Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000541158
Querying Taster for transcript #2: ENST00000342443
Querying Taster for transcript #3: ENST00000554263
Querying Taster for transcript #4: ENST00000554435
Querying Taster for transcript #5: ENST00000298171
MT speed 0 s - this script 4.441215 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TSHRpolymorphism_automatic1.47992729182533e-13simple_aaeaffectedR248Ssingle base exchangers3783941show file
TSHRpolymorphism_automatic1.47992729182533e-13simple_aaeaffectedR269Ssingle base exchangers3783941show file
TSHRpolymorphism_automatic2.1296531982351e-08without_aaeaffectedsingle base exchangers3783941show file
TSHRpolymorphism_automatic2.1296531982351e-08without_aaeaffectedsingle base exchangers3783941show file
TSHRpolymorphism_automatic2.1296531982351e-08without_aaeaffectedsingle base exchangers3783941show file

Taster files

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 increased153668wt: 0.27 / mu: 0.93wt: GAAGGCCCCACGCTC
mu: GAAGGCCCCAAGCTC		 AGGC|ccca
Donor increased153674wt: 0.52 / mu: 0.62wt: CCCACGCTCCAGTAT
mu: CCCAAGCTCCAGTAT		 CACG|ctcc
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 1.13 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
back to results table
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 ENST00000554435
Genbank transcript ID NM_001142626
UniProt peptide P16473
alteration type single base exchange
alteration region CDS
DNA changes c.805C>A
cDNA.831C>A
g.153673C>A
AA changes R269S Score: 110 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 269
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 increased153668wt: 0.27 / mu: 0.93wt: GAAGGCCCCACGCTC
mu: GAAGGCCCCAAGCTC		 AGGC|ccca
Donor increased153674wt: 0.52 / mu: 0.62wt: CCCACGCTCCAGTAT
mu: CCCAAGCTCCAGTAT		 CACG|ctcc
distance from splice site 113
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      269KSLSFETQKAPRSSMPS*
mutated  not conserved    269KSLSFETQKAPSSSMPS
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
250271REPEATLRR 7.lost
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 825 / 825
position (AA) of stopcodon in wt / mu AA sequence 275 / 275
position of stopcodon in wt / mu cDNA 851 / 851
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 27 / 27
chromosome 14
strand 1
last intron/exon boundary 719
theoretical NMD boundary in CDS 642
length of CDS 825
coding sequence (CDS) position 805
cDNA position
(for ins/del: last normal base / first normal base)		 831
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 LVENVAVSGK
GFCKSLFSWL YRLPLGRKSL SFETQKAPRS SMPS*
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 LVENVAVSGK
GFCKSLFSWL YRLPLGRKSL SFETQKAPSS SMPS*
speed 1.22 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999978703468 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • 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 ENST00000554263
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.927C>A
g.153673C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
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 splice site change occurs after stopcodon (at aa 298) splice site change occurs after stopcodon (at aa 300)
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased153668wt: 0.27 / mu: 0.93wt: GAAGGCCCCACGCTC
mu: GAAGGCCCCAAGCTC		 AGGC|ccca
Donor increased153674wt: 0.52 / mu: 0.62wt: CCCACGCTCCAGTAT
mu: CCCAAGCTCCAGTAT		 CACG|ctcc
distance from splice site 258
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
poly(A) signal signal is predicted to be ok
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 27 / 27
chromosome 14
strand 1
last intron/exon boundary 641
theoretical NMD boundary in CDS 564
length of CDS 696
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 927
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 L*
mutated AA sequence N/A
speed 0.46 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999978703468 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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 ENST00000541158
Genbank transcript ID NM_000369
UniProt peptide P16473
alteration type single base exchange
alteration region intron
DNA changes g.153673C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
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 increased153668wt: 0.27 / mu: 0.93wt: GAAGGCCCCACGCTC
mu: GAAGGCCCCAAGCTC		 AGGC|ccca
Donor increased153674wt: 0.52 / mu: 0.62wt: CCCACGCTCCAGTAT
mu: CCCAAGCTCCAGTAT		 CACG|ctcc
distance from splice site 209
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
21413TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
227248REPEATLRR 6.might get lost (downstream of altered splice site)
229232STRANDmight get lost (downstream of altered splice site)
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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 323 / 323
chromosome 14
strand 1
last intron/exon boundary 1204
theoretical NMD boundary in CDS 831
length of CDS 2295
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
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 N/A
altered cDNA sequence snippet N/A
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 LDVSQTSVTA
LPSKGLEHLK ELIARNTWTL KKLPLSLSFL HLTRADLSYP SHCCAFKNQK KIRGILESLM
CNESSMQSLR QRKSVNALNS PLHQEYEENL GDSIVGYKEK SKFQDTHNNA HYYVFFEEQE
DEIIGFGQEL KNPQEETLQA FDSHYDYTIC GDSEDMVCTP KSDEFNPCED IMGYKFLRIV
VWFVSLLALL GNVFVLLILL TSHYKLNVPR FLMCNLAFAD FCMGMYLLLI ASVDLYTHSE
YYNHAIDWQT GPGCNTAGFF TVFASELSVY TLTVITLERW YAITFAMRLD RKIRLRHACA
IMVGGWVCCF LLALLPLVGI SSYAKVSICL PMDTETPLAL AYIVFVLTLN IVAFVIVCCC
YVKIYITVRN PQYNPGDKDT KIAKRMAVLI FTDFICMAPI SFYALSAILN KPLITVSNSK
ILLVLFYPLN SCANPFLYAI FTKAFQRDVF ILLSKFGICK RQAQAYRGQR VPPKNSTDIQ
VQKVTHEMRQ GLHNMEDVYE LIENSHLTPK KQGQISEEYM QTVL*
mutated AA sequence N/A
speed 0.80 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999978703468 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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 ENST00000298171
Genbank transcript ID NM_000369
UniProt peptide P16473
alteration type single base exchange
alteration region intron
DNA changes g.153673C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
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 increased153668wt: 0.27 / mu: 0.93wt: GAAGGCCCCACGCTC
mu: GAAGGCCCCAAGCTC		 AGGC|ccca
Donor increased153674wt: 0.52 / mu: 0.62wt: CCCACGCTCCAGTAT
mu: CCCAAGCTCCAGTAT		 CACG|ctcc
distance from splice site 209
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
21413TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
227248REPEATLRR 6.might get lost (downstream of altered splice site)
229232STRANDmight get lost (downstream of altered splice site)
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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 157 / 157
chromosome 14
strand 1
last intron/exon boundary 1038
theoretical NMD boundary in CDS 831
length of CDS 2295
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
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 N/A
altered cDNA sequence snippet N/A
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 LDVSQTSVTA
LPSKGLEHLK ELIARNTWTL KKLPLSLSFL HLTRADLSYP SHCCAFKNQK KIRGILESLM
CNESSMQSLR QRKSVNALNS PLHQEYEENL GDSIVGYKEK SKFQDTHNNA HYYVFFEEQE
DEIIGFGQEL KNPQEETLQA FDSHYDYTIC GDSEDMVCTP KSDEFNPCED IMGYKFLRIV
VWFVSLLALL GNVFVLLILL TSHYKLNVPR FLMCNLAFAD FCMGMYLLLI ASVDLYTHSE
YYNHAIDWQT GPGCNTAGFF TVFASELSVY TLTVITLERW YAITFAMRLD RKIRLRHACA
IMVGGWVCCF LLALLPLVGI SSYAKVSICL PMDTETPLAL AYIVFVLTLN IVAFVIVCCC
YVKIYITVRN PQYNPGDKDT KIAKRMAVLI FTDFICMAPI SFYALSAILN KPLITVSNSK
ILLVLFYPLN SCANPFLYAI FTKAFQRDVF ILLSKFGICK RQAQAYRGQR VPPKNSTDIQ
VQKVTHEMRQ GLHNMEDVYE LIENSHLTPK KQGQISEEYM QTVL*
mutated AA sequence N/A
speed 0.65 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
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Problems