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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: ENST00000378842
Querying Taster for transcript #2: ENST00000450095
MT speed 2.8 s - this script 5.39599 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GALTdisease_causing_automatic0.999999976717223simple_aaeaffected0F117Ssingle base exchangers111033679show file
GALTdisease_causing_automatic1without_aaeaffected0single base exchangers111033679show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999976717223 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990633)
  • known disease mutation: rs25160 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34647675T>CN/A show variant in all transcripts   IGV
HGNC symbol GALT
Ensembl transcript ID ENST00000378842
Genbank transcript ID NM_000155
UniProt peptide P07902
alteration type single base exchange
alteration region CDS
DNA changes c.350T>C
cDNA.392T>C
g.9546T>C
AA changes F117S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS
117
frameshift no
known variant Reference ID: rs111033679
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs25160 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)
regulatory features H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0061
4.5331
(flanking)0.6421
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased9547wt: 0.6134 / mu: 0.6412 (marginal change - not scored)wt: CCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAGG
mu: CCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAGG
 tttc|CAAG
Donor marginally increased9550wt: 0.9990 / mu: 0.9991 (marginal change - not scored)wt: TTCCAAGCAAAGTCT
mu: TCCCAAGCAAAGTCT
 CCAA|gcaa
Donor increased9545wt: 0.53 / mu: 0.79wt: CCCTTTTCCAAGCAA
mu: CCCTTTCCCAAGCAA
 CTTT|tcca
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      117APSPGPSDHPLFQAKSARGVCKVM
mutated  not conserved    117APSPGPSDHPLSQAK
Ptroglodytes  all identical  ENSPTRG00000020886  117APSPGPSDHPLFQAK
Mmulatta  all identical  ENSMMUG00000020789  117APSPGPSDHPLFQAK
Fcatus  all identical  ENSFCAG00000016304  117APSPGPSDHPLFKAE
Mmusculus  all identical  ENSMUSG00000036073  98APDPGPSDHPLFRAEAARGVCKV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  102APDPASDQHPLFQSKAARGVCKV
Drerio  all identical  ENSDARG00000069543  102APDPGSDHHPLFQSKAARGVCKV
Dmelanogaster  all identical  FBgn0263200  96VPVPPNNDDPLFQIAPARGNCRV
Celegans  all identical  ZK1058.3  97EECAGKDENDDLFKQHEVKGVCKV
Xtropicalis  all conserved  ENSXETG00000013206  92APVFAPG---LYKSKCP------
protein features
start (aa)end (aa)featuredetails 
184184METALZinc (Potential).might get lost (downstream of altered splice site)
186186ACT_SITETele-UMP-histidine intermediate (By similarity).might get lost (downstream of altered splice site)
202202METALIron (Potential).might get lost (downstream of altered splice site)
258259CONFLICTRR -> VG (in Ref. 1; AAC83409).might get lost (downstream of altered splice site)
301301METALIron (Potential).might get lost (downstream of altered splice site)
319319METALIron (Potential).might get lost (downstream of altered splice site)
321321METALIron (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1140 / 1140
position (AA) of stopcodon in wt / mu AA sequence 380 / 380
position of stopcodon in wt / mu cDNA 1182 / 1182
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 9
strand 1
last intron/exon boundary 1102
theoretical NMD boundary in CDS 1009
length of CDS 1140
coding sequence (CDS) position 350
cDNA position
(for ins/del: last normal base / first normal base)
392
gDNA position
(for ins/del: last normal base / first normal base)
9546
chromosomal position
(for ins/del: last normal base / first normal base)
34647675
original gDNA sequence snippet ACCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAG
altered gDNA sequence snippet ACCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAG
original cDNA sequence snippet ACCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAG
altered cDNA sequence snippet ACCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAG
wildtype AA sequence MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
mutated AA sequence MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLSQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 1.68 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM990633)
  • known disease mutation: rs25160 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34647675T>CN/A show variant in all transcripts   IGV
HGNC symbol GALT
Ensembl transcript ID ENST00000450095
Genbank transcript ID NM_001258332
UniProt peptide P07902
alteration type single base exchange
alteration region intron
DNA changes g.9546T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs111033679
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs25160 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)
regulatory features H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0061
4.5331
(flanking)0.6421
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased9547wt: 0.6134 / mu: 0.6412 (marginal change - not scored)wt: CCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAGG
mu: CCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAGG
 tttc|CAAG
Donor marginally increased9550wt: 0.9990 / mu: 0.9991 (marginal change - not scored)wt: TTCCAAGCAAAGTCT
mu: TCCCAAGCAAAGTCT
 CCAA|gcaa
Donor increased9545wt: 0.53 / mu: 0.79wt: CCCTTTTCCAAGCAA
mu: CCCTTTCCCAAGCAA
 CTTT|tcca
distance from splice site 154
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
7575METALZinc (Potential).might get lost (downstream of altered splice site)
184184METALZinc (Potential).might get lost (downstream of altered splice site)
186186ACT_SITETele-UMP-histidine intermediate (By similarity).might get lost (downstream of altered splice site)
202202METALIron (Potential).might get lost (downstream of altered splice site)
258259CONFLICTRR -> VG (in Ref. 1; AAC83409).might get lost (downstream of altered splice site)
301301METALIron (Potential).might get lost (downstream of altered splice site)
319319METALIron (Potential).might get lost (downstream of altered splice site)
321321METALIron (Potential).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 272 / 272
chromosome 9
strand 1
last intron/exon boundary 1004
theoretical NMD boundary in CDS 682
length of CDS 813
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
9546
chromosomal position
(for ins/del: last normal base / first normal base)
34647675
original gDNA sequence snippet ACCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAG
altered gDNA sequence snippet ACCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MTLSTLCVLG PSEPTESKVM CFHPWSDVTL PLMSVPEIRA VVDAWASVTE ELGAQYPWVQ
IFENKGAMMG CSNPHPHCQV WASSFLPDIA QREERSQQAY KSQHGEPLLM EYSRQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
mutated AA sequence N/A
speed 1.12 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