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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000378842
Querying Taster for transcript #2: ENST00000450095
MT speed 0 s - this script 4.379615 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GALTdisease_causing0.999999975881096simple_aaeE271Gsingle base exchangers111033765show file
GALTdisease_causing0.999999975881096simple_aaeE162Gsingle base exchangers111033765show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999975881096      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs25267 (probable pathogenic)
  • known disease mutation at this position (HGMD CM074209)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648883A>GN/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.812A>G
cDNA.854A>G
g.10754A>G
AA changes E271G Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 271
frameshift no
known variant Reference ID: rs111033765
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs25267 (probable pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not specified|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074209)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074209)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074209)
regulatory features H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5481
4.5911
(flanking)1.5861
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 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      271HVRRLPELTPAERDDLASIMKKLL
mutated  not conserved    271HVRRLPELTPAGRDDLASIMKKL
Ptroglodytes  all identical  ENSPTRG00000020886  271HVRRLPELTPAERDDLASIMKKL
Mmulatta  all identical  ENSMMUG00000020789  271HVQRLPELTPAERDDLASIMKKL
Fcatus  all identical  ENSFCAG00000016304  271HVRRLPELTPAERDDLACIMKKL
Mmusculus  all identical  ENSMUSG00000036073  252VRRLPELNPAERDDLASIMKKL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  256RITELTAEERKGLADIMKRL
Drerio  all identical  ENSDARG00000069543  256RLPDLTTQERDSLASIMKRL
Dmelanogaster  all conserved  FBgn0263200  250INDLTAEQRYNLALTIKEL
Celegans  all identical  ZK1058.3  252LGEVEKQSLSEILRSL
Xtropicalis  not conserved  ENSXETG00000013206  235QLR-LQDLSQRRAPGLASIMKRL
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 812
cDNA position
(for ins/del: last normal base / first normal base)		 854
gDNA position
(for ins/del: last normal base / first normal base)		 10754
chromosomal position
(for ins/del: last normal base / first normal base)		 34648883
original gDNA sequence snippet ACCTGAGCTGACCCCTGCTGAGCGTGATGGTCAGTCTCCCA
altered gDNA sequence snippet ACCTGAGCTGACCCCTGCTGGGCGTGATGGTCAGTCTCCCA
original cDNA sequence snippet ACCTGAGCTGACCCCTGCTGAGCGTGATGATCTAGCCTCCA
altered cDNA sequence snippet ACCTGAGCTGACCCCTGCTGGGCGTGATGATCTAGCCTCCA
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 GRDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 1.21 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: 0.999999975881096      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs25267 (probable pathogenic)
  • known disease mutation at this position (HGMD CM074209)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648883A>GN/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.485A>G
cDNA.756A>G
g.10754A>G
AA changes E162G Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 162
frameshift no
known variant Reference ID: rs111033765
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs25267 (probable pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not specified|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074209)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074209)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074209)
regulatory features H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5481
4.5911
(flanking)1.5861
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 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      162HVRRLPELTPAERDDLASIMKKLL
mutated  not conserved    162HVRRLPELTPAGRDDLASIMKKL
Ptroglodytes  all identical  ENSPTRG00000020886  271HVRRLPELTPAERDDLASIMKKL
Mmulatta  all identical  ENSMMUG00000020789  271HVQRLPELTPAERDDLASIMKKL
Fcatus  all identical  ENSFCAG00000016304  271HVRRLPELTPAERDDLACIMKKL
Mmusculus  all identical  ENSMUSG00000036073  252HVRRLPELNPAERDDLASIMKKL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  256HILRITELTAEERKGLADIMKRL
Drerio  all identical  ENSDARG00000069543  256HVLRLPDLTTQERDSLASIMKRL
Dmelanogaster  all conserved  FBgn0263200  250NNKRINDLTAEQRYNLALTIKEL
Celegans  all identical  ZK1058.3  252HVERFTDLGEVEKQSLSEILRSL
Xtropicalis  not conserved  ENSXETG00000013206  234QLR-LQDLSQRRAPGLASIMKRL
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 485
cDNA position
(for ins/del: last normal base / first normal base)		 756
gDNA position
(for ins/del: last normal base / first normal base)		 10754
chromosomal position
(for ins/del: last normal base / first normal base)		 34648883
original gDNA sequence snippet ACCTGAGCTGACCCCTGCTGAGCGTGATGGTCAGTCTCCCA
altered gDNA sequence snippet ACCTGAGCTGACCCCTGCTGGGCGTGATGGTCAGTCTCCCA
original cDNA sequence snippet ACCTGAGCTGACCCCTGCTGAGCGTGATGATCTAGCCTCCA
altered cDNA sequence snippet ACCTGAGCTGACCCCTGCTGGGCGTGATGATCTAGCCTCCA
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 AGRDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
speed 1.22 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