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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 0 s - this script 4.088217 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GALTdisease_causing_automatic0.999948293202923simple_aaeaffected0I32Nsingle base exchangers111033644show file
GALTdisease_causing_automatic1without_aaeaffected0single base exchangers111033644show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999948293202923 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970609)
  • known disease mutation: rs25123 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34647098T>AN/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.95T>A
cDNA.137T>A
g.8969T>A
AA changes I32N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 32
frameshift no
known variant Reference ID: rs111033644
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs25123 (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 CM970609)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970609)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970609)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-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
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6571
4.8791
(flanking)-0.3230.934
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased8971wt: 0.75 / mu: 0.86wt: ATATCCGCTACAACC
mu: ATAACCGCTACAACC		 ATCC|gcta
Donor increased8963wt: 0.69 / mu: 0.81wt: CCATCAGCATATCCG
mu: CCATCAGCATAACCG		 ATCA|gcat
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      32AATFRANDHQHIRYNPLQDEWVLV
mutated  not conserved    32AATFRANDHQHNRYNPLQDEWVL
Ptroglodytes  all identical  ENSPTRG00000020886  32AATFRANDHQHIRYNPLQDEWVL
Mmulatta  all identical  ENSMMUG00000020789  32AATFRASDHQHIRYNPLQDEWVL
Fcatus  all identical  ENSFCAG00000016304  32ATAFRASEHQHIRYNPLQDEWVL
Mmusculus  all identical  ENSMUSG00000036073  13AATFRASEHQHIRYNPLQDEWVL
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000016445  17SFDPKEHQHLRYNPLRDTWVL
Drerio  all conserved  ENSDARG00000069543  17TFDPKEHQHLRYNPLRDSWVL
Dmelanogaster  not conserved  FBgn0263200  11FVASEHPHRRLNPLNGQWVL
Celegans  no alignment  ZK1058.3  n/a
Xtropicalis  all identical  ENSXETG00000013206  7EHQHIRYNPLRDDWLL
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 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 95
cDNA position
(for ins/del: last normal base / first normal base)		 137
gDNA position
(for ins/del: last normal base / first normal base)		 8969
chromosomal position
(for ins/del: last normal base / first normal base)		 34647098
original gDNA sequence snippet GCCCCCAGACCATCAGCATATCCGCTACAACCCGCTGCAGG
altered gDNA sequence snippet GCCCCCAGACCATCAGCATAACCGCTACAACCCGCTGCAGG
original cDNA sequence snippet GGCAAACGACCATCAGCATATCCGCTACAACCCGCTGCAGG
altered cDNA sequence snippet GGCAAACGACCATCAGCATAACCGCTACAACCCGCTGCAGG
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 HNRYNPLQDE 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*
speed 1.04 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 CM970609)
  • known disease mutation: rs25123 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34647098T>AN/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 5'UTR
DNA changes cDNA.164T>A
g.8969T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs111033644
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs25123 (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 CM970609)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970609)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970609)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-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
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6571
4.8791
(flanking)-0.3230.934
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -37) | splice site change before start ATG (at aa -35) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased8971wt: 0.75 / mu: 0.86wt: ATATCCGCTACAACC
mu: ATAACCGCTACAACC		 ATCC|gcta
Donor increased8963wt: 0.69 / mu: 0.81wt: CCATCAGCATATCCG
mu: CCATCAGCATAACCG		 ATCA|gcat
distance from splice site 13
Kozak consensus sequence altered? no
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)		 164
gDNA position
(for ins/del: last normal base / first normal base)		 8969
chromosomal position
(for ins/del: last normal base / first normal base)		 34647098
original gDNA sequence snippet GCCCCCAGACCATCAGCATATCCGCTACAACCCGCTGCAGG
altered gDNA sequence snippet GCCCCCAGACCATCAGCATAACCGCTACAACCCGCTGCAGG
original cDNA sequence snippet GGCAAACGACCATCAGCATATCCGCTACAACCCGCTGCAGG
altered cDNA sequence snippet GGCAAACGACCATCAGCATAACCGCTACAACCCGCTGCAGG
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 1.01 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

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