Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999999 (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) chr7:74212311G>TN/A show variant in all transcripts   IGV
HGNC symbol GTF2IRD2
Ensembl transcript ID ENST00000451013
Genbank transcript ID N/A
UniProt peptide Q86UP8
alteration type single base exchange
alteration region CDS
DNA changes c.181C>A
cDNA.421C>A
g.55537C>A
AA changes H61N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 61
frameshift no
known variant Reference ID: rs187868539
databasehomozygous (T/T)heterozygousallele carriers
1000G21102702380
ExAC80541548208
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)1.1440.001
-1.1870
(flanking)-1.2360
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained555330.60mu: GTGTTTGCAAACCCA GTTT|gcaa
distance from splice site 294
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      61TECPEQKQVFAHPSPTQKSPVQPV
mutated  all conserved    61NPSPTQKSPVQP
Ptroglodytes  all conserved  ENSPTRG00000019295  514NPSPTQKSPVQP
Mmulatta  all conserved  ENSMMUG00000017270  509NASPTQKSPVQP
Fcatus  all conserved  ENSFCAG00000002626  223NASPDEDAAAQP
Mmusculus  all conserved  ENSMUSG00000015942  508NASPPTNSAVQP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
98192REPEATGTF2I-like 1.might get lost (downstream of altered splice site)
323417REPEATGTF2I-like 2.might get lost (downstream of altered splice site)
500500CONFLICTL -> S (in Ref. 4; BAF84120).might get lost (downstream of altered splice site)
716716CONFLICTR -> C (in Ref. 5; CAD38861).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1491 / 1491
position (AA) of stopcodon in wt / mu AA sequence 497 / 497
position of stopcodon in wt / mu cDNA 1731 / 1731
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 241 / 241
chromosome 7
strand -1
last intron/exon boundary 128
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1491
coding sequence (CDS) position 181
cDNA position
(for ins/del: last normal base / first normal base)		 421
gDNA position
(for ins/del: last normal base / first normal base)		 55537
chromosomal position
(for ins/del: last normal base / first normal base)		 74212311
original gDNA sequence snippet AGCAAAAACAAGTGTTTGCACACCCAAGTCCAACCCAGAAA
altered gDNA sequence snippet AGCAAAAACAAGTGTTTGCAAACCCAAGTCCAACCCAGAAA
original cDNA sequence snippet AGCAAAAACAAGTGTTTGCACACCCAAGTCCAACCCAGAAA
altered cDNA sequence snippet AGCAAAAACAAGTGTTTGCAAACCCAAGTCCAACCCAGAAA
wildtype AA sequence MSVSKEYNLR RHYQTNHSKH YDQYMERMRD EKLHELKKGL RKYLLGLSDT ECPEQKQVFA
HPSPTQKSPV QPVEDLAGNL WEKLREKIRS FVAYSIAIDE ITDINNTTQL AIFIRGVDEN
FDVSEELLDT VPMTGTKSGN EIFSRVEKSL KKFCIDWSKL VSVASTGTPA MVDANNGLVT
KLKSRVATFC KGAELKSICC IIHPESLCAQ KLKMDHVMDV VVKSVNWICS RGLNHSEFTT
LLYELDSQYG SLLYYTEIKW LSRGLVLKRF FESLEEIDSF MSSRGKPLPQ LSSIDWIRDL
AFLVDMTMHL NALNISLQGH SQIVTQMYDL IRAFLAKLCL WETHLTRNNL AHFPTLKLAS
RNESDGLNYI PKIAELKTEF QKRLSDFKLY ESELTLFSSP FSTKIDSVHE ELQMEVIDLQ
CNTVLKTKYD KVGIPEFYKY LWGSYPKYKH HCAKILSMFG STYICEQLFS IMKLSKTKYC
SQLKDSQWDS VLHIAT*
mutated AA sequence MSVSKEYNLR RHYQTNHSKH YDQYMERMRD EKLHELKKGL RKYLLGLSDT ECPEQKQVFA
NPSPTQKSPV QPVEDLAGNL WEKLREKIRS FVAYSIAIDE ITDINNTTQL AIFIRGVDEN
FDVSEELLDT VPMTGTKSGN EIFSRVEKSL KKFCIDWSKL VSVASTGTPA MVDANNGLVT
KLKSRVATFC KGAELKSICC IIHPESLCAQ KLKMDHVMDV VVKSVNWICS RGLNHSEFTT
LLYELDSQYG SLLYYTEIKW LSRGLVLKRF FESLEEIDSF MSSRGKPLPQ LSSIDWIRDL
AFLVDMTMHL NALNISLQGH SQIVTQMYDL IRAFLAKLCL WETHLTRNNL AHFPTLKLAS
RNESDGLNYI PKIAELKTEF QKRLSDFKLY ESELTLFSSP FSTKIDSVHE ELQMEVIDLQ
CNTVLKTKYD KVGIPEFYKY LWGSYPKYKH HCAKILSMFG STYICEQLFS IMKLSKTKYC
SQLKDSQWDS VLHIAT*
speed 0.72 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