Yum, tasty mutations...

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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000374375
Querying Taster for transcript #2: ENST00000374369
Querying Taster for transcript #3: ENST00000374372
MT speed 0 s - this script 3.90021 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GDF5disease_causing_automatic0.999999998228993simple_aae0P436Tsingle base exchangers121909351show file
GDF5disease_causing_automatic0.999999998228993simple_aae0P436Tsingle base exchangers121909351show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998228993 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM085445)
  • known disease mutation: rs8394 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:34021907G>TN/A show variant in all transcripts   IGV
HGNC symbol GDF5
Ensembl transcript ID ENST00000374369
Genbank transcript ID NM_000557
UniProt peptide P43026
alteration type single base exchange
alteration region CDS
DNA changes c.1306C>A
cDNA.1621C>A
g.20662C>A
AA changes P436T Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 436
frameshift no
known variant Reference ID: rs121909351
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8394 (pathogenic for Fibular hypoplasia and complex brachydactyly) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085445)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085445)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085445)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6531
5.6531
(flanking)1.6231
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 675
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      436EAFHCEGLCEFPLRSHLEPTNHAV
mutated  not conserved    436EAFHCEGLCEFTLRSHLEPTNHA
Ptroglodytes  all identical  ENSPTRG00000013439  436EAFHCEGLCEFPLRSHLEPTNHA
Mmulatta  all identical  ENSMMUG00000007333  434EAFHCEGLCEFPLRSHLEPTNHA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038259  430EAFHCEGLCEFPLRSHLEPTNHA
Ggallus  all identical  ENSGALG00000001786  435EAYHCEGLCEFPLRSHLEPTNHA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000002760  409EAFHCDGVCDFPIRSHLEPTNHA
Dmelanogaster  all identical  FBgn0000490  523DAYYCHGKCPFPLADHFNSTNHA
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021223  431EAYHCEGLCEFPLRSHLEPTNHA
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1506 / 1506
position (AA) of stopcodon in wt / mu AA sequence 502 / 502
position of stopcodon in wt / mu cDNA 1821 / 1821
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 316 / 316
chromosome 20
strand -1
last intron/exon boundary 947
theoretical NMD boundary in CDS 581
length of CDS 1506
coding sequence (CDS) position 1306
cDNA position
(for ins/del: last normal base / first normal base)		 1621
gDNA position
(for ins/del: last normal base / first normal base)		 20662
chromosomal position
(for ins/del: last normal base / first normal base)		 34021907
original gDNA sequence snippet GCGAGGGGCTGTGCGAGTTCCCATTGCGCTCCCACCTGGAG
altered gDNA sequence snippet GCGAGGGGCTGTGCGAGTTCACATTGCGCTCCCACCTGGAG
original cDNA sequence snippet GCGAGGGGCTGTGCGAGTTCCCATTGCGCTCCCACCTGGAG
altered cDNA sequence snippet GCGAGGGGCTGTGCGAGTTCACATTGCGCTCCCACCTGGAG
wildtype AA sequence MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
mutated AA sequence MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFTLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
speed 1.09 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: 0.999999998228993 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM085445)
  • known disease mutation: rs8394 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:34021907G>TN/A show variant in all transcripts   IGV
HGNC symbol GDF5
Ensembl transcript ID ENST00000374372
Genbank transcript ID N/A
UniProt peptide P43026
alteration type single base exchange
alteration region CDS
DNA changes c.1306C>A
cDNA.1810C>A
g.20662C>A
AA changes P436T Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 436
frameshift no
known variant Reference ID: rs121909351
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8394 (pathogenic for Fibular hypoplasia and complex brachydactyly) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085445)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085445)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085445)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6531
5.6531
(flanking)1.6231
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 675
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      436EAFHCEGLCEFPLRSHLEPTNHAV
mutated  not conserved    436EAFHCEGLCEFTLRSHLEPTNHA
Ptroglodytes  all identical  ENSPTRG00000013439  436EAFHCEGLCEFPLRSHLEPTNHA
Mmulatta  all identical  ENSMMUG00000007333  434EAFHCEGLCEFPLRSHLEPTNHA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038259  430EAFHCEGLCEFPLRSHLEPTNHA
Ggallus  all identical  ENSGALG00000001786  435EAYHCEGLCEFPLRSHLEPTNHA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000002760  409EAFHCDGVCDFPIRSHLEPTNHA
Dmelanogaster  all identical  FBgn0000490  523DAYYCHGKCPFPLADHFNSTNHA
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021223  431EAYHCEGLCEFPLRSHLEPTNHA
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1506 / 1506
position (AA) of stopcodon in wt / mu AA sequence 502 / 502
position of stopcodon in wt / mu cDNA 2010 / 2010
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 505 / 505
chromosome 20
strand -1
last intron/exon boundary 1136
theoretical NMD boundary in CDS 581
length of CDS 1506
coding sequence (CDS) position 1306
cDNA position
(for ins/del: last normal base / first normal base)		 1810
gDNA position
(for ins/del: last normal base / first normal base)		 20662
chromosomal position
(for ins/del: last normal base / first normal base)		 34021907
original gDNA sequence snippet GCGAGGGGCTGTGCGAGTTCCCATTGCGCTCCCACCTGGAG
altered gDNA sequence snippet GCGAGGGGCTGTGCGAGTTCACATTGCGCTCCCACCTGGAG
original cDNA sequence snippet GCGAGGGGCTGTGCGAGTTCCCATTGCGCTCCCACCTGGAG
altered cDNA sequence snippet GCGAGGGGCTGTGCGAGTTCACATTGCGCTCCCACCTGGAG
wildtype AA sequence MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
mutated AA sequence MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFTLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
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
back to results table

Problems

data problem

back to results table