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 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 3.870913 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GDF5disease_causing_automatic0.99997642364062simple_aaeaffected0L373Rsingle base exchangers121909349show file
GDF5disease_causing_automatic0.99997642364062simple_aaeaffected0L373Rsingle base exchangers121909349show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99997642364062 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM081282)
  • known disease mutation: rs8392 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:34022095A>CN/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.1118T>G
cDNA.1433T>G
g.20474T>G
AA changes L373R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 373
frameshift no
known variant Reference ID: rs121909349
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs8392 (pathogenic for Symphalangism, proximal, 1B) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081282)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081282)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081282)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4251
3.9951
(flanking)0.8631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased20474wt: 0.52 / mu: 0.62wt: GTACCTGTTCAGCCA
mu: GTACCGGTTCAGCCA		 ACCT|gttc
distance from splice site 487
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      373SGQDDKTVYEYLFSQRRKRRAPLA
mutated  not conserved    373SGQDDKTVYEYRFSQRRKRRAPL
Ptroglodytes  all identical  ENSPTRG00000013439  373SGQDDKTVYEYLFSQRRKRRAPL
Mmulatta  all identical  ENSMMUG00000007333  371SGQDDKTVYEYLFSQRRKRRAPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038259  367SGQDDKTVYEYLFSQRRKRRAPL
Ggallus  all identical  ENSGALG00000001786  372SGQDDKTVYEYLFNQRRKRRAPL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000002760  348SGHDNKTVYEYLFTQRRMRRAPL
Dmelanogaster  not conserved  FBgn0000490  465SIRDVSGGEGGGKGGRNKRQPRR
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021223  368SGQDDKTVYEYLFNQRRKRRAPL
protein features
start (aa)end (aa)featuredetails 
28381PROPEPPotential. /FTId=PRO_0000033912.lost
384384CONFLICTL -> S (in Ref. 2; AAA57007).might get lost (downstream of altered splice site)
399403STRANDmight get lost (downstream of altered splice site)
400400DISULFIDmight get lost (downstream of altered splice site)
406408STRANDmight get lost (downstream of altered splice site)
410412HELIXmight get lost (downstream of altered splice site)
414416HELIXmight get lost (downstream of altered splice site)
418420STRANDmight get lost (downstream of altered splice site)
422425STRANDmight get lost (downstream of altered splice site)
428432STRANDmight get lost (downstream of altered splice site)
429429DISULFIDmight get lost (downstream of altered splice site)
433433DISULFIDmight get lost (downstream of altered splice site)
439441HELIXmight get lost (downstream of altered splice site)
445456HELIXmight get lost (downstream of altered splice site)
458460TURNmight get lost (downstream of altered splice site)
465465DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
465465DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
466466DISULFIDmight get lost (downstream of altered splice site)
466479STRANDmight get lost (downstream of altered splice site)
481483STRANDmight get lost (downstream of altered splice site)
485500STRANDmight get lost (downstream of altered splice site)
498498DISULFIDmight get lost (downstream of altered splice site)
500500DISULFIDmight get lost (downstream of altered splice site)
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 1118
cDNA position
(for ins/del: last normal base / first normal base)		 1433
gDNA position
(for ins/del: last normal base / first normal base)		 20474
chromosomal position
(for ins/del: last normal base / first normal base)		 34022095
original gDNA sequence snippet TAAGACCGTGTATGAGTACCTGTTCAGCCAGCGGCGAAAAC
altered gDNA sequence snippet TAAGACCGTGTATGAGTACCGGTTCAGCCAGCGGCGAAAAC
original cDNA sequence snippet TAAGACCGTGTATGAGTACCTGTTCAGCCAGCGGCGAAAAC
altered cDNA sequence snippet TAAGACCGTGTATGAGTACCGGTTCAGCCAGCGGCGAAAAC
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 EYRFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
speed 0.72 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: 0.99997642364062 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM081282)
  • known disease mutation: rs8392 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:34022095A>CN/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.1118T>G
cDNA.1622T>G
g.20474T>G
AA changes L373R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 373
frameshift no
known variant Reference ID: rs121909349
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs8392 (pathogenic for Symphalangism, proximal, 1B) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081282)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081282)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081282)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4251
3.9951
(flanking)0.8631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased20474wt: 0.52 / mu: 0.62wt: GTACCTGTTCAGCCA
mu: GTACCGGTTCAGCCA		 ACCT|gttc
distance from splice site 487
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      373SGQDDKTVYEYLFSQRRKRRAPLA
mutated  not conserved    373SGQDDKTVYEYRFSQRRKRRAPL
Ptroglodytes  all identical  ENSPTRG00000013439  373SGQDDKTVYEYLFSQRRKRRAPL
Mmulatta  all identical  ENSMMUG00000007333  371SGQDDKTVYEYLFSQRRKRRAPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038259  367SGQDDKTVYEYLFSQRRKRRAPL
Ggallus  all identical  ENSGALG00000001786  372SGQDDKTVYEYLFNQRRKRRAPL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000002760  348SGHDNKTVYEYLFTQRRMRRAPL
Dmelanogaster  not conserved  FBgn0000490  465SIRDVSGGEGGGKGGRNKRQPRR
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021223  368SGQDDKTVYEYLFNQRRKRRAPL
protein features
start (aa)end (aa)featuredetails 
28381PROPEPPotential. /FTId=PRO_0000033912.lost
384384CONFLICTL -> S (in Ref. 2; AAA57007).might get lost (downstream of altered splice site)
399403STRANDmight get lost (downstream of altered splice site)
400400DISULFIDmight get lost (downstream of altered splice site)
406408STRANDmight get lost (downstream of altered splice site)
410412HELIXmight get lost (downstream of altered splice site)
414416HELIXmight get lost (downstream of altered splice site)
418420STRANDmight get lost (downstream of altered splice site)
422425STRANDmight get lost (downstream of altered splice site)
428432STRANDmight get lost (downstream of altered splice site)
429429DISULFIDmight get lost (downstream of altered splice site)
433433DISULFIDmight get lost (downstream of altered splice site)
439441HELIXmight get lost (downstream of altered splice site)
445456HELIXmight get lost (downstream of altered splice site)
458460TURNmight get lost (downstream of altered splice site)
465465DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
465465DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
466466DISULFIDmight get lost (downstream of altered splice site)
466479STRANDmight get lost (downstream of altered splice site)
481483STRANDmight get lost (downstream of altered splice site)
485500STRANDmight get lost (downstream of altered splice site)
498498DISULFIDmight get lost (downstream of altered splice site)
500500DISULFIDmight get lost (downstream of altered splice site)
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 1118
cDNA position
(for ins/del: last normal base / first normal base)		 1622
gDNA position
(for ins/del: last normal base / first normal base)		 20474
chromosomal position
(for ins/del: last normal base / first normal base)		 34022095
original gDNA sequence snippet TAAGACCGTGTATGAGTACCTGTTCAGCCAGCGGCGAAAAC
altered gDNA sequence snippet TAAGACCGTGTATGAGTACCGGTTCAGCCAGCGGCGAAAAC
original cDNA sequence snippet TAAGACCGTGTATGAGTACCTGTTCAGCCAGCGGCGAAAAC
altered cDNA sequence snippet TAAGACCGTGTATGAGTACCGGTTCAGCCAGCGGCGAAAAC
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 EYRFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
speed 0.78 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