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 ENST00000337248
Genbank transcript ID NM_001199013
UniProt peptide Q5TH74
alteration type single base exchange
alteration region CDS
DNA changes c.313A>G
cDNA.448A>G
g.37133A>G
AA changes I105V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 105
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      105FPSMCARLDTIISKYPAANAYTIP
mutated  all conserved    105FPSMCARLDTIVSKYPAANAYTI
Ptroglodytes  all identical  ENSPTRG00000000345  58FPSMCARLDTIISKYPAANAYTI
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  87FASKGGRVPRSFQRLSPGPDAYNL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000031811  119FPSKAPRTLQRKIARTPAPNAYLL
protein features
start (aa)end (aa)featuredetails 
105105CONFLICTI -> V (in Ref. 2; AAH35061).lost
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 1005 / 1005
position (AA) of stopcodon in wt / mu AA sequence 335 / 335
position of stopcodon in wt / mu cDNA 1140 / 1140
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 136 / 136
chromosome 1
strand -1
last intron/exon boundary 1064
theoretical NMD boundary in CDS 878
length of CDS 1005
coding sequence (CDS) position 313
cDNA position
(for ins/del: last normal base / first normal base)		 448
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 MDNSAQKNER TGKHPRRASE VQKGFTAAYP TQSSIPFKSQ ASVIPESEKK GFNSQAKRFP
HKKNDIPGPG FYNVIHQSPV SNSVSLSKKG TCMFPSMCAR LDTIISKYPA ANAYTIPSDF
ISKRDFSNSC SSMFQLPSFM KALKFETPAP NYYNASVSCC KQRNNVCTRA GFMSKTQRGS
FAFADKGPPP GHYDINESLV KQSPNTLMSC FKSKTNRGLK LTSTGPGPGY YNPSDCTKVP
KKTLFPKNPI LNFSAQPSPL PPKPPFPGPG QYEIVDYLGP RKHFISSASF VSNTSRWTAA
PPQPGLPGPA TYKPELPGKQ SFLYNEDKKW IPVL*
mutated AA sequence MDNSAQKNER TGKHPRRASE VQKGFTAAYP TQSSIPFKSQ ASVIPESEKK GFNSQAKRFP
HKKNDIPGPG FYNVIHQSPV SNSVSLSKKG TCMFPSMCAR LDTIVSKYPA ANAYTIPSDF
ISKRDFSNSC SSMFQLPSFM KALKFETPAP NYYNASVSCC KQRNNVCTRA GFMSKTQRGS
FAFADKGPPP GHYDINESLV KQSPNTLMSC FKSKTNRGLK LTSTGPGPGY YNPSDCTKVP
KKTLFPKNPI LNFSAQPSPL PPKPPFPGPG QYEIVDYLGP RKHFISSASF VSNTSRWTAA
PPQPGLPGPA TYKPELPGKQ SFLYNEDKKW IPVL*
speed 0.76 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