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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000576910
Querying Taster for transcript #2: ENST00000393456
Querying Taster for transcript #3: ENST00000415811
Querying Taster for transcript #4: ENST00000575949
Querying Taster for transcript #5: ENST00000225567
Querying Taster for transcript #6: ENST00000439730
MT speed 4.78 s - this script 5.164503 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GOSR2polymorphism_automatic0.00209928034486895simple_aaeaffectedR67Ksingle base exchangers197922show file
GOSR2polymorphism_automatic0.00209928034486895simple_aaeaffectedR67Ksingle base exchangers197922show file
GOSR2polymorphism_automatic0.00209928034486895simple_aaeaffectedR67Ksingle base exchangers197922show file
GOSR2polymorphism_automatic0.00209928034486895simple_aaeaffectedR67Ksingle base exchangers197922show file
GOSR2polymorphism_automatic0.00209928034486895simple_aaeaffectedR67Ksingle base exchangers197922show file
GOSR2polymorphism_automatic0.00209928034486895simple_aaeaffectedR67Ksingle base exchangers197922show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.997900719655131 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM091892)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:45008570G>AN/A show variant in all transcripts   IGV
HGNC symbol GOSR2
Ensembl transcript ID ENST00000576910
Genbank transcript ID N/A
UniProt peptide O14653
alteration type single base exchange
alteration region CDS
DNA changes c.200G>A
cDNA.276G>A
g.8088G>A
AA changes R67K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 67
frameshift no
known variant Reference ID: rs197922
databasehomozygous (A/A)heterozygousallele carriers
1000G31810971415
ExAC75061775525261

known disease mutation at this position, please check HGMD for details (HGMD ID CM091892)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.251
2.7131
(flanking)2.0761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost8090sequence motif lost- wt: GACT|gtaa
 mu: AACT.gtaa
Donor increased8083wt: 0.41 / mu: 0.95wt: CAAAATGCCAGACTG
mu: CAAAATGCCAAACTG		 AAAT|gcca
Donor marginally decreased8090wt: 0.9750 / mu: 0.9713 (marginal change - not scored)wt: CCAGACTGTAAGTGC
mu: CCAAACTGTAAGTGC		 AGAC|tgta
Donor increased8091wt: 0.34 / mu: 0.61wt: CAGACTGTAAGTGCT
mu: CAAACTGTAAGTGCT		 GACT|gtaa
Donor gained80840.78mu: AAAATGCCAAACTGT AATG|ccaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      67SKEPPNKRQNARLRVDQLKYDVQH
mutated  all conserved    67NKRQNAKLRVDQLKYDVQ
Ptroglodytes  all conserved  ENSPTRG00000009323  67NKRQNAKLRVDQLKYDVQ
Mmulatta  all conserved  ENSMMUG00000018689  67NKRQNAKLRVDQLKYDVQ
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000020946  67NRRQNAKLRVDQLKYDVQ
Ggallus  all conserved  ENSGALG00000001107  67NKRQNAKLRVDQLKYDVQ
Trubripes  all conserved  ENSTRUG00000014249  67NRRQNAKLRVDQLKYDVQ
Drerio  all conserved  ENSDARG00000053070  67NRRQNAKLRVDQLKYDVQ
Dmelanogaster  all conserved  FBgn0260856  67SQRQSSKLRVDQLKYDLR
Celegans  all identical  B0272.2  68PARRQAARMRVDQLRADVH
Xtropicalis  all conserved  ENSXETG00000014258  67SKRQNAKLRVDQLKYDVQ
protein features
start (aa)end (aa)featuredetails 
1190TOPO_DOMCytoplasmic (Potential).lost
61107COILEDPotential.lost
106106CONFLICTS -> C (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
113113CONFLICTD -> G (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
117119STRANDmight get lost (downstream of altered splice site)
166166CONFLICTL -> P (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
191211TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
212212TOPO_DOMVesicular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 498 / 498
position (AA) of stopcodon in wt / mu AA sequence 166 / 166
position of stopcodon in wt / mu cDNA 574 / 574
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 77 / 77
chromosome 17
strand 1
last intron/exon boundary 413
theoretical NMD boundary in CDS 286
length of CDS 498
coding sequence (CDS) position 200
cDNA position
(for ins/del: last normal base / first normal base)		 276
gDNA position
(for ins/del: last normal base / first normal base)		 8088
chromosomal position
(for ins/del: last normal base / first normal base)		 45008570
original gDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTGTAAGTGCTGACCTCTG
altered gDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTGTAAGTGCTGACCTCTG
original cDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTTCGGGTTGACCAGTTAA
altered cDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTTCGGGTTGACCAGTTAA
wildtype AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNARLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNGTQKKILD
IANMLGLSNT VMRLIEKRAF QDKYFMIGGM LLTCVVMFLV VQYLT*
mutated AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNAKLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNGTQKKILD
IANMLGLSNT VMRLIEKRAF QDKYFMIGGM LLTCVVMFLV VQYLT*
speed 0.79 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: 0.997900719655131 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM091892)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:45008570G>AN/A show variant in all transcripts   IGV
HGNC symbol GOSR2
Ensembl transcript ID ENST00000393456
Genbank transcript ID NM_004287
UniProt peptide O14653
alteration type single base exchange
alteration region CDS
DNA changes c.200G>A
cDNA.257G>A
g.8088G>A
AA changes R67K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 67
frameshift no
known variant Reference ID: rs197922
databasehomozygous (A/A)heterozygousallele carriers
1000G31810971415
ExAC75061775525261

known disease mutation at this position, please check HGMD for details (HGMD ID CM091892)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.251
2.7131
(flanking)2.0761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost8090sequence motif lost- wt: GACT|gtaa
 mu: AACT.gtaa
Donor increased8083wt: 0.41 / mu: 0.95wt: CAAAATGCCAGACTG
mu: CAAAATGCCAAACTG		 AAAT|gcca
Donor marginally decreased8090wt: 0.9750 / mu: 0.9713 (marginal change - not scored)wt: CCAGACTGTAAGTGC
mu: CCAAACTGTAAGTGC		 AGAC|tgta
Donor increased8091wt: 0.34 / mu: 0.61wt: CAGACTGTAAGTGCT
mu: CAAACTGTAAGTGCT		 GACT|gtaa
Donor gained80840.78mu: AAAATGCCAAACTGT AATG|ccaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      67SKEPPNKRQNARLRVDQLKYDVQH
mutated  all conserved    67NKRQNAKLRVDQLKYDVQ
Ptroglodytes  all conserved  ENSPTRG00000009323  67NKRQNAKLRVDQLKYDVQ
Mmulatta  all conserved  ENSMMUG00000018689  67NKRQNAKLRVDQLKYDVQ
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000020946  67NRRQNAKLRVDQLKYDVQ
Ggallus  all conserved  ENSGALG00000001107  67NKRQNAKLRVDQLKYDVQ
Trubripes  all conserved  ENSTRUG00000014249  67NRRQNAKLRVDQLKYDVQ
Drerio  all conserved  ENSDARG00000053070  67NRRQNAKLRVDQLKYDVQ
Dmelanogaster  all conserved  FBgn0260856  67SQRQSSKLRVDQLKYDLR
Celegans  all identical  B0272.2  68PARRQAARMRVDQLRADVH
Xtropicalis  all conserved  ENSXETG00000014258  67SKRQNAKLRVDQLKYDVQ
protein features
start (aa)end (aa)featuredetails 
1190TOPO_DOMCytoplasmic (Potential).lost
61107COILEDPotential.lost
106106CONFLICTS -> C (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
113113CONFLICTD -> G (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
117119STRANDmight get lost (downstream of altered splice site)
166166CONFLICTL -> P (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
191211TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
212212TOPO_DOMVesicular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 639 / 639
position (AA) of stopcodon in wt / mu AA sequence 213 / 213
position of stopcodon in wt / mu cDNA 696 / 696
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 58 / 58
chromosome 17
strand 1
last intron/exon boundary 535
theoretical NMD boundary in CDS 427
length of CDS 639
coding sequence (CDS) position 200
cDNA position
(for ins/del: last normal base / first normal base)		 257
gDNA position
(for ins/del: last normal base / first normal base)		 8088
chromosomal position
(for ins/del: last normal base / first normal base)		 45008570
original gDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTGTAAGTGCTGACCTCTG
altered gDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTGTAAGTGCTGACCTCTG
original cDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTTCGGGTTGACCAGTTAA
altered cDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTTCGGGTTGACCAGTTAA
wildtype AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNARLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKG TQKKILDIAN MLGLSNTVMR
LIEKRAFQDK YFMIGGMLLT CVVMFLVVQY LT*
mutated AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNAKLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKG TQKKILDIAN MLGLSNTVMR
LIEKRAFQDK YFMIGGMLLT CVVMFLVVQY LT*
speed 0.87 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: 0.997900719655131 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM091892)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:45008570G>AN/A show variant in all transcripts   IGV
HGNC symbol GOSR2
Ensembl transcript ID ENST00000415811
Genbank transcript ID NM_001012511
UniProt peptide O14653
alteration type single base exchange
alteration region CDS
DNA changes c.200G>A
cDNA.255G>A
g.8088G>A
AA changes R67K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 67
frameshift no
known variant Reference ID: rs197922
databasehomozygous (A/A)heterozygousallele carriers
1000G31810971415
ExAC75061775525261

known disease mutation at this position, please check HGMD for details (HGMD ID CM091892)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.251
2.7131
(flanking)2.0761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost8090sequence motif lost- wt: GACT|gtaa
 mu: AACT.gtaa
Donor increased8083wt: 0.41 / mu: 0.95wt: CAAAATGCCAGACTG
mu: CAAAATGCCAAACTG		 AAAT|gcca
Donor marginally decreased8090wt: 0.9750 / mu: 0.9713 (marginal change - not scored)wt: CCAGACTGTAAGTGC
mu: CCAAACTGTAAGTGC		 AGAC|tgta
Donor increased8091wt: 0.34 / mu: 0.61wt: CAGACTGTAAGTGCT
mu: CAAACTGTAAGTGCT		 GACT|gtaa
Donor gained80840.78mu: AAAATGCCAAACTGT AATG|ccaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      67SKEPPNKRQNARLRVDQLKYDVQH
mutated  all conserved    67NKRQNAKLRVDQLKYDVQ
Ptroglodytes  all conserved  ENSPTRG00000009323  67NKRQNAKLRVDQLKYDVQ
Mmulatta  all conserved  ENSMMUG00000018689  67NKRQNAKLRVDQLKYDVQ
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000020946  67NRRQNAKLRVDQLKYDVQ
Ggallus  all conserved  ENSGALG00000001107  67NKRQNAKLRVDQLKYDVQ
Trubripes  all conserved  ENSTRUG00000014249  67NRRQNAKLRVDQLKYDVQ
Drerio  all conserved  ENSDARG00000053070  67NRRQNAKLRVDQLKYDVQ
Dmelanogaster  all conserved  FBgn0260856  67SQRQSSKLRVDQLKYDLR
Celegans  all identical  B0272.2  68PARRQAARMRVDQLRADVH
Xtropicalis  all conserved  ENSXETG00000014258  67SKRQNAKLRVDQLKYDVQ
protein features
start (aa)end (aa)featuredetails 
1190TOPO_DOMCytoplasmic (Potential).lost
61107COILEDPotential.lost
106106CONFLICTS -> C (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
113113CONFLICTD -> G (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
117119STRANDmight get lost (downstream of altered splice site)
166166CONFLICTL -> P (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
191211TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
212212TOPO_DOMVesicular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 588 / 588
position (AA) of stopcodon in wt / mu AA sequence 196 / 196
position of stopcodon in wt / mu cDNA 643 / 643
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 56 / 56
chromosome 17
strand 1
last intron/exon boundary 392
theoretical NMD boundary in CDS 286
length of CDS 588
coding sequence (CDS) position 200
cDNA position
(for ins/del: last normal base / first normal base)		 255
gDNA position
(for ins/del: last normal base / first normal base)		 8088
chromosomal position
(for ins/del: last normal base / first normal base)		 45008570
original gDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTGTAAGTGCTGACCTCTG
altered gDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTGTAAGTGCTGACCTCTG
original cDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTTCGGGTTGACCAGTTAA
altered cDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTTCGGGTTGACCAGTTAA
wildtype AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNARLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKV GSLLGDREKA SCFSLIQQFS
NCVYILITCP QIVIF*
mutated AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNAKLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKV GSLLGDREKA SCFSLIQQFS
NCVYILITCP QIVIF*
speed 0.47 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: 0.997900719655131 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM091892)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:45008570G>AN/A show variant in all transcripts   IGV
HGNC symbol GOSR2
Ensembl transcript ID ENST00000575949
Genbank transcript ID N/A
UniProt peptide O14653
alteration type single base exchange
alteration region CDS
DNA changes c.200G>A
cDNA.240G>A
g.8088G>A
AA changes R67K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 67
frameshift no
known variant Reference ID: rs197922
databasehomozygous (A/A)heterozygousallele carriers
1000G31810971415
ExAC75061775525261

known disease mutation at this position, please check HGMD for details (HGMD ID CM091892)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.251
2.7131
(flanking)2.0761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost8090sequence motif lost- wt: GACT|gtaa
 mu: AACT.gtaa
Donor increased8083wt: 0.41 / mu: 0.95wt: CAAAATGCCAGACTG
mu: CAAAATGCCAAACTG		 AAAT|gcca
Donor marginally decreased8090wt: 0.9750 / mu: 0.9713 (marginal change - not scored)wt: CCAGACTGTAAGTGC
mu: CCAAACTGTAAGTGC		 AGAC|tgta
Donor increased8091wt: 0.34 / mu: 0.61wt: CAGACTGTAAGTGCT
mu: CAAACTGTAAGTGCT		 GACT|gtaa
Donor gained80840.78mu: AAAATGCCAAACTGT AATG|ccaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      67SKEPPNKRQNARLRVDQLKYDVQH
mutated  all conserved    67NKRQNAKLRVDQLKYDVQ
Ptroglodytes  all conserved  ENSPTRG00000009323  67NKRQNAKLRVDQLKYDVQ
Mmulatta  all conserved  ENSMMUG00000018689  67NKRQNAKLRVDQLKYDVQ
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000020946  67NRRQNAKLRVDQLKYDVQ
Ggallus  all conserved  ENSGALG00000001107  67NKRQNAKLRVDQLKYDVQ
Trubripes  all conserved  ENSTRUG00000014249  67NRRQNAKLRVDQLKYDVQ
Drerio  all conserved  ENSDARG00000053070  67NRRQNAKLRVDQLKYDVQ
Dmelanogaster  all conserved  FBgn0260856  67SQRQSSKLRVDQLKYDLR
Celegans  all identical  B0272.2  68PARRQAARMRVDQLRADVH
Xtropicalis  all conserved  ENSXETG00000014258  67SKRQNAKLRVDQLKYDVQ
protein features
start (aa)end (aa)featuredetails 
1190TOPO_DOMCytoplasmic (Potential).lost
61107COILEDPotential.lost
106106CONFLICTS -> C (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
113113CONFLICTD -> G (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
117119STRANDmight get lost (downstream of altered splice site)
166166CONFLICTL -> P (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
191211TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
212212TOPO_DOMVesicular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 432 / 432
position (AA) of stopcodon in wt / mu AA sequence 144 / 144
position of stopcodon in wt / mu cDNA 472 / 472
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 41 / 41
chromosome 17
strand 1
last intron/exon boundary 244
theoretical NMD boundary in CDS 153
length of CDS 432
coding sequence (CDS) position 200
cDNA position
(for ins/del: last normal base / first normal base)		 240
gDNA position
(for ins/del: last normal base / first normal base)		 8088
chromosomal position
(for ins/del: last normal base / first normal base)		 45008570
original gDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTGTAAGTGCTGACCTCTG
altered gDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTGTAAGTGCTGACCTCTG
original cDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTTCGGGTTGACCAGTTAA
altered cDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTTCGGGTTGACCAGTTAA
wildtype AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNARLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNVSQARGEG
RPALDRSWGL EFRSLSAICF GGV*
mutated AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNAKLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNVSQARGEG
RPALDRSWGL EFRSLSAICF GGV*
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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.997900719655131 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM091892)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:45008570G>AN/A show variant in all transcripts   IGV
HGNC symbol GOSR2
Ensembl transcript ID ENST00000225567
Genbank transcript ID NM_054022
UniProt peptide O14653
alteration type single base exchange
alteration region CDS
DNA changes c.200G>A
cDNA.231G>A
g.8088G>A
AA changes R67K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 67
frameshift no
known variant Reference ID: rs197922
databasehomozygous (A/A)heterozygousallele carriers
1000G31810971415
ExAC75061775525261

known disease mutation at this position, please check HGMD for details (HGMD ID CM091892)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.251
2.7131
(flanking)2.0761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost8090sequence motif lost- wt: GACT|gtaa
 mu: AACT.gtaa
Donor increased8083wt: 0.41 / mu: 0.95wt: CAAAATGCCAGACTG
mu: CAAAATGCCAAACTG		 AAAT|gcca
Donor marginally decreased8090wt: 0.9750 / mu: 0.9713 (marginal change - not scored)wt: CCAGACTGTAAGTGC
mu: CCAAACTGTAAGTGC		 AGAC|tgta
Donor increased8091wt: 0.34 / mu: 0.61wt: CAGACTGTAAGTGCT
mu: CAAACTGTAAGTGCT		 GACT|gtaa
Donor gained80840.78mu: AAAATGCCAAACTGT AATG|ccaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      67SKEPPNKRQNARLRVDQLKYDVQH
mutated  all conserved    67NKRQNAKLRVDQLKYDVQ
Ptroglodytes  all conserved  ENSPTRG00000009323  67NKRQNAKLRVDQLKYDVQ
Mmulatta  all conserved  ENSMMUG00000018689  67NKRQNAKLRVDQLKYDVQ
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000020946  67NRRQNAKLRVDQLKYDVQ
Ggallus  all conserved  ENSGALG00000001107  67NKRQNAKLRVDQLKYDVQ
Trubripes  all conserved  ENSTRUG00000014249  67NRRQNAKLRVDQLKYDVQ
Drerio  all conserved  ENSDARG00000053070  67NRRQNAKLRVDQLKYDVQ
Dmelanogaster  all conserved  FBgn0260856  67SQRQSSKLRVDQLKYDLR
Celegans  all identical  B0272.2  68PARRQAARMRVDQLRADVH
Xtropicalis  all conserved  ENSXETG00000014258  67SKRQNAKLRVDQLKYDVQ
protein features
start (aa)end (aa)featuredetails 
1190TOPO_DOMCytoplasmic (Potential).lost
61107COILEDPotential.lost
106106CONFLICTS -> C (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
113113CONFLICTD -> G (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
117119STRANDmight get lost (downstream of altered splice site)
166166CONFLICTL -> P (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
191211TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
212212TOPO_DOMVesicular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 642 / 642
position (AA) of stopcodon in wt / mu AA sequence 214 / 214
position of stopcodon in wt / mu cDNA 673 / 673
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 32 / 32
chromosome 17
strand 1
last intron/exon boundary 615
theoretical NMD boundary in CDS 533
length of CDS 642
coding sequence (CDS) position 200
cDNA position
(for ins/del: last normal base / first normal base)		 231
gDNA position
(for ins/del: last normal base / first normal base)		 8088
chromosomal position
(for ins/del: last normal base / first normal base)		 45008570
original gDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTGTAAGTGCTGACCTCTG
altered gDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTGTAAGTGCTGACCTCTG
original cDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTTCGGGTTGACCAGTTAA
altered cDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTTCGGGTTGACCAGTTAA
wildtype AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNARLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKG TQKKILDIAN MLGLSNTVMR
LIEKRAFQDK YFMIGTQGSC QTAHFGGRSA GSS*
mutated AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNAKLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKG TQKKILDIAN MLGLSNTVMR
LIEKRAFQDK YFMIGTQGSC QTAHFGGRSA GSS*
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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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.997900719655131 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM091892)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:45008570G>AN/A show variant in all transcripts   IGV
HGNC symbol GOSR2
Ensembl transcript ID ENST00000439730
Genbank transcript ID N/A
UniProt peptide O14653
alteration type single base exchange
alteration region CDS
DNA changes c.200G>A
cDNA.260G>A
g.8088G>A
AA changes R67K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 67
frameshift no
known variant Reference ID: rs197922
databasehomozygous (A/A)heterozygousallele carriers
1000G31810971415
ExAC75061775525261

known disease mutation at this position, please check HGMD for details (HGMD ID CM091892)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.251
2.7131
(flanking)2.0761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost8090sequence motif lost- wt: GACT|gtaa
 mu: AACT.gtaa
Donor increased8083wt: 0.41 / mu: 0.95wt: CAAAATGCCAGACTG
mu: CAAAATGCCAAACTG		 AAAT|gcca
Donor marginally decreased8090wt: 0.9750 / mu: 0.9713 (marginal change - not scored)wt: CCAGACTGTAAGTGC
mu: CCAAACTGTAAGTGC		 AGAC|tgta
Donor increased8091wt: 0.34 / mu: 0.61wt: CAGACTGTAAGTGCT
mu: CAAACTGTAAGTGCT		 GACT|gtaa
Donor gained80840.78mu: AAAATGCCAAACTGT AATG|ccaa
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      67SKEPPNKRQNARLRVDQLKYDVQH
mutated  all conserved    67NKRQNAKLRVDQLKYDVQ
Ptroglodytes  all conserved  ENSPTRG00000009323  67NKRQNAKLRVDQLKYDVQ
Mmulatta  all conserved  ENSMMUG00000018689  67NKRQNAKLRVDQLKYDVQ
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000020946  67NRRQNAKLRVDQLKYDVQ
Ggallus  all conserved  ENSGALG00000001107  67NKRQNAKLRVDQLKYDVQ
Trubripes  all conserved  ENSTRUG00000014249  67NRRQNAKLRVDQLKYDVQ
Drerio  all conserved  ENSDARG00000053070  67NRRQNAKLRVDQLKYDVQ
Dmelanogaster  all conserved  FBgn0260856  67SQRQSSKLRVDQLKYDLR
Celegans  all identical  B0272.2  68PARRQAARMRVDQLRADVH
Xtropicalis  all conserved  ENSXETG00000014258  67SKRQNAKLRVDQLKYDVQ
protein features
start (aa)end (aa)featuredetails 
1190TOPO_DOMCytoplasmic (Potential).lost
61107COILEDPotential.lost
106106CONFLICTS -> C (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
113113CONFLICTD -> G (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
117119STRANDmight get lost (downstream of altered splice site)
166166CONFLICTL -> P (in Ref. 1; AAB82651).might get lost (downstream of altered splice site)
191211TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
212212TOPO_DOMVesicular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 699 / 699
position (AA) of stopcodon in wt / mu AA sequence 233 / 233
position of stopcodon in wt / mu cDNA 759 / 759
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 61 / 61
chromosome 17
strand 1
last intron/exon boundary 809
theoretical NMD boundary in CDS 698
length of CDS 699
coding sequence (CDS) position 200
cDNA position
(for ins/del: last normal base / first normal base)		 260
gDNA position
(for ins/del: last normal base / first normal base)		 8088
chromosomal position
(for ins/del: last normal base / first normal base)		 45008570
original gDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTGTAAGTGCTGACCTCTG
altered gDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTGTAAGTGCTGACCTCTG
original cDNA sequence snippet TAACAAAAGGCAAAATGCCAGACTTCGGGTTGACCAGTTAA
altered cDNA sequence snippet TAACAAAAGGCAAAATGCCAAACTTCGGGTTGACCAGTTAA
wildtype AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNARLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKG TQKKILDIAN MLGLSNTVMR
LIEKRAFQDK YFMIETRSHH VAQNGPELLS SRDPPASASR SAGIIEFSEK IT*
mutated AA sequence MDPLFQQTHK QVHEIQSCMG RLETADKQSV HIVENEIQAS IDQIFSRLER LEILSSKEPP
NKRQNAKLRV DQLKYDVQHL QTALRNFQHR RHAREQQERQ REELLSRTFT TNDSDTTIPM
DESLQFNSSL QKVHNGMDDL ILDGHNILDG LRTQRLTLKG TQKKILDIAN MLGLSNTVMR
LIEKRAFQDK YFMIETRSHH VAQNGPELLS SRDPPASASR SAGIIEFSEK IT*
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

Problems