Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999988000592683 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM063843)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:20925154T>GN/A show variant in all transcripts   IGV
HGNC symbol APEX1
Ensembl transcript ID ENST00000216714
Genbank transcript ID NM_001244249
UniProt peptide P27695
alteration type single base exchange
alteration region CDS
DNA changes c.444T>G
cDNA.712T>G
g.1805T>G
AA changes D148E Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 148
frameshift no
known variant Reference ID: rs1130409
databasehomozygous (G/G)heterozygousallele carriers
1000G38211171499
ExAC109681083121799

known disease mutation at this position, please check HGMD for details (HGMD ID CM063843)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1520.969
-0.4830.751
(flanking)5.8921
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 increased1795wt: 0.4893 / mu: 0.5123 (marginal change - not scored)wt: ATGCTAATTCTGTTTCATTTCTATAGGCGATGAGGAGCATG
mu: ATGCTAATTCTGTTTCATTTCTATAGGCGAGGAGGAGCATG		 tttc|TATA
Acc marginally increased1798wt: 0.8895 / mu: 0.9204 (marginal change - not scored)wt: CTAATTCTGTTTCATTTCTATAGGCGATGAGGAGCATGATC
mu: CTAATTCTGTTTCATTTCTATAGGCGAGGAGGAGCATGATC		 ctat|AGGC
Acc marginally increased1797wt: 0.9186 / mu: 0.9492 (marginal change - not scored)wt: GCTAATTCTGTTTCATTTCTATAGGCGATGAGGAGCATGAT
mu: GCTAATTCTGTTTCATTTCTATAGGCGAGGAGGAGCATGAT		 tcta|TAGG
Acc marginally increased1799wt: 0.9467 / mu: 0.9533 (marginal change - not scored)wt: TAATTCTGTTTCATTTCTATAGGCGATGAGGAGCATGATCA
mu: TAATTCTGTTTCATTTCTATAGGCGAGGAGGAGCATGATCA		 tata|GGCG
Donor marginally increased1802wt: 0.9736 / mu: 0.9842 (marginal change - not scored)wt: ATAGGCGATGAGGAG
mu: ATAGGCGAGGAGGAG		 AGGC|gatg
Donor increased1799wt: 0.23 / mu: 0.99wt: TCTATAGGCGATGAG
mu: TCTATAGGCGAGGAG		 TATA|ggcg
Donor marginally decreased1800wt: 0.9838 / mu: 0.9392 (marginal change - not scored)wt: CTATAGGCGATGAGG
mu: CTATAGGCGAGGAGG		 ATAG|gcga
Donor marginally increased1807wt: 0.4967 / mu: 0.5311 (marginal change - not scored)wt: CGATGAGGAGCATGA
mu: CGAGGAGGAGCATGA		 ATGA|ggag
Acc gained18040.60mu: CTGTTTCATTTCTATAGGCGAGGAGGAGCATGATCAGGAAG gcga|GGAG
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      148QCPLKVSYGIGDEEHDQEGRVIVA
mutated  all conserved    148QCPLKVSYGIGEEEHDQEGRVIV
Ptroglodytes  all conserved  ENSPTRG00000006093  148QCPLKVSYGIGEEEHDQEGRVIV
Mmulatta  all conserved  ENSMMUG00000019123  148HCPLKVSYGIGEEEHDQEGRVIV
Fcatus  all conserved  ENSFCAG00000006932  148QCPLKVSYGIGEEEHDQEGRVIV
Mmusculus  all conserved  ENSMUSG00000035960  147QCPLKVSYGIGEEEHDQEGRVIV
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000004268  145TEPIKVTYGIGKEEHDKEGRVIT
Drerio  not conserved  ENSDARG00000045843  141TEPLNVTYGIGKEEHDKEGRVIT
Dmelanogaster  all conserved  FBgn0004584  537HVEYGIGNEEFDDVGRMIT
Celegans  all identical  R09B3.1  118CAPMKVHKGIGDPEFDTAGRLII
Xtropicalis  not conserved  ENSXETG00000024773  147DKPVNVTYGIGIEEHDKEGRVIT
protein features
start (aa)end (aa)featuredetails 
149151HELIXmight get lost (downstream of altered splice site)
152154STRANDmight get lost (downstream of altered splice site)
157161STRANDmight get lost (downstream of altered splice site)
166171STRANDmight get lost (downstream of altered splice site)
177179HELIXmight get lost (downstream of altered splice site)
182200HELIXmight get lost (downstream of altered splice site)
197197MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
205210STRANDmight get lost (downstream of altered splice site)
208208MUTAGENC->A: Does not abolish the redox activity.might get lost (downstream of altered splice site)
210210MUTAGEND->A: Abolishes the AP endodeoxyribonuclease activity. Reduces protection from granzyme A-mediated cell death; when associated with A-31 and A- 65.might get lost (downstream of altered splice site)
210210METALMagnesium or manganese.might get lost (downstream of altered splice site)
212212MUTAGENN->Q,D: Decreases AP endodeoxyribonuclease activity.might get lost (downstream of altered splice site)
212212MUTAGENN->A: Abolishes AP endodeoxyribonuclease activity.might get lost (downstream of altered splice site)
212212METALMagnesium or manganese.might get lost (downstream of altered splice site)
217219HELIXmight get lost (downstream of altered splice site)
223225TURNmight get lost (downstream of altered splice site)
227229STRANDmight get lost (downstream of altered splice site)
230232TURNmight get lost (downstream of altered splice site)
233233MOD_RESPhosphothreonine; by CDK5 (By similarity).might get lost (downstream of altered splice site)
234246HELIXmight get lost (downstream of altered splice site)
249251STRANDmight get lost (downstream of altered splice site)
252256HELIXmight get lost (downstream of altered splice site)
257259STRANDmight get lost (downstream of altered splice site)
262262MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
270272HELIXmight get lost (downstream of altered splice site)
273276HELIXmight get lost (downstream of altered splice site)
283287STRANDmight get lost (downstream of altered splice site)
289294HELIXmight get lost (downstream of altered splice site)
289318REGIONMitochondrial targeting sequence (MTS).might get lost (downstream of altered splice site)
295300STRANDmight get lost (downstream of altered splice site)
296296MUTAGENC->A: Does not abolish the redox activity.might get lost (downstream of altered splice site)
299299MUTAGENK->A: Reduces the interaction with TOMM20. Abolishes localization in the mitochondria; when associated with A-301.might get lost (downstream of altered splice site)
301301MUTAGENR->A: Reduces the interaction with TOMM20. Abolishes localization in the mitochondria; when associated with A-299.might get lost (downstream of altered splice site)
303303MUTAGENK->A: Reduces the interaction with TOMM20.might get lost (downstream of altered splice site)
306306CONFLICTG -> A (in Ref. 2; AAA58371).might get lost (downstream of altered splice site)
306309STRANDmight get lost (downstream of altered splice site)
308308METALMagnesium or manganese.might get lost (downstream of altered splice site)
309309METALMagnesium or manganese.might get lost (downstream of altered splice site)
309309MUTAGENH->N: Lacks MYC CRD RNA cleavage activity.might get lost (downstream of altered splice site)
309309ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
310310MOD_RESS-nitrosocysteine.might get lost (downstream of altered splice site)
310310MUTAGENC->A: Does not abolish the redox activity.might get lost (downstream of altered splice site)
310310MUTAGENC->S: Does not abolish NO-induced nitrosylation. Abolishes NO-induced nitrosylation and translocation from the nucleus to the cytoplasm; when associated with S-93.might get lost (downstream of altered splice site)
312316STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 957 / 957
position (AA) of stopcodon in wt / mu AA sequence 319 / 319
position of stopcodon in wt / mu cDNA 1225 / 1225
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 269 / 269
chromosome 14
strand 1
last intron/exon boundary 708
theoretical NMD boundary in CDS 389
length of CDS 957
coding sequence (CDS) position 444
cDNA position
(for ins/del: last normal base / first normal base)		 712
gDNA position
(for ins/del: last normal base / first normal base)		 1805
chromosomal position
(for ins/del: last normal base / first normal base)		 20925154
original gDNA sequence snippet TGTTTCATTTCTATAGGCGATGAGGAGCATGATCAGGAAGG
altered gDNA sequence snippet TGTTTCATTTCTATAGGCGAGGAGGAGCATGATCAGGAAGG
original cDNA sequence snippet GTTTCTTACGGCATAGGCGATGAGGAGCATGATCAGGAAGG
altered cDNA sequence snippet GTTTCTTACGGCATAGGCGAGGAGGAGCATGATCAGGAAGG
wildtype AA sequence MPKRGKKGAV AEDGDELRTE PEAKKSKTAA KKNDKEAAGE GPALYEDPPD QKTSPSGKPA
TLKICSWNVD GLRAWIKKKG LDWVKEEAPD ILCLQETKCS ENKLPAELQE LPGLSHQYWS
APSDKEGYSG VGLLSRQCPL KVSYGIGDEE HDQEGRVIVA EFDSFVLVTA YVPNAGRGLV
RLEYRQRWDE AFRKFLKGLA SRKPLVLCGD LNVAHEEIDL RNPKGNKKNA GFTPQERQGF
GELLQAVPLA DSFRHLYPNT PYAYTFWTYM MNARSKNVGW RLDYFLLSHS LLPALCDSKI
RSKALGSDHC PITLYLAL*
mutated AA sequence MPKRGKKGAV AEDGDELRTE PEAKKSKTAA KKNDKEAAGE GPALYEDPPD QKTSPSGKPA
TLKICSWNVD GLRAWIKKKG LDWVKEEAPD ILCLQETKCS ENKLPAELQE LPGLSHQYWS
APSDKEGYSG VGLLSRQCPL KVSYGIGEEE HDQEGRVIVA EFDSFVLVTA YVPNAGRGLV
RLEYRQRWDE AFRKFLKGLA SRKPLVLCGD LNVAHEEIDL RNPKGNKKNA GFTPQERQGF
GELLQAVPLA DSFRHLYPNT PYAYTFWTYM MNARSKNVGW RLDYFLLSHS LLPALCDSKI
RSKALGSDHC PITLYLAL*
speed 0.53 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