Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999260371 (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) chr1:24706292T>CN/A show variant in all transcripts   IGV
HGNC symbol STPG1
Ensembl transcript ID ENST00000003583
Genbank transcript ID NM_178122
UniProt peptide Q5TH74
alteration type single base exchange
alteration region CDS
DNA changes c.172A>G
cDNA.314A>G
g.37133A>G
AA changes I58V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 58
frameshift no
known variant Reference ID: rs1142057
databasehomozygous (C/C)heterozygousallele carriers
1000G36810951463
ExAC75511766525216
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3040
-0.0850
(flanking)0.0440
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 increased37140wt: 0.7861 / mu: 0.8396 (marginal change - not scored)wt: ATTGGACACCATCATTTCTAAATACCCTGCAGCGAATGCAT
mu: ATTGGACACCATCGTTTCTAAATACCCTGCAGCGAATGCAT		 ctaa|ATAC
Donor gained371270.54mu: TGGACACCATCGTTT GACA|ccat
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      58FPSMCARLDTIISKYPAANAYTIP
mutated  all conserved    58FPSMCARLDTIVSK
Ptroglodytes  all identical  ENSPTRG00000000345  58FPSMCARLDTIISK
Mmulatta  all identical  ENSMMUG00000004464  105FPSMRARLDTIISKYPAANAYTI
Fcatus  all identical  ENSFCAG00000002066  105FPSMRARLDTIISKYPAANAYTI
Mmusculus  all identical  ENSMUSG00000028801  111FPSTCARLGPIISKNPAANAYTI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000059171  88FASKGGRVPRSFQRLSPGPDAYNL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000031811  119FPSKAPRTLQRKIARTPAPNAYLL
protein features
start (aa)end (aa)featuredetails 
6774REPEATSTPGR 1.might get lost (downstream of altered splice site)
7272MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
9393CONFLICTM -> T (in Ref. 2; AAH35061).might get lost (downstream of altered splice site)
105105CONFLICTI -> V (in Ref. 2; AAH35061).might get lost (downstream of altered splice site)
163163CONFLICTR -> I (in Ref. 2; AAH17650).might get lost (downstream of altered splice site)
187206REPEATSTPGR 2.might get lost (downstream of altered splice site)
225257REPEATSTPGR 3.might get lost (downstream of altered splice site)
233233CONFLICTP -> T (in Ref. 2; AAH35061).might get lost (downstream of altered splice site)
267282REPEATSTPGR 4.might get lost (downstream of altered splice site)
306316REPEATSTPGR 5.might get lost (downstream of altered splice site)
332332CONFLICTP -> R (in Ref. 2; AAH35061).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 864 / 864
position (AA) of stopcodon in wt / mu AA sequence 288 / 288
position of stopcodon in wt / mu cDNA 1006 / 1006
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 143 / 143
chromosome 1
strand -1
last intron/exon boundary 930
theoretical NMD boundary in CDS 737
length of CDS 864
coding sequence (CDS) position 172
cDNA position
(for ins/del: last normal base / first normal base)		 314
gDNA position
(for ins/del: last normal base / first normal base)		 37133
chromosomal position
(for ins/del: last normal base / first normal base)		 24706292
original gDNA sequence snippet GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG
altered gDNA sequence snippet GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG
original cDNA sequence snippet GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG
altered cDNA sequence snippet GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG
wildtype AA sequence MNALANIPDV PVKYRKNDIP GPGFYNVIHQ SPVSNSVSLS KKGTCMFPSM CARLDTIISK
YPAANAYTIP SDFISKRDFS NSCSSMFQLP SFMKALKFET PAPNYYNASV SCCKQRNNVC
TRAGFMSKTQ RGSFAFADKG PPPGHYDINE SLVKQSPNTL MSCFKSKTNR GLKLTSTGPG
PGYYNPSDCT KVPKKTLFPK NPILNFSAQP SPLPPKPPFP GPGQYEIVDY LGPRKHFISS
ASFVSNTSRW TAAPPQPGLP GPATYKPELP GKQSFLYNED KKWIPVL*
mutated AA sequence MNALANIPDV PVKYRKNDIP GPGFYNVIHQ SPVSNSVSLS KKGTCMFPSM CARLDTIVSK
YPAANAYTIP SDFISKRDFS NSCSSMFQLP SFMKALKFET PAPNYYNASV SCCKQRNNVC
TRAGFMSKTQ RGSFAFADKG PPPGHYDINE SLVKQSPNTL MSCFKSKTNR GLKLTSTGPG
PGYYNPSDCT KVPKKTLFPK NPILNFSAQP SPLPPKPPFP GPGQYEIVDY LGPRKHFISS
ASFVSNTSRW TAAPPQPGLP GPATYKPELP GKQSFLYNED KKWIPVL*
speed 0.99 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