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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 4.01 s - this script 7.92163 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GALTdisease_causing_automatic0.999999999734514simple_aae0A320Tsingle base exchangers111033795show file
GALTdisease_causing_automatic0.999999999734514simple_aae0A211Tsingle base exchangers111033795show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999734514 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012764)
  • known disease mutation at this position (HGMD CM950557)
  • known disease mutation: rs25298 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34649460G>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.958G>A
cDNA.1000G>A
g.11331G>A
AA changes A320T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
320
frameshift no
known variant Reference ID: rs111033795
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs25298 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0570.997
5.6731
(flanking)5.6731
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 54
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      320AGANWNHWQLHAHYYPPLLRSATV
mutated  not conserved    320AGANWNHWQLHTHYYPPLLRSAT
Ptroglodytes  all identical  ENSPTRG00000020886  320AGANWDHWQLHAHYYPPLLRSAT
Mmulatta  all identical  ENSMMUG00000020789  320AGANWDHWQLHAHYYPPLLRSAT
Fcatus  all identical  ENSFCAG00000016304  320AGANWDHWQLHAHYYPPLLRSAT
Mmusculus  all identical  ENSMUSG00000036073  301TGATCDHWQLHAHYYPPLLRSAT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  305LKEDHSHWQLHAHY
Drerio  all identical  ENSDARG00000069543  305LNKNMSHWQLHAHY
Dmelanogaster  all identical  FBgn0263200  299AHASSAHWTLHAIY
Celegans  not conserved  ZK1058.3  301LTENCSFWQLHLSFFPPL
Xtropicalis  all identical  ENSXETG00000013206  283SHWQLHAHFYPPLLRSAT
protein features no protein features affected
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 958
cDNA position
(for ins/del: last normal base / first normal base)
1000
gDNA position
(for ins/del: last normal base / first normal base)
11331
chromosomal position
(for ins/del: last normal base / first normal base)
34649460
original gDNA sequence snippet GGAACCATTGGCAGCTGCACGCTCATTACTACCCTCCGCTC
altered gDNA sequence snippet GGAACCATTGGCAGCTGCACACTCATTACTACCCTCCGCTC
original cDNA sequence snippet GGAACCATTGGCAGCTGCACGCTCATTACTACCCTCCGCTC
altered cDNA sequence snippet GGAACCATTGGCAGCTGCACACTCATTACTACCCTCCGCTC
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 PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHT HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 2.07 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: 0.999999999734514 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012764)
  • known disease mutation at this position (HGMD CM950557)
  • known disease mutation: rs25298 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34649460G>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 CDS
DNA changes c.631G>A
cDNA.902G>A
g.11331G>A
AA changes A211T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
211
frameshift no
known variant Reference ID: rs111033795
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs25298 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012764)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950557)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0570.997
5.6731
(flanking)5.6731
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 54
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      211AGANWNHWQLHAHYYPPLLRSATV
mutated  not conserved    211AGANWNHWQLHTHYYPPLLRSAT
Ptroglodytes  all identical  ENSPTRG00000020886  320AGANWDHWQLHAHYYPPLLRSAT
Mmulatta  all identical  ENSMMUG00000020789  320AGANWDHWQLHAHYYPPLLRSAT
Fcatus  all identical  ENSFCAG00000016304  320AGANWDHWQLHAHYYPPLLRSAT
Mmusculus  all identical  ENSMUSG00000036073  301TGATCDHWQLHAHYYPPLLRSAT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  305LKEDHSHWQLHAHYYPPLLRSAT
Drerio  all identical  ENSDARG00000069543  305LNKNMSHWQLHAHYYPPLLRSAN
Dmelanogaster  all identical  FBgn0263200  299AHASSAHWTLHAIYYPPLLRSAS
Celegans  not conserved  ZK1058.3  301LTENCSFWQLHLSFFPPLLRSAT
Xtropicalis  all identical  ENSXETG00000013206  283LGEDCSHWQLHAHFYPPLLRSAT
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 1084 / 1084
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 631
cDNA position
(for ins/del: last normal base / first normal base)
902
gDNA position
(for ins/del: last normal base / first normal base)
11331
chromosomal position
(for ins/del: last normal base / first normal base)
34649460
original gDNA sequence snippet GGAACCATTGGCAGCTGCACGCTCATTACTACCCTCCGCTC
altered gDNA sequence snippet GGAACCATTGGCAGCTGCACACTCATTACTACCCTCCGCTC
original cDNA sequence snippet GGAACCATTGGCAGCTGCACGCTCATTACTACCCTCCGCTC
altered cDNA sequence snippet GGAACCATTGGCAGCTGCACACTCATTACTACCCTCCGCTC
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 MTLSTLCVLG PSEPTESKVM CFHPWSDVTL PLMSVPEIRA VVDAWASVTE ELGAQYPWVQ
IFENKGAMMG CSNPHPHCQV WASSFLPDIA QREERSQQAY KSQHGEPLLM EYSRQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH THYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
speed 1.94 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