Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999984499      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs25124 (probable pathogenic)
  • known disease mutation at this position (HGMD CM065206)
  • known disease mutation at this position (HGMD CM151305)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34647101G>AN/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.98G>A
cDNA.140G>A
g.8972G>A
AA changes R33H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 33
frameshift no
known variant Reference ID: rs111033829
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs25124 (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 CM065206)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065206)
known disease mutation at this position, please check HGMD for details (HGMD ID CM151305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065206)
known disease mutation at this position, please check HGMD for details (HGMD ID CM151305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065206)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-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
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2020.998
5.9081
(flanking)0.311
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 increased8963wt: 0.6939 / mu: 0.7620 (marginal change - not scored)wt: CCATCAGCATATCCG
mu: CCATCAGCATATCCA		 ATCA|gcat
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      33ATFRANDHQHIRYNPLQDEWVLVS
mutated  not conserved    33ATFRANDHQHIHYNPLQDEWVLV
Ptroglodytes  all identical  ENSPTRG00000020886  33ATFRANDHQHIRYNPLQDEWVLV
Mmulatta  all identical  ENSMMUG00000020789  33ATFRASDHQHIRYNPLQDEWVLV
Fcatus  all identical  ENSFCAG00000016304  33TAFRASEHQHIRYNPLQDEWVLV
Mmusculus  all identical  ENSMUSG00000036073  14ATFRASEHQHIRYNPLQDEWVLV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  18SFDPKEHQHLRYNPLRDTWVLV
Drerio  all identical  ENSDARG00000069543  18TFDPKEHQHLRYNPLRDSWVLV
Dmelanogaster  all identical  FBgn0263200  12FVASEHPHRRLNPLNGQWVLV
Celegans  all identical  ZK1058.3  9RYNPLIDEWVIV
Xtropicalis  all identical  ENSXETG00000013206  8EHQHIRYNPLRDDWLLV
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 98
cDNA position
(for ins/del: last normal base / first normal base)		 140
gDNA position
(for ins/del: last normal base / first normal base)		 8972
chromosomal position
(for ins/del: last normal base / first normal base)		 34647101
original gDNA sequence snippet CCCAGACCATCAGCATATCCGCTACAACCCGCTGCAGGATG
altered gDNA sequence snippet CCCAGACCATCAGCATATCCACTACAACCCGCTGCAGGATG
original cDNA sequence snippet AAACGACCATCAGCATATCCGCTACAACCCGCTGCAGGATG
altered cDNA sequence snippet AAACGACCATCAGCATATCCACTACAACCCGCTGCAGGATG
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 HIHYNPLQDE 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*
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