Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999672573 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM125426)
  • known disease mutation: rs25281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34649046A>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.545A>T
cDNA.816A>T
g.10917A>T
AA changes E182V Score: 121 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 182
frameshift no
known variant Reference ID: rs111033841
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs25281 (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 CM125426)
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)5.8551
4.8361
(flanking)1.4751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased10915wt: 0.9947 / mu: 0.9949 (marginal change - not scored)wt: CTCTTTGAGACGTCC
mu: CTCTTTGTGACGTCC		 CTTT|gaga
Acc gained109270.36mu: AACCTCTTTGTGACGTCCTTTCCCTACTCCATGGGCTGGCA cttt|CCCT
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      182KKLLTKYDNLFETSFPYSMGWHGA
mutated  not conserved    182FVTSFPYSMGWHG
Ptroglodytes  all identical  ENSPTRG00000020886  291KKLLTKYDNLFETSFPYSMGWHG
Mmulatta  all identical  ENSMMUG00000020789  291KKLLTKYDNLFETSFPYSMGWHG
Fcatus  all identical  ENSFCAG00000016304  291KKLLTKYDNLFETSFPYSMGWHG
Mmusculus  all identical  ENSMUSG00000036073  272KKLLTKYDNLFETSFPYSMGWHG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  276KRLLTKYDNLFEVSFPYSMGWHG
Drerio  all identical  ENSDARG00000069543  276KRLLTKYDNLFEVSFPYSMGWHG
Dmelanogaster  all conserved  FBgn0263200  270KELTTKYDNLFQCSFPYSMGWHG
Celegans  all identical  ZK1058.3  272RSLLIKYDNVFECSFPYMMGWSG
Xtropicalis  all identical  ENSXETG00000013206  254KRLLSKYDNLFEI
protein features
start (aa)end (aa)featuredetails 
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 545
cDNA position
(for ins/del: last normal base / first normal base)		 816
gDNA position
(for ins/del: last normal base / first normal base)		 10917
chromosomal position
(for ins/del: last normal base / first normal base)		 34649046
original gDNA sequence snippet CAAGTATGACAACCTCTTTGAGACGTCCTTTCCCTACTCCA
altered gDNA sequence snippet CAAGTATGACAACCTCTTTGTGACGTCCTTTCCCTACTCCA
original cDNA sequence snippet CAAGTATGACAACCTCTTTGAGACGTCCTTTCCCTACTCCA
altered cDNA sequence snippet CAAGTATGACAACCTCTTTGTGACGTCCTTTCCCTACTCCA
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
FVTSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
speed 1.00 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