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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 4.366125 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GALTdisease_causing0.999999993035484simple_aaeaffectedL282Vsingle base exchangers111033772show file
GALTdisease_causing0.999999993035484simple_aaeaffectedL173Vsingle base exchangers111033772show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993035484      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs25276 (probable pathogenic)
  • known disease mutation at this position (HGMD CM990665)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34649018C>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.844C>G
cDNA.886C>G
g.10889C>G
AA changes L282V Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 282
frameshift no
known variant Reference ID: rs111033772
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs25276 (probable 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 CM990665)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990665)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990665)
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)0.9911
4.1961
(flanking)4.8360.999
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 increased10881wt: 0.2568 / mu: 0.3051 (marginal change - not scored)wt: TCCAGATCTAGCCTCCATCATGAAGAAGCTCTTGACCAAGT
mu: TCCAGATCTAGCCTCCATCATGAAGAAGGTCTTGACCAAGT		 tcat|GAAG
Donor gained108830.93mu: TCATGAAGAAGGTCT ATGA|agaa
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      282ERDDLASIMKKLLTKYDNLFETSF
mutated  all conserved    282ERDDLASIMKKVLTKYDNLFETS
Ptroglodytes  all identical  ENSPTRG00000020886  282ERDDLASIMKKLLTKYDNLFETS
Mmulatta  all identical  ENSMMUG00000020789  282ERDDLASIMKKLLTKYDNLFETS
Fcatus  all identical  ENSFCAG00000016304  282ERDDLACIMKKLLTKYDNLFETS
Mmusculus  all identical  ENSMUSG00000036073  263ERDDLASIMKKLLTKYDNLFETS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  267ERKGLADIMKRLLTKYDNLFEVS
Drerio  all identical  ENSDARG00000069543  267ERDSLASIMKRLLTKYDNLFEVS
Dmelanogaster  all identical  FBgn0263200  261QRYNLALTIKELTTKYDNLFQCS
Celegans  all identical  ZK1058.3  263EKQSLSEILRSLLIKYDNVFECS
Xtropicalis  all identical  ENSXETG00000013206  246RAPGLASIMKRLLSKYDNLFEIS
protein features
start (aa)end (aa)featuredetails 
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 844
cDNA position
(for ins/del: last normal base / first normal base)		 886
gDNA position
(for ins/del: last normal base / first normal base)		 10889
chromosomal position
(for ins/del: last normal base / first normal base)		 34649018
original gDNA sequence snippet TAGCCTCCATCATGAAGAAGCTCTTGACCAAGTATGACAAC
altered gDNA sequence snippet TAGCCTCCATCATGAAGAAGGTCTTGACCAAGTATGACAAC
original cDNA sequence snippet TAGCCTCCATCATGAAGAAGCTCTTGACCAAGTATGACAAC
altered cDNA sequence snippet TAGCCTCCATCATGAAGAAGGTCTTGACCAAGTATGACAAC
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 KVLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 1.17 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: 0.999999993035484      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs25276 (probable pathogenic)
  • known disease mutation at this position (HGMD CM990665)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34649018C>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.517C>G
cDNA.788C>G
g.10889C>G
AA changes L173V Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 173
frameshift no
known variant Reference ID: rs111033772
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs25276 (probable 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 CM990665)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990665)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990665)
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)0.9911
4.1961
(flanking)4.8360.999
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 increased10881wt: 0.2568 / mu: 0.3051 (marginal change - not scored)wt: TCCAGATCTAGCCTCCATCATGAAGAAGCTCTTGACCAAGT
mu: TCCAGATCTAGCCTCCATCATGAAGAAGGTCTTGACCAAGT		 tcat|GAAG
Donor gained108830.93mu: TCATGAAGAAGGTCT ATGA|agaa
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      173ERDDLASIMKKLLTKYDNLFETSF
mutated  all conserved    173ERDDLASIMKKVLTKYDNL
Ptroglodytes  all identical  ENSPTRG00000020886  282ERDDLASIMKKLLTKYDNLFETS
Mmulatta  all identical  ENSMMUG00000020789  282ERDDLASIMKKLLTKYDNLFETS
Fcatus  all identical  ENSFCAG00000016304  282ERDDLACIMKKLLTKYDNLFETS
Mmusculus  all identical  ENSMUSG00000036073  263ERDDLASIMKKLLTKYDNLFETS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  267ERKGLADIMKRLLTKYDNLFEVS
Drerio  all identical  ENSDARG00000069543  267ERDSLASIMKRLLTKYDNLFEVS
Dmelanogaster  all identical  FBgn0263200  261QRYNLALTIKELTTKYDNLFQCS
Celegans  all identical  ZK1058.3  263EKQSLSEILRSLLIKYDNVFECS
Xtropicalis  all identical  ENSXETG00000013206  245RAPGLASIMKRLLSKYDNLFEI
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 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 517
cDNA position
(for ins/del: last normal base / first normal base)		 788
gDNA position
(for ins/del: last normal base / first normal base)		 10889
chromosomal position
(for ins/del: last normal base / first normal base)		 34649018
original gDNA sequence snippet TAGCCTCCATCATGAAGAAGCTCTTGACCAAGTATGACAAC
altered gDNA sequence snippet TAGCCTCCATCATGAAGAAGGTCTTGACCAAGTATGACAAC
original cDNA sequence snippet TAGCCTCCATCATGAAGAAGCTCTTGACCAAGTATGACAAC
altered cDNA sequence snippet TAGCCTCCATCATGAAGAAGGTCTTGACCAAGTATGACAAC
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 KKVLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
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

Problems