Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.937043664172609 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:25876011G>AN/A show variant in all transcripts   IGV
HGNC symbol NUP58
Ensembl transcript ID ENST00000463407
Genbank transcript ID N/A
UniProt peptide Q9BVL2
alteration type single base exchange
alteration region CDS
DNA changes c.100G>A
cDNA.243G>A
g.350G>A
AA changes A34T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 34
frameshift no
known variant Reference ID: rs11556093
databasehomozygous (A/A)heterozygousallele carriers
1000G4319771408
ExAC14263424118504
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
Gabp, Transcription Factor, Gabp TF binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.7560
-0.0550.025
(flanking)3.010.373
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 increased340wt: 0.9377 / mu: 0.9441 (marginal change - not scored)wt: ACAGGCGGCGTTTTCTCCTTCGGAACGGGAGCGTCTAGGTA
mu: ACAGGCGGCGTTTTCTCCTTCGGAACGGGAACGTCTAGGTA		 cttc|GGAA
Acc marginally increased341wt: 0.9733 / mu: 0.9759 (marginal change - not scored)wt: CAGGCGGCGTTTTCTCCTTCGGAACGGGAGCGTCTAGGTAA
mu: CAGGCGGCGTTTTCTCCTTCGGAACGGGAACGTCTAGGTAA		 ttcg|GAAC
Acc marginally increased345wt: 0.8248 / mu: 0.8332 (marginal change - not scored)wt: CGGCGTTTTCTCCTTCGGAACGGGAGCGTCTAGGTAACCGC
mu: CGGCGTTTTCTCCTTCGGAACGGGAACGTCTAGGTAACCGC		 gaac|GGGA
Donor marginally increased346wt: 0.9438 / mu: 0.9969 (marginal change - not scored)wt: GGAACGGGAGCGTCT
mu: GGAACGGGAACGTCT		 AACG|ggag
Donor increased351wt: 0.41 / mu: 0.69wt: GGGAGCGTCTAGGTA
mu: GGGAACGTCTAGGTA		 GAGC|gtct
Donor gained3450.84mu: CGGAACGGGAACGTC GAAC|ggga
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      34STGGVFSFGTGASSNPSVGLNFGN
mutated  not conserved    34STGGVFSFGTGTSSNPSVGLNFG
Ptroglodytes  all identical  ENSPTRG00000005719  34STGGGFSFGTGASSNPSVGLNFG
Mmulatta  all identical  ENSMMUG00000018420  34GTGGGFSFGTGASSNPSVGLNFG
Fcatus  no alignment  ENSFCAG00000001580  n/a
Mmusculus  all identical  ENSMUSG00000063895  34GAGSGFSFGTVASSTPSVGLNFG
Ggallus  all identical  ENSGALG00000017111  34GGGGGFSFGTTAPSSTG-GLNFG
Trubripes  all identical  ENSTRUG00000001476  34-TGGGLSFGTAARATSSGGFSFG
Drerio  all identical  ENSDARG00000033965  33AGGGGFSFGA-ATSTPAAGTGGFSFG
Dmelanogaster  not conserved  FBgn0038722  26AATGAFAFGARPATTTAPPPSFG
Celegans  not conserved  Y54E5A.4  82STSSVPLFGSTTTTASPSGGLFGA
Xtropicalis  all identical  ENSXETG00000010681  34GAAAPFSFGGTPAASNTGTAGGLGFG
protein features
start (aa)end (aa)featuredetails 
7579REGION14 X 2 AA repeats of F-G.lost
3031REPEAT2.might get lost (downstream of altered splice site)
4445REPEAT3.might get lost (downstream of altered splice site)
6364REPEAT4.might get lost (downstream of altered splice site)
6869REPEAT5.might get lost (downstream of altered splice site)
256276COILEDPotential.might get lost (downstream of altered splice site)
314381COILEDPotential.might get lost (downstream of altered splice site)
488489REPEAT6.might get lost (downstream of altered splice site)
492493REPEAT7.might get lost (downstream of altered splice site)
513514REPEAT8.might get lost (downstream of altered splice site)
519520REPEAT9.might get lost (downstream of altered splice site)
529530REPEAT10.might get lost (downstream of altered splice site)
531532REPEAT11.might get lost (downstream of altered splice site)
545546REPEAT12.might get lost (downstream of altered splice site)
568569REPEAT13.might get lost (downstream of altered splice site)
578579REPEAT14.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1458 / 1458
position (AA) of stopcodon in wt / mu AA sequence 486 / 486
position of stopcodon in wt / mu cDNA 1601 / 1601
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 144 / 144
chromosome 13
strand 1
last intron/exon boundary 1377
theoretical NMD boundary in CDS 1183
length of CDS 1458
coding sequence (CDS) position 100
cDNA position
(for ins/del: last normal base / first normal base)		 243
gDNA position
(for ins/del: last normal base / first normal base)		 350
chromosomal position
(for ins/del: last normal base / first normal base)		 25876011
original gDNA sequence snippet TTTTCTCCTTCGGAACGGGAGCGTCTAGGTAACCGCACTTT
altered gDNA sequence snippet TTTTCTCCTTCGGAACGGGAACGTCTAGGTAACCGCACTTT
original cDNA sequence snippet TTTTCTCCTTCGGAACGGGAGCGTCTAGCAACCCTTCTGTG
altered cDNA sequence snippet TTTTCTCCTTCGGAACGGGAACGTCTAGCAACCCTTCTGTG
wildtype AA sequence MSTGFSFGSG TLGSTTVAAG GTSTGGVFSF GTGASSNPSV GLNFGNLGST STPATTSAPS
SGFGTGLFGS KPATGFTLGG TNTGIATTIT TGLTLGTPAT TSAATTGFSL GFNKPAASAT
PFALPITSTS ASGLTLSSAL TSTPAASTGF TLNNLGGTTA TTTTASTGLS LGGALAGLGG
SLFQSTNTGT SGLGQNALGL TLGTTAATST AGNEGLGGID FSSSSDKKSD KTGTRPEDSK
ALKDENLPPV ICQDVENLQK FVKEQKQVQE EISRMSSKAM LKVQEDIKAL KQLLSLAANG
IQRNTLNIDK LKIETAQELK NAEIALRTQK TPPGLQHEYA APADYFRILV QQFEVQLQQY
RQQIEELENH LATQANNSHI TPQDLSMAMQ KIYQTFVALA AQLQSIHENV KVLKEQYLGY
RKMFLGDAVD VFETRRAEAK KWQNTPRVTT GPTPFSTMPN AAAVAMAATL TQQQQPATGL
NAFKL*
mutated AA sequence MSTGFSFGSG TLGSTTVAAG GTSTGGVFSF GTGTSSNPSV GLNFGNLGST STPATTSAPS
SGFGTGLFGS KPATGFTLGG TNTGIATTIT TGLTLGTPAT TSAATTGFSL GFNKPAASAT
PFALPITSTS ASGLTLSSAL TSTPAASTGF TLNNLGGTTA TTTTASTGLS LGGALAGLGG
SLFQSTNTGT SGLGQNALGL TLGTTAATST AGNEGLGGID FSSSSDKKSD KTGTRPEDSK
ALKDENLPPV ICQDVENLQK FVKEQKQVQE EISRMSSKAM LKVQEDIKAL KQLLSLAANG
IQRNTLNIDK LKIETAQELK NAEIALRTQK TPPGLQHEYA APADYFRILV QQFEVQLQQY
RQQIEELENH LATQANNSHI TPQDLSMAMQ KIYQTFVALA AQLQSIHENV KVLKEQYLGY
RKMFLGDAVD VFETRRAEAK KWQNTPRVTT GPTPFSTMPN AAAVAMAATL TQQQQPATGL
NAFKL*
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