Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 3.06141895622736e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:100219374T>AN/A show variant in all transcripts   IGV
HGNC symbol HPSE2
Ensembl transcript ID ENST00000370552
Genbank transcript ID NM_021828
UniProt peptide Q8WWQ2
alteration type single base exchange
alteration region CDS
DNA changes c.1736A>T
cDNA.1796A>T
g.776246A>T
AA changes Y579F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 579
frameshift no
known variant Reference ID: rs10883100
databasehomozygous (A/A)heterozygousallele carriers
1000G74111751916
ExAC15537169317230
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gata2, Transcription Factor, Gata2 Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6921
4.6171
(flanking)4.6991
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 increased776249wt: 0.8688 / mu: 0.8785 (marginal change - not scored)wt: AGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATGCTT
mu: AGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTT		 atgt|GGTC
Acc marginally increased776239wt: 0.4793 / mu: 0.5256 (marginal change - not scored)wt: TCATCCCTCCAGTCACCATGGGCTTTTATGTGGTCAAGAAT
mu: TCATCCCTCCAGTCACCATGGGCTTTTTTGTGGTCAAGAAT		 atgg|GCTT
Acc increased776255wt: 0.26 / mu: 0.79wt: CATGGGCTTTTATGTGGTCAAGAATGTCAATGCTTTGGCCT
mu: CATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTTTGGCCT		 tcaa|GAAT
Acc marginally increased776247wt: 0.8379 / mu: 0.8408 (marginal change - not scored)wt: CCAGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATGC
mu: CCAGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATGC		 ttat|GTGG
Acc gained7762540.61mu: CCATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTTTGGCC gtca|AGAA
Acc gained7762510.41mu: TCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTTTG gtgg|TCAA
distance from splice site 123
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      579TLVIPPVTMGFYVVKNVNALACRY
mutated  all conserved    579TLVIPPVTMGFFVVKNVNALACR
Ptroglodytes  all identical  ENSPTRG00000002826  579TLVIPPVTMGFYVVKNVNALACR
Mmulatta  all identical  ENSMMUG00000020605  578TLVIPPVTMGFYVVKNVNALACR
Fcatus  all identical  ENSFCAG00000009349  579TLVIPPVTMGFYVVKNVNALACR
Mmusculus  all identical  ENSMUSG00000074852  579TLVIPPVTMGFYVVKNVNALACR
Ggallus  all identical  ENSGALG00000007508  580TLVIPPLTMSFYVVKNVNALACR
Trubripes  all identical  ENSTRUG00000007806  553TIVMPPMTIGFYVIKNINAYACR
Drerio  all identical  ENSDARG00000078163  581TIAMPPVSIGFYVIKNINAYACR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018422  556TLVIPPLNIGFYVVKNVNAVACR
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1779 / 1779
position (AA) of stopcodon in wt / mu AA sequence 593 / 593
position of stopcodon in wt / mu cDNA 1839 / 1839
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 61 / 61
chromosome 10
strand -1
last intron/exon boundary 1674
theoretical NMD boundary in CDS 1563
length of CDS 1779
coding sequence (CDS) position 1736
cDNA position
(for ins/del: last normal base / first normal base)		 1796
gDNA position
(for ins/del: last normal base / first normal base)		 776246
chromosomal position
(for ins/del: last normal base / first normal base)		 100219374
original gDNA sequence snippet TCCAGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATG
altered gDNA sequence snippet TCCAGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATG
original cDNA sequence snippet TCCAGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATG
altered cDNA sequence snippet TCCAGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATG
wildtype AA sequence MRVLCAFPEA MPSSNSRPPA CLAPGALYLA LLLHLSLSSQ AGDRRPLPVD RAAGLKEKTL
ILLDVSTKNP VRTVNENFLS LQLDPSIIHD GWLDFLSSKR LVTLARGLSP AFLRFGGKRT
DFLQFQNLRN PAKSRGGPGP DYYLKNYEDD IVRSDVALDK QKGCKIAQHP DVMLELQREK
AAQMHLVLLK EQFSNTYSNL ILTARSLDKL YNFADCSGLH LIFALNALRR NPNNSWNSSS
ALSLLKYSAS KKYNISWELG NEPNNYRTMH GRAVNGSQLG KDYIQLKSLL QPIRIYSRAS
LYGPNIGRPR KNVIALLDGF MKVAGSTVDA VTWQHCYIDG RVVKVMDFLK TRLLDTLSDQ
IRKIQKVVNT YTPGKKIWLE GVVTTSAGGT NNLSDSYAAG FLWLNTLGML ANQGIDVVIR
HSFFDHGYNH LVDQNFNPLP DYWLSLLYKR LIGPKVLAVH VAGLQRKPRP GRVIRDKLRI
YAHCTNHHNH NYVRGSITLF IINLHRSRKK IKLAGTLRDK LVHQYLLQPY GQEGLKSKSV
QLNGQPLVMV DDGTLPELKP RPLRAGRTLV IPPVTMGFYV VKNVNALACR YR*
mutated AA sequence MRVLCAFPEA MPSSNSRPPA CLAPGALYLA LLLHLSLSSQ AGDRRPLPVD RAAGLKEKTL
ILLDVSTKNP VRTVNENFLS LQLDPSIIHD GWLDFLSSKR LVTLARGLSP AFLRFGGKRT
DFLQFQNLRN PAKSRGGPGP DYYLKNYEDD IVRSDVALDK QKGCKIAQHP DVMLELQREK
AAQMHLVLLK EQFSNTYSNL ILTARSLDKL YNFADCSGLH LIFALNALRR NPNNSWNSSS
ALSLLKYSAS KKYNISWELG NEPNNYRTMH GRAVNGSQLG KDYIQLKSLL QPIRIYSRAS
LYGPNIGRPR KNVIALLDGF MKVAGSTVDA VTWQHCYIDG RVVKVMDFLK TRLLDTLSDQ
IRKIQKVVNT YTPGKKIWLE GVVTTSAGGT NNLSDSYAAG FLWLNTLGML ANQGIDVVIR
HSFFDHGYNH LVDQNFNPLP DYWLSLLYKR LIGPKVLAVH VAGLQRKPRP GRVIRDKLRI
YAHCTNHHNH NYVRGSITLF IINLHRSRKK IKLAGTLRDK LVHQYLLQPY GQEGLKSKSV
QLNGQPLVMV DDGTLPELKP RPLRAGRTLV IPPVTMGFFV VKNVNALACR YR*
speed 1.48 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