Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999990038292      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs37357 (probable pathogenic)
  • known disease mutation at this position (HGMD CM990640)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34647845C>TN/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.67C>T
cDNA.338C>T
g.9716C>T
AA changes H23Y Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 23
frameshift no
known variant Reference ID: rs111033688
Allele 'T' was neither found in ExAC nor 1000G.
known as potential disease variant: rs37357 (probable 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 CM990640)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990640)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990640)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-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
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
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)3.4741
5.0611
(flanking)4.1961
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased9722wt: 0.27 / mu: 0.35wt: AGGTCATGTGCTTCCACCCCTGGTCGGATGTAACGCTGCCA
mu: AGGTCATGTGCTTCTACCCCTGGTCGGATGTAACGCTGCCA		 ccct|GGTC
Acc increased9720wt: 0.79 / mu: 0.88wt: TAAGGTCATGTGCTTCCACCCCTGGTCGGATGTAACGCTGC
mu: TAAGGTCATGTGCTTCTACCCCTGGTCGGATGTAACGCTGC		 accc|CTGG
Acc marginally increased9727wt: 0.2553 / mu: 0.3292 (marginal change - not scored)wt: ATGTGCTTCCACCCCTGGTCGGATGTAACGCTGCCACTCAT
mu: ATGTGCTTCTACCCCTGGTCGGATGTAACGCTGCCACTCAT		 gtcg|GATG
Acc gained97240.37mu: GTCATGTGCTTCTACCCCTGGTCGGATGTAACGCTGCCACT ctgg|TCGG
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      23SEPTESKVMCFHPWSDVTLPLMSV
mutated  all conserved    23SEPTESKVMCFYPWSDVTLPLMS
Ptroglodytes  all identical  ENSPTRG00000020886  132KVMCFHPWSDVTLPLMS
Mmulatta  all identical  ENSMMUG00000020789  132KVMCFHPWSDVTLPLMS
Fcatus  all identical  ENSFCAG00000016304  132KVMCFHPWSDVTLPLMS
Mmusculus  all identical  ENSMUSG00000036073  113KVMCFHPWSDVTLPLMS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  117KVMCFHPWSDVTLPLMK
Drerio  all identical  ENSDARG00000069543  117KVMCFHPWSDITLPLMQ
Dmelanogaster  all identical  FBgn0263200  111RVMCFHPKSNLTLPTMS
Celegans  all identical  ZK1058.3  113KVICYHPNSQLTLATMD
Xtropicalis  no alignment  ENSXETG00000013206  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 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 67
cDNA position
(for ins/del: last normal base / first normal base)		 338
gDNA position
(for ins/del: last normal base / first normal base)		 9716
chromosomal position
(for ins/del: last normal base / first normal base)		 34647845
original gDNA sequence snippet CCAGTAAGGTCATGTGCTTCCACCCCTGGTCGGATGTAACG
altered gDNA sequence snippet CCAGTAAGGTCATGTGCTTCTACCCCTGGTCGGATGTAACG
original cDNA sequence snippet AGAGTAAGGTCATGTGCTTCCACCCCTGGTCGGATGTAACG
altered cDNA sequence snippet AGAGTAAGGTCATGTGCTTCTACCCCTGGTCGGATGTAACG
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 CFYPWSDVTL PLMSVPEIRA VVDAWASVTE ELGAQYPWVQ
IFENKGAMMG CSNPHPHCQV WASSFLPDIA QREERSQQAY KSQHGEPLLM EYSRQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
speed 0.95 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