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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 5.241499 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GALTdisease_causing_automatic0.999999994932066simple_aaeaffected0L108Psingle base exchangers111033741show file
GALTdisease_causing_automatic0.999999999630569simple_aaeaffected0L217Psingle base exchangers111033741show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999994932066 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990657)
  • known disease mutation: rs25236 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648416T>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 CDS
DNA changes c.323T>C
cDNA.594T>C
g.10287T>C
AA changes L108P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS
108
frameshift no
known variant Reference ID: rs111033741
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs25236 (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 CM990657)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990657)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990657)
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
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9531
3.5170.999
(flanking)0.7680.932
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased10291wt: 0.88 / mu: 0.98wt: CTGCTAATGGAGTAC
mu: CCGCTAATGGAGTAC
 GCTA|atgg
Donor increased10287wt: 0.50 / mu: 0.85wt: GCCCCTGCTAATGGA
mu: GCCCCCGCTAATGGA
 CCCT|gcta
distance from splice site 38
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      108QQAYKSQHGEPLLMEYSRQELLRK
mutated  not conserved    108QQAYKSQHGEPPLMEYSRQELLR
Ptroglodytes  all identical  ENSPTRG00000020886  217QQAYKSQHGEPLLMEYSRQELLR
Mmulatta  all identical  ENSMMUG00000020789  217QQTYKSQHGEPLLMEYSRQELLR
Fcatus  all identical  ENSFCAG00000016304  217QRAYQSQHGEPLLMEYGHQELLR
Mmusculus  all identical  ENSMUSG00000036073  198QQTYHSQHGKPLLLEYGHQELLR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  202QRAFHQKHGEPLLLQYAREEAAK
Drerio  all conserved  ENSDARG00000069543  202QRDFLQKHGEPMLVQYARMEAQA
Dmelanogaster  all conserved  FBgn0263200  196LRAYYATNERPMLADYVERELQR
Celegans  all conserved  ZK1058.3  198QKKHFEKHGKVMLMDYLEQETLK
Xtropicalis  no alignment  ENSXETG00000013206  n/a
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 323
cDNA position
(for ins/del: last normal base / first normal base)
594
gDNA position
(for ins/del: last normal base / first normal base)
10287
chromosomal position
(for ins/del: last normal base / first normal base)
34648416
original gDNA sequence snippet GAGTCAGCATGGAGAGCCCCTGCTAATGGAGTACAGCCGCC
altered gDNA sequence snippet GAGTCAGCATGGAGAGCCCCCGCTAATGGAGTACAGCCGCC
original cDNA sequence snippet GAGTCAGCATGGAGAGCCCCTGCTAATGGAGTACAGCCGCC
altered cDNA sequence snippet GAGTCAGCATGGAGAGCCCCCGCTAATGGAGTACAGCCGCC
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 KSQHGEPPLM EYSRQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
speed 1.70 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: 0.999999999630569 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990657)
  • known disease mutation: rs25236 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648416T>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.650T>C
cDNA.692T>C
g.10287T>C
AA changes L217P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS
217
frameshift no
known variant Reference ID: rs111033741
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs25236 (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 CM990657)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990657)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990657)
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
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9531
3.5170.999
(flanking)0.7680.932
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased10291wt: 0.88 / mu: 0.98wt: CTGCTAATGGAGTAC
mu: CCGCTAATGGAGTAC
 GCTA|atgg
Donor increased10287wt: 0.50 / mu: 0.85wt: GCCCCTGCTAATGGA
mu: GCCCCCGCTAATGGA
 CCCT|gcta
distance from splice site 38
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      217QQAYKSQHGEPLLMEYSRQELLRK
mutated  not conserved    217QQAYKSQHGEPPLMEYSRQELLR
Ptroglodytes  all identical  ENSPTRG00000020886  217QQAYKSQHGEPLLMEYSRQELLR
Mmulatta  all identical  ENSMMUG00000020789  217QQTYKSQHGEPLLMEYSRQELLR
Fcatus  all identical  ENSFCAG00000016304  217QRAYQSQHGEPLLMEYGHQELLR
Mmusculus  all identical  ENSMUSG00000036073  198QQTYHSQHGKPLLLEYGHQELLR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  202QRAFHQKHGEPLLLQYAREEAAK
Drerio  all conserved  ENSDARG00000069543  202QRDFLQKHGEPMLVQYARMEAQA
Dmelanogaster  all conserved  FBgn0263200  196LRAYYATNERPMLADYVERELQR
Celegans  all conserved  ZK1058.3  198KKHFEKHGKVMLMDYLEQETLK
Xtropicalis  all identical  ENSXETG00000013206  180PVLTPGLVIIKQMPLSLPLANAPVFT
protein features
start (aa)end (aa)featuredetails 
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 650
cDNA position
(for ins/del: last normal base / first normal base)
692
gDNA position
(for ins/del: last normal base / first normal base)
10287
chromosomal position
(for ins/del: last normal base / first normal base)
34648416
original gDNA sequence snippet GAGTCAGCATGGAGAGCCCCTGCTAATGGAGTACAGCCGCC
altered gDNA sequence snippet GAGTCAGCATGGAGAGCCCCCGCTAATGGAGTACAGCCGCC
original cDNA sequence snippet GAGTCAGCATGGAGAGCCCCTGCTAATGGAGTACAGCCGCC
altered cDNA sequence snippet GAGTCAGCATGGAGAGCCCCCGCTAATGGAGTACAGCCGCC
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 SQHGEPPLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 1.55 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