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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000324695
Querying Taster for transcript #2: ENST00000433712
MT speed 0 s - this script 4.261659 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TRPM8polymorphism_automatic5.74047323598226e-06simple_aaeaffectedS419Nsingle base exchangers7593557show file
TRPM8polymorphism_automatic5.74047323598226e-06simple_aaeaffectedS107Nsingle base exchangers7593557show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999994259526764 (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) chr2:234863788G>AN/A show variant in all transcripts   IGV
HGNC symbol TRPM8
Ensembl transcript ID ENST00000324695
Genbank transcript ID NM_024080
UniProt peptide Q7Z2W7
alteration type single base exchange
alteration region CDS
DNA changes c.1256G>A
cDNA.1296G>A
g.37746G>A
AA changes S419N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 419
frameshift no
known variant Reference ID: rs7593557
databasehomozygous (A/A)heterozygousallele carriers
1000G4099071316
ExAC32421227515517
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.6281
2.6921
(flanking)-0.1510.991
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 increased37736wt: 0.3317 / mu: 0.3561 (marginal change - not scored)wt: TTTCCTGCCCTCTCACAGCCTTCAGCACCAGTGAGCAAGAC
mu: TTTCCTGCCCTCTCACAGCCTTCAGCACCAATGAGCAAGAC		 gcct|TCAG
Acc marginally increased37740wt: 0.2965 / mu: 0.2994 (marginal change - not scored)wt: CTGCCCTCTCACAGCCTTCAGCACCAGTGAGCAAGACAAGG
mu: CTGCCCTCTCACAGCCTTCAGCACCAATGAGCAAGACAAGG		 tcag|CACC
Donor increased37744wt: 0.42 / mu: 0.67wt: AGCACCAGTGAGCAA
mu: AGCACCAATGAGCAA		 CACC|agtg
Donor increased37742wt: 0.31 / mu: 0.87wt: TCAGCACCAGTGAGC
mu: TCAGCACCAATGAGC		 AGCA|ccag
Donor increased37749wt: 0.74 / mu: 0.86wt: CAGTGAGCAAGACAA
mu: CAATGAGCAAGACAA		 GTGA|gcaa
Donor increased37748wt: 0.30 / mu: 0.62wt: CCAGTGAGCAAGACA
mu: CCAATGAGCAAGACA		 AGTG|agca
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      419ISYALYKAFSTSEQDKDNWNGQLK
mutated  all conserved    419ISYALYKAFSTNEQDKDNWNGQL
Ptroglodytes  all conserved  ENSPTRG00000013063  367ISYALYKAFSTNEQDKDNWNGQL
Mmulatta  no alignment  ENSMMUG00000021224  n/a
Fcatus  all conserved  ENSFCAG00000009701  418ISYALYKAFSTNEQDKDNWNGQL
Mmusculus  all conserved  ENSMUSG00000036251  419ISYALYKAFSTNEQDKDNWNGQL
Ggallus  all conserved  ENSGALG00000004116  421NEHNRDNWNEQL
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no alignment  ZK512.3  n/a
Xtropicalis  all conserved  ENSXETG00000026873  460ISFALYKAYSTNEQDKDNWNAQL
protein features
start (aa)end (aa)featuredetails 
1691TOPO_DOMCytoplasmic (Potential).lost
692712TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
693693CONFLICTW -> R (in Ref. 5; BAB86335).might get lost (downstream of altered splice site)
713734TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
735755TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
756759TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
760780TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
781794TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
795795CONFLICTT -> A (in Ref. 2; AAP92167).might get lost (downstream of altered splice site)
795815TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
816829TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
830850TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
851958TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
959979TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
9801104TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3315 / 3315
position (AA) of stopcodon in wt / mu AA sequence 1105 / 1105
position of stopcodon in wt / mu cDNA 3355 / 3355
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 41 / 41
chromosome 2
strand 1
last intron/exon boundary 3398
theoretical NMD boundary in CDS 3307
length of CDS 3315
coding sequence (CDS) position 1256
cDNA position
(for ins/del: last normal base / first normal base)		 1296
gDNA position
(for ins/del: last normal base / first normal base)		 37746
chromosomal position
(for ins/del: last normal base / first normal base)		 234863788
original gDNA sequence snippet TCTCACAGCCTTCAGCACCAGTGAGCAAGACAAGGATAACT
altered gDNA sequence snippet TCTCACAGCCTTCAGCACCAATGAGCAAGACAAGGATAACT
original cDNA sequence snippet ATACAAAGCCTTCAGCACCAGTGAGCAAGACAAGGATAACT
altered cDNA sequence snippet ATACAAAGCCTTCAGCACCAATGAGCAAGACAAGGATAACT
wildtype AA sequence MSFRAARLSM RNRRNDTLDS TRTLYSSASR STDLSYSESD LVNFIQANFK KRECVFFTKD
SKATENVCKC GYAQSQHMEG TQINQSEKWN YKKHTKEFPT DAFGDIQFET LGKKGKYIRL
SCDTDAEILY ELLTQHWHLK TPNLVISVTG GAKNFALKPR MRKIFSRLIY IAQSKGAWIL
TGGTHYGLMK YIGEVVRDNT ISRSSEENIV AIGIAAWGMV SNRDTLIRNC DAEGYFLAQY
LMDDFTRDPL YILDNNHTHL LLVDNGCHGH PTVEAKLRNQ LEKYISERTI QDSNYGGKIP
IVCFAQGGGK ETLKAINTSI KNKIPCVVVE GSGQIADVIA SLVEVEDALT SSAVKEKLVR
FLPRTVSRLP EEETESWIKW LKEILECSHL LTVIKMEEAG DEIVSNAISY ALYKAFSTSE
QDKDNWNGQL KLLLEWNQLD LANDEIFTND RRWESADLQE VMFTALIKDR PKFVRLFLEN
GLNLRKFLTH DVLTELFSNH FSTLVYRNLQ IAKNSYNDAL LTFVWKLVAN FRRGFRKEDR
NGRDEMDIEL HDVSPITRHP LQALFIWAIL QNKKELSKVI WEQTRGCTLA ALGASKLLKT
LAKVKNDINA AGESEELANE YETRAVELFT ECYSSDEDLA EQLLVYSCEA WGGSNCLELA
VEATDQHFIA QPGVQNFLSK QWYGEISRDT KNWKIILCLF IIPLVGCGFV SFRKKPVDKH
KKLLWYYVAF FTSPFVVFSW NVVFYIAFLL LFAYVLLMDF HSVPHPPELV LYSLVFVLFC
DEVRQWYVNG VNYFTDLWNV MDTLGLFYFI AGIVFRLHSS NKSSLYSGRV IFCLDYIIFT
LRLIHIFTVS RNLGPKIIML QRMLIDVFFF LFLFAVWMVA FGVARQGILR QNEQRWRWIF
RSVIYEPYLA MFGQVPSDVD GTTYDFAHCT FTGNESKPLC VELDEHNLPR FPEWITIPLV
CIYMLSTNIL LVNLLVAMFG YTVGTVQENN DQVWKFQRYF LVQEYCSRLN IPFPFIVFAY
FYMVVKKCFK CCCKEKNMES SVCCFKNEDN ETLAWEGVMK ENYLVKINTK ANDTSEEMRH
RFRQLDTKLN DLKGLLKEIA NKIK*
mutated AA sequence MSFRAARLSM RNRRNDTLDS TRTLYSSASR STDLSYSESD LVNFIQANFK KRECVFFTKD
SKATENVCKC GYAQSQHMEG TQINQSEKWN YKKHTKEFPT DAFGDIQFET LGKKGKYIRL
SCDTDAEILY ELLTQHWHLK TPNLVISVTG GAKNFALKPR MRKIFSRLIY IAQSKGAWIL
TGGTHYGLMK YIGEVVRDNT ISRSSEENIV AIGIAAWGMV SNRDTLIRNC DAEGYFLAQY
LMDDFTRDPL YILDNNHTHL LLVDNGCHGH PTVEAKLRNQ LEKYISERTI QDSNYGGKIP
IVCFAQGGGK ETLKAINTSI KNKIPCVVVE GSGQIADVIA SLVEVEDALT SSAVKEKLVR
FLPRTVSRLP EEETESWIKW LKEILECSHL LTVIKMEEAG DEIVSNAISY ALYKAFSTNE
QDKDNWNGQL KLLLEWNQLD LANDEIFTND RRWESADLQE VMFTALIKDR PKFVRLFLEN
GLNLRKFLTH DVLTELFSNH FSTLVYRNLQ IAKNSYNDAL LTFVWKLVAN FRRGFRKEDR
NGRDEMDIEL HDVSPITRHP LQALFIWAIL QNKKELSKVI WEQTRGCTLA ALGASKLLKT
LAKVKNDINA AGESEELANE YETRAVELFT ECYSSDEDLA EQLLVYSCEA WGGSNCLELA
VEATDQHFIA QPGVQNFLSK QWYGEISRDT KNWKIILCLF IIPLVGCGFV SFRKKPVDKH
KKLLWYYVAF FTSPFVVFSW NVVFYIAFLL LFAYVLLMDF HSVPHPPELV LYSLVFVLFC
DEVRQWYVNG VNYFTDLWNV MDTLGLFYFI AGIVFRLHSS NKSSLYSGRV IFCLDYIIFT
LRLIHIFTVS RNLGPKIIML QRMLIDVFFF LFLFAVWMVA FGVARQGILR QNEQRWRWIF
RSVIYEPYLA MFGQVPSDVD GTTYDFAHCT FTGNESKPLC VELDEHNLPR FPEWITIPLV
CIYMLSTNIL LVNLLVAMFG YTVGTVQENN DQVWKFQRYF LVQEYCSRLN IPFPFIVFAY
FYMVVKKCFK CCCKEKNMES SVCCFKNEDN ETLAWEGVMK ENYLVKINTK ANDTSEEMRH
RFRQLDTKLN DLKGLLKEIA NKIK*
speed 1.10 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: 0.999994259526764 (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) chr2:234863788G>AN/A show variant in all transcripts   IGV
HGNC symbol TRPM8
Ensembl transcript ID ENST00000433712
Genbank transcript ID N/A
UniProt peptide Q7Z2W7
alteration type single base exchange
alteration region CDS
DNA changes c.320G>A
cDNA.1546G>A
g.37746G>A
AA changes S107N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 107
frameshift no
known variant Reference ID: rs7593557
databasehomozygous (A/A)heterozygousallele carriers
1000G4099071316
ExAC32421227515517
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.6281
2.6921
(flanking)-0.1510.991
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 increased37736wt: 0.3317 / mu: 0.3561 (marginal change - not scored)wt: TTTCCTGCCCTCTCACAGCCTTCAGCACCAGTGAGCAAGAC
mu: TTTCCTGCCCTCTCACAGCCTTCAGCACCAATGAGCAAGAC		 gcct|TCAG
Acc marginally increased37740wt: 0.2965 / mu: 0.2994 (marginal change - not scored)wt: CTGCCCTCTCACAGCCTTCAGCACCAGTGAGCAAGACAAGG
mu: CTGCCCTCTCACAGCCTTCAGCACCAATGAGCAAGACAAGG		 tcag|CACC
Donor increased37744wt: 0.42 / mu: 0.67wt: AGCACCAGTGAGCAA
mu: AGCACCAATGAGCAA		 CACC|agtg
Donor increased37742wt: 0.31 / mu: 0.87wt: TCAGCACCAGTGAGC
mu: TCAGCACCAATGAGC		 AGCA|ccag
Donor increased37749wt: 0.74 / mu: 0.86wt: CAGTGAGCAAGACAA
mu: CAATGAGCAAGACAA		 GTGA|gcaa
Donor increased37748wt: 0.30 / mu: 0.62wt: CCAGTGAGCAAGACA
mu: CCAATGAGCAAGACA		 AGTG|agca
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      107ISYALYKAFSTSEQDKDNWNGQLK
mutated  all conserved    107ISYALYKAFSTNEQDKDNWNGQL
Ptroglodytes  all conserved  ENSPTRG00000013063  367ISYALYKAFSTNEQDKDNWNGQL
Mmulatta  no alignment  ENSMMUG00000021224  n/a
Fcatus  all conserved  ENSFCAG00000009701  418ISYALYKAFSTNEQDKDNWNGQL
Mmusculus  all conserved  ENSMUSG00000036251  419ISYALYKAFSTNEQDKDNWNGQL
Ggallus  all conserved  ENSGALG00000004116  420IAFALYKAAFSTNEHNRDNWNEQL
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no alignment  ZK512.3  n/a
Xtropicalis  all conserved  ENSXETG00000026873  460ISFALYKAYSTNEQDKDNWNAQL
protein features
start (aa)end (aa)featuredetails 
1691TOPO_DOMCytoplasmic (Potential).lost
187195REGIONEpitope; activates specific cytotoxic T lymphocytes.might get lost (downstream of altered splice site)
692712TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
693693CONFLICTW -> R (in Ref. 5; BAB86335).might get lost (downstream of altered splice site)
713734TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
735755TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
756759TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
760780TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
781794TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
795795CONFLICTT -> A (in Ref. 2; AAP92167).might get lost (downstream of altered splice site)
795815TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
816829TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
830850TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
851958TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
959979TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
9801104TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2049 / 2049
position (AA) of stopcodon in wt / mu AA sequence 683 / 683
position of stopcodon in wt / mu cDNA 3275 / 3275
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 1227 / 1227
chromosome 2
strand 1
last intron/exon boundary 3318
theoretical NMD boundary in CDS 2041
length of CDS 2049
coding sequence (CDS) position 320
cDNA position
(for ins/del: last normal base / first normal base)		 1546
gDNA position
(for ins/del: last normal base / first normal base)		 37746
chromosomal position
(for ins/del: last normal base / first normal base)		 234863788
original gDNA sequence snippet TCTCACAGCCTTCAGCACCAGTGAGCAAGACAAGGATAACT
altered gDNA sequence snippet TCTCACAGCCTTCAGCACCAATGAGCAAGACAAGGATAACT
original cDNA sequence snippet ATACAAAGCCTTCAGCACCAGTGAGCAAGACAAGGATAACT
altered cDNA sequence snippet ATACAAAGCCTTCAGCACCAATGAGCAAGACAAGGATAACT
wildtype AA sequence MQAINTSIKN KIPCVVVEGS GQIADVIASL VEVEDALTSS AVKEKLVRFL PRTVSRLPEE
ETESWIKWLK EILECSHLLT VIKMEEAGDE IVSNAISYAL YKAFSTSEQD KDNWNGQLKL
LLEWNQLDLA NDEIFTNDRR WESADLQEVM FTALIKDRPK FVRLFLENGL NLRKFLTHDV
LTELFSNHFS TLVYRNLQIA KNSYNDALLT FVWKLVANFR RGFRKEDRNG RDEMDIELHD
VSPITRHPLQ ALFIWAILQN KKELSKVIWE QTRGCTLAAL GASKLLKTLA KVKNDINAAG
ESEELANEYE TRAVELFTEC YSSDEDLAEQ LLVYSCEAWG GSNCLELAVE ATDQHFIAQP
GVQWYVNGVN YFTDLWNVMD TLGLFYFIAG IVFRLHSSNK SSLYSGRVIF CLDYIIFTLR
LIHIFTVSRN LGPKIIMLQR MLIDVFFFLF LFAVWMVAFG VARQGILRQN EQRWRWIFRS
VIYEPYLAMF GQVPSDVDGT TYDFAHCTFT GNESKPLCVE LDEHNLPRFP EWITIPLVCI
YMLSTNILLV NLLVAMFGYT VGTVQENNDQ VWKFQRYFLV QEYCSRLNIP FPFIVFAYFY
MVVKKCFKCC CKEKNMESSV CCFKNEDNET LAWEGVMKEN YLVKINTKAN DTSEEMRHRF
RQLDTKLNDL KGLLKEIANK IK*
mutated AA sequence MQAINTSIKN KIPCVVVEGS GQIADVIASL VEVEDALTSS AVKEKLVRFL PRTVSRLPEE
ETESWIKWLK EILECSHLLT VIKMEEAGDE IVSNAISYAL YKAFSTNEQD KDNWNGQLKL
LLEWNQLDLA NDEIFTNDRR WESADLQEVM FTALIKDRPK FVRLFLENGL NLRKFLTHDV
LTELFSNHFS TLVYRNLQIA KNSYNDALLT FVWKLVANFR RGFRKEDRNG RDEMDIELHD
VSPITRHPLQ ALFIWAILQN KKELSKVIWE QTRGCTLAAL GASKLLKTLA KVKNDINAAG
ESEELANEYE TRAVELFTEC YSSDEDLAEQ LLVYSCEAWG GSNCLELAVE ATDQHFIAQP
GVQWYVNGVN YFTDLWNVMD TLGLFYFIAG IVFRLHSSNK SSLYSGRVIF CLDYIIFTLR
LIHIFTVSRN LGPKIIMLQR MLIDVFFFLF LFAVWMVAFG VARQGILRQN EQRWRWIFRS
VIYEPYLAMF GQVPSDVDGT TYDFAHCTFT GNESKPLCVE LDEHNLPRFP EWITIPLVCI
YMLSTNILLV NLLVAMFGYT VGTVQENNDQ VWKFQRYFLV QEYCSRLNIP FPFIVFAYFY
MVVKKCFKCC CKEKNMESSV CCFKNEDNET LAWEGVMKEN YLVKINTKAN DTSEEMRHRF
RQLDTKLNDL KGLLKEIANK IK*
speed 1.15 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

Problems