Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999852 (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) chr14:81575005C>AN/A show variant in all transcripts   IGV
HGNC symbol TSHR
Ensembl transcript ID ENST00000342443
Genbank transcript ID NM_001018036
UniProt peptide P16473
alteration type single base exchange
alteration region CDS
DNA changes c.742C>A
cDNA.992C>A
g.153673C>A
AA changes R248S Score: 110 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 248
frameshift no
known variant Reference ID: rs3783941
databasehomozygous (A/A)heterozygousallele carriers
1000G96611242090
ExAC25847-189276920
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3680
-2.3250
(flanking)-0.260
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased153674wt: 0.52 / mu: 0.62wt: CCCACGCTCCAGTAT
mu: CCCAAGCTCCAGTAT		 CACG|ctcc
Donor increased153668wt: 0.27 / mu: 0.93wt: GAAGGCCCCACGCTC
mu: GAAGGCCCCAAGCTC		 AGGC|ccca
distance from splice site 50
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      248KSLSFETQKAPRSSMPS*
mutated  not conserved    248FETQKAPSSSMPS
Ptroglodytes  no alignment  ENSPTRG00000006595  n/a
Mmulatta  no alignment  ENSMMUG00000019713  n/a
Fcatus  no alignment  ENSFCAG00000011083  n/a
Mmusculus  no alignment  ENSMUSG00000020963  n/a
Ggallus  no alignment  ENSGALG00000010572  n/a
Trubripes  no alignment  ENSTRUG00000017972  n/a
Drerio  no alignment  ENSDARG00000037195  n/a
Dmelanogaster  no alignment  FBgn0016650  n/a
Celegans  no alignment  C50H2.1  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
21413TOPO_DOMExtracellular (Potential).lost
227248REPEATLRR 6.lost
250253STRANDmight get lost (downstream of altered splice site)
250271REPEATLRR 7.might get lost (downstream of altered splice site)
257257CONFLICTT -> S (in Ref. 4; AAA70232).might get lost (downstream of altered splice site)
264264CONFLICTP -> A (in Ref. 4; AAA70232).might get lost (downstream of altered splice site)
302302CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
306308CONFLICTMQS -> IET (in Ref. 4; AAA70232).might get lost (downstream of altered splice site)
414441TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
442450TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
451473TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
474494TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
494494DISULFIDBy similarity.might get lost (downstream of altered splice site)
495517TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
518537TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
528528CONFLICTR -> A (in Ref. 4; AAA70232).might get lost (downstream of altered splice site)
538560TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
561580TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
569569DISULFIDBy similarity.might get lost (downstream of altered splice site)
581602TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
601601CONFLICTY -> H (in Ref. 1; AAA36783).might get lost (downstream of altered splice site)
603625TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
626649TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
635635CONFLICTI -> T (in Ref. 4; AAA70232).might get lost (downstream of altered splice site)
645645CONFLICTL -> V (in Ref. 4; AAA70232).might get lost (downstream of altered splice site)
650660TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
661682TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
669669CONFLICTL -> I (in Ref. 4; AAA70232).might get lost (downstream of altered splice site)
683764TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
744744CONFLICTN -> K (in Ref. 3; AAA61236).might get lost (downstream of altered splice site)
762764MOTIFPDZ-binding.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 762 / 762
position (AA) of stopcodon in wt / mu AA sequence 254 / 254
position of stopcodon in wt / mu cDNA 1012 / 1012
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 251 / 251
chromosome 14
strand 1
last intron/exon boundary 943
theoretical NMD boundary in CDS 642
length of CDS 762
coding sequence (CDS) position 742
cDNA position
(for ins/del: last normal base / first normal base)		 992
gDNA position
(for ins/del: last normal base / first normal base)		 153673
chromosomal position
(for ins/del: last normal base / first normal base)		 81575005
original gDNA sequence snippet TTGAGACTCAGAAGGCCCCACGCTCCAGTATGCCATCATGA
altered gDNA sequence snippet TTGAGACTCAGAAGGCCCCAAGCTCCAGTATGCCATCATGA
original cDNA sequence snippet TTGAGACTCAGAAGGCCCCACGCTCCAGTATGCCATCATGA
altered cDNA sequence snippet TTGAGACTCAGAAGGCCCCAAGCTCCAGTATGCCATCATGA
wildtype AA sequence MRPADLLQLV LLLDLPRDLG GMGCSSPPCE CHQEEDFRVT CKDIQRIPSL PPSTQTLKLI
ETHLRTIPSH AFSNLPNISR IYVSIDVTLQ QLESHSFYNL SKVTHIEIRN TRNLTYIDPD
ALKELPLLKF LGIFNTGLKM FPDLTKVYST DIFFILEITD NPYMTSIPVN AFQGLCNETL
TLKLYNNGFT SVQGYAFNGT KLDAVYLNKN KYLTVIDKDA FGGVYSGPSL LLPLGRKSLS
FETQKAPRSS MPS*
mutated AA sequence MRPADLLQLV LLLDLPRDLG GMGCSSPPCE CHQEEDFRVT CKDIQRIPSL PPSTQTLKLI
ETHLRTIPSH AFSNLPNISR IYVSIDVTLQ QLESHSFYNL SKVTHIEIRN TRNLTYIDPD
ALKELPLLKF LGIFNTGLKM FPDLTKVYST DIFFILEITD NPYMTSIPVN AFQGLCNETL
TLKLYNNGFT SVQGYAFNGT KLDAVYLNKN KYLTVIDKDA FGGVYSGPSL LLPLGRKSLS
FETQKAPSSS MPS*
speed 1.18 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