGTGCGCTCTGGACTGCTCA
wildtype AA sequence MWNATPSEEP GFNLTLADLD WDASPGNDSL GDELLQLFPA PLLAGVTATC VALFVVGIAG
NLLTMLVVSR FRELRTTTNL YLSSMAFSDL LIFLCMPLDL VRLWQYRPWN FGDLLCKLFQ
FVSESCTYAT VLTITALSVE RYFAICFPLR AKVVVTKGRV KLVIFVIWAV AFCSAGPIFV
LVGVEHENGT DPWDTNECRP TEFAVRSGLL TVMVWVSSIF FFLPVFCLTV LYSLIGRKLW
RRRRGDAVVG ASLRDQNHKQ TVKMLAVVVF AFILCWLPFH VGRYLFSKSF EPGSLEIAQI
SQYCNLVSFV LFYLSAAINP ILYNIMSKKY RVAVFRLLGF EPFSQRKLST LKDESSRAWT
ESSINT*
mutated AA sequence MWNATPSEEP GFNLTLADLD WDASPGNDSL GDELLQLFPA PLLAGVTATC VALFVVGIAG
NLLTMLVVSR FRELRTTTNL YLSSMAFSDL LIFLCMPLDL VRLWQYRPWN FGDLLCKLFQ
FVSESCTYAT VLTITALSVE RYFAICFPLR AKVVVTKGRV KLVIFVIWAV AFCSAGPIFV
LVGVEHENGT DPWDTNECRP TEFEVRSGLL TVMVWVSSIF FFLPVFCLTV LYSLIGRKLW
RRRRGDAVVG ASLRDQNHKQ TVKMLAVVVF AFILCWLPFH VGRYLFSKSF EPGSLEIAQI
SQYCNLVSFV LFYLSAAINP ILYNIMSKKY RVAVFRLLGF EPFSQRKLST LKDESSRAWT
ESSINT*
speed 1.45 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: 0.999999999972726      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs7632 (probable pathogenic)
  • known disease mutation at this position (HGMD CM061011)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:172165593G>TN/A show variant in all transcripts   IGV
HGNC symbol GHSR
Ensembl transcript ID ENST00000427970
Genbank transcript ID NM_004122
UniProt peptide Q92847
alteration type single base exchange
alteration region CDS
DNA changes c.611C>A
cDNA.653C>A
g.654C>A
AA changes A204E Score: 107 explain score(s)
position(s) of altered AA
if AA alteration in CDS
204
frameshift no
known variant Reference ID: rs121917883
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC033

known as potential disease variant: rs7632 (probable pathogenic for Short stature due to growth hormone secretagogue receptor deficiency|Inborn genetic diseases) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM061011)

known disease mutation at this position, please check HGMD for details (HGMD ID CM061011)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061011)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.340.924
6.0971
(flanking)6.0971
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained6540.69mu: GTTTGAGGTGCGCTC TTGA|ggtg
Donor gained6500.31mu: CCGAGTTTGAGGTGC GAGT|ttga
distance from splice site 260
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      204WDTNECRPTEFAVRSGLLTVMVWV
mutated  not conserved    204WDTNECRPTEFEVRSGLLTVMVW
Ptroglodytes  all identical  ENSPTRG00000015630  204WDTNECRPTEFAVRSGLLTVMVW
Mmulatta  all identical  ENSMMUG00000004194  204WDTNECRPTEFAVRSGLLTVMVW
Fcatus  all identical  ENSFCAG00000011266  155RDTNECRATEFAVRSGLLTVMVW
Mmusculus  all identical  ENSMUSG00000051136  203RDTNECRATEFAVRSGLLTVMVW
Ggallus  all identical  ENSGALG00000009187  184EYAIRSGLLTIMVW
Trubripes  all identical  ENSTRUG00000012927  220WPLEAVDTRECRMTQYAV
Drerio  all identical  ENSDARG00000056230  198WDTNECKATEYAIRSGLLT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023610  204LDTNECKATEYAIKSGLLTIMVW
protein features
start (aa)end (aa)featuredetails 
184211TOPO_DOMExtracellular (Potential).lost
212235TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
236263TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
264285TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
286302TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
303326TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
327366TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 870 / 870
position (AA) of stopcodon in wt / mu AA sequence 290 / 290
position of stopcodon in wt / mu cDNA 912 / 912
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 43 / 43
chromosome 3
strand -1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 870
coding sequence (CDS) position 611
cDNA position
(for ins/del: last normal base / first normal base)
653
gDNA position
(for ins/del: last normal base / first normal base)
654
chromosomal position
(for ins/del: last normal base / first normal base)
172165593
original gDNA sequence snippet GTGCCGCCCCACCGAGTTTGCGGTGCGCTCTGGACTGCTCA
altered gDNA sequence snippet GTGCCGCCCCACCGAGTTTGAGGTGCGCTCTGGACTGCTCA
original cDNA sequence snippet GTGCCGCCCCACCGAGTTTGCGGTGCGCTCTGGACTGCTCA
altered cDNA sequence snippet GTGCCGCCCCACCGAGTTTGAGGTGCGCTCTGGACTGCTCA
wildtype AA sequence MWNATPSEEP GFNLTLADLD WDASPGNDSL GDELLQLFPA PLLAGVTATC VALFVVGIAG
NLLTMLVVSR FRELRTTTNL YLSSMAFSDL LIFLCMPLDL VRLWQYRPWN FGDLLCKLFQ
FVSESCTYAT VLTITALSVE RYFAICFPLR AKVVVTKGRV KLVIFVIWAV AFCSAGPIFV
LVGVEHENGT DPWDTNECRP TEFAVRSGLL TVMVWVSSIF FFLPVFCLTV LYSLIGRKLW
RRRRGDAVVG ASLRDQNHKQ TVKMLGGSQR ALRLSLAGPI LSLCLLPSL*
mutated AA sequence MWNATPSEEP GFNLTLADLD WDASPGNDSL GDELLQLFPA PLLAGVTATC VALFVVGIAG
NLLTMLVVSR FRELRTTTNL YLSSMAFSDL LIFLCMPLDL VRLWQYRPWN FGDLLCKLFQ
FVSESCTYAT VLTITALSVE RYFAICFPLR AKVVVTKGRV KLVIFVIWAV AFCSAGPIFV
LVGVEHENGT DPWDTNECRP TEFEVRSGLL TVMVWVSSIF FFLPVFCLTV LYSLIGRKLW
RRRRGDAVVG ASLRDQNHKQ TVKMLGGSQR ALRLSLAGPI LSLCLLPSL*
speed 1.44 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