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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000490131
Querying Taster for transcript #2: ENST00000498619
Querying Taster for transcript #3: ENST00000296154
MT speed 0 s - this script 2.72718 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CASRdisease_causing_automatic0.999999999784697simple_aaeaffected0R62Msingle base exchangers121909265show file
CASRdisease_causing_automatic0.999999999784697simple_aaeaffected0R62Msingle base exchangers121909265show file
CASRdisease_causing_automatic0.999999999784697simple_aaeaffected0R62Msingle base exchangers121909265show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999784697 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950199)
  • known disease mutation: rs8334 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:121973221G>TN/A show variant in all transcripts   IGV
HGNC symbol CASR
Ensembl transcript ID ENST00000490131
Genbank transcript ID NM_000388
UniProt peptide P41180
alteration type single base exchange
alteration region CDS
DNA changes c.185G>T
cDNA.557G>T
g.70692G>T
AA changes R62M Score: 91 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 62
frameshift no
known variant Reference ID: rs121909265
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8334 (pathogenic for Hypocalciuric hypercalcemia, familial, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2131
5.9181
(flanking)5.9181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost70691sequence motif lost- wt: TCAG|gtaa
 mu: TCAT.gtaa
Donor marginally decreased70691wt: 0.9981 / mu: 0.9199 (marginal change - not scored)wt: GTATCAGGTAAGAAG
mu: GTATCATGTAAGAAG		 ATCA|ggta
Donor marginally increased70694wt: 0.8205 / mu: 0.8923 (marginal change - not scored)wt: TCAGGTAAGAAGAGG
mu: TCATGTAAGAAGAGG		 AGGT|aaga
Donor increased70687wt: 0.22 / mu: 0.28wt: GAATGTATCAGGTAA
mu: GAATGTATCATGTAA		 ATGT|atca
Donor marginally increased70696wt: 0.9935 / mu: 0.9943 (marginal change - not scored)wt: AGGTAAGAAGAGGGG
mu: ATGTAAGAAGAGGGG		 GTAA|gaag
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      62LKSRPESVECIRYNFRGFRWLQAM
mutated  not conserved    62IMYNFRGFRWLQA
Ptroglodytes  all identical  ENSPTRG00000015289  62IRYNFRGFRWLQA
Mmulatta  all identical  ENSMMUG00000007886  62IRYNFRGFRWLQA
Fcatus  all identical  ENSFCAG00000008717  62IRYNFRGFRWLQA
Mmusculus  all identical  ENSMUSG00000051980  62IRYNFRGFRWLQA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016870  63LAARPESTKCVRFNFRGF
Drerio  all identical  ENSDARG00000013649  62VRYNFRGFRWLQS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011400  62LESRPESLECVRYNFRGFR
protein features
start (aa)end (aa)featuredetails 
20612TOPO_DOMExtracellular (Potential).lost
9090CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
130130CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
261261CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
287287CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
386386CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
400400CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
446446CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
468468CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
488488CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
541541CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
594594CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
613635TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
636649TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
650670TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
671681TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
682700TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
701724TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
725745TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
746769TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
770792TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
793805TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
806828TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
829836TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
837862TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
857857CONFLICTI -> T (in Ref. 3; BAA09453).might get lost (downstream of altered splice site)
8631078TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
878878CONFLICTA -> R (in Ref. 3; BAA09453).might get lost (downstream of altered splice site)
880900REGIONInteraction with RNF19A.might get lost (downstream of altered splice site)
926926CONFLICTQ -> R (in Ref. 2; AAA86503).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3237 / 3237
position (AA) of stopcodon in wt / mu AA sequence 1079 / 1079
position of stopcodon in wt / mu cDNA 3609 / 3609
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 373 / 373
chromosome 3
strand 1
last intron/exon boundary 2105
theoretical NMD boundary in CDS 1682
length of CDS 3237
coding sequence (CDS) position 185
cDNA position
(for ins/del: last normal base / first normal base)		 557
gDNA position
(for ins/del: last normal base / first normal base)		 70692
chromosomal position
(for ins/del: last normal base / first normal base)		 121973221
original gDNA sequence snippet GGAGTCTGTGGAATGTATCAGGTAAGAAGAGGGGCCTAATC
altered gDNA sequence snippet GGAGTCTGTGGAATGTATCATGTAAGAAGAGGGGCCTAATC
original cDNA sequence snippet GGAGTCTGTGGAATGTATCAGGTATAATTTCCGTGGGTTTC
altered cDNA sequence snippet GGAGTCTGTGGAATGTATCATGTATAATTTCCGTGGGTTTC
wildtype AA sequence MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC
IRYNFRGFRW LQAMIFAIEE INSSPALLPN LTLGYRIFDT CNTVSKALEA TLSFVAQNKI
DSLNLDEFCN CSEHIPSTIA VVGATGSGVS TAVANLLGLF YIPQVSYASS SRLLSNKNQF
KSFLRTIPND EHQATAMADI IEYFRWNWVG TIAADDDYGR PGIEKFREEA EERDICIDFS
ELISQYSDEE EIQHVVEVIQ NSTAKVIVVF SSGPDLEPLI KEIVRRNITG KIWLASEAWA
SSSLIAMPQY FHVVGGTIGF ALKAGQIPGF REFLKKVHPR KSVHNGFAKE FWEETFNCHL
QEGAKGPLPV DTFLRGHEES GDRFSNSSTA FRPLCTGDEN ISSVETPYID YTHLRISYNV
YLAVYSIAHA LQDIYTCLPG RGLFTNGSCA DIKKVEAWQV LKHLRHLNFT NNMGEQVTFD
ECGDLVGNYS IINWHLSPED GSIVFKEVGY YNVYAKKGER LFINEEKILW SGFSREVPFS
NCSRDCLAGT RKGIIEGEPT CCFECVECPD GEYSDETDAS ACNKCPDDFW SNENHTSCIA
KEIEFLSWTE PFGIALTLFA VLGIFLTAFV LGVFIKFRNT PIVKATNREL SYLLLFSLLC
CFSSSLFFIG EPQDWTCRLR QPAFGISFVL CISCILVKTN RVLLVFEAKI PTSFHRKWWG
LNLQFLLVFL CTFMQIVICV IWLYTAPPSS YRNQELEDEI IFITCHEGSL MALGFLIGYT
CLLAAICFFF AFKSRKLPEN FNEAKFITFS MLIFFIVWIS FIPAYASTYG KFVSAVEVIA
ILAASFGLLA CIFFNKIYII LFKPSRNTIE EVRCSTAAHA FKVAARATLR RSNVSRKRSS
SLGGSTGSTP SSSISSKSNS EDPFPQPERQ KQQQPLALTQ QEQQQQPLTL PQQQRSQQQP
RCKQKVIFGS GTVTFSLSFD EPQKNAMAHR NSTHQNSLEA QKSSDTLTRH EPLLPLQCGE
TDLDLTVQET GLQGPVGGDQ RPEVEDPEEL SPALVVSSSQ SFVISGGGST VTENVVNS*
mutated AA sequence MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC
IMYNFRGFRW LQAMIFAIEE INSSPALLPN LTLGYRIFDT CNTVSKALEA TLSFVAQNKI
DSLNLDEFCN CSEHIPSTIA VVGATGSGVS TAVANLLGLF YIPQVSYASS SRLLSNKNQF
KSFLRTIPND EHQATAMADI IEYFRWNWVG TIAADDDYGR PGIEKFREEA EERDICIDFS
ELISQYSDEE EIQHVVEVIQ NSTAKVIVVF SSGPDLEPLI KEIVRRNITG KIWLASEAWA
SSSLIAMPQY FHVVGGTIGF ALKAGQIPGF REFLKKVHPR KSVHNGFAKE FWEETFNCHL
QEGAKGPLPV DTFLRGHEES GDRFSNSSTA FRPLCTGDEN ISSVETPYID YTHLRISYNV
YLAVYSIAHA LQDIYTCLPG RGLFTNGSCA DIKKVEAWQV LKHLRHLNFT NNMGEQVTFD
ECGDLVGNYS IINWHLSPED GSIVFKEVGY YNVYAKKGER LFINEEKILW SGFSREVPFS
NCSRDCLAGT RKGIIEGEPT CCFECVECPD GEYSDETDAS ACNKCPDDFW SNENHTSCIA
KEIEFLSWTE PFGIALTLFA VLGIFLTAFV LGVFIKFRNT PIVKATNREL SYLLLFSLLC
CFSSSLFFIG EPQDWTCRLR QPAFGISFVL CISCILVKTN RVLLVFEAKI PTSFHRKWWG
LNLQFLLVFL CTFMQIVICV IWLYTAPPSS YRNQELEDEI IFITCHEGSL MALGFLIGYT
CLLAAICFFF AFKSRKLPEN FNEAKFITFS MLIFFIVWIS FIPAYASTYG KFVSAVEVIA
ILAASFGLLA CIFFNKIYII LFKPSRNTIE EVRCSTAAHA FKVAARATLR RSNVSRKRSS
SLGGSTGSTP SSSISSKSNS EDPFPQPERQ KQQQPLALTQ QEQQQQPLTL PQQQRSQQQP
RCKQKVIFGS GTVTFSLSFD EPQKNAMAHR NSTHQNSLEA QKSSDTLTRH EPLLPLQCGE
TDLDLTVQET GLQGPVGGDQ RPEVEDPEEL SPALVVSSSQ SFVISGGGST VTENVVNS*
speed 0.28 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

disease causing

 Model: simple_aae, prob: 0.999999999784697 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950199)
  • known disease mutation: rs8334 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:121973221G>TN/A show variant in all transcripts   IGV
HGNC symbol CASR
Ensembl transcript ID ENST00000498619
Genbank transcript ID NM_001178065
UniProt peptide P41180
alteration type single base exchange
alteration region CDS
DNA changes c.185G>T
cDNA.623G>T
g.70692G>T
AA changes R62M Score: 91 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 62
frameshift no
known variant Reference ID: rs121909265
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8334 (pathogenic for Hypocalciuric hypercalcemia, familial, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2131
5.9181
(flanking)5.9181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost70691sequence motif lost- wt: TCAG|gtaa
 mu: TCAT.gtaa
Donor marginally decreased70691wt: 0.9981 / mu: 0.9199 (marginal change - not scored)wt: GTATCAGGTAAGAAG
mu: GTATCATGTAAGAAG		 ATCA|ggta
Donor marginally increased70694wt: 0.8205 / mu: 0.8923 (marginal change - not scored)wt: TCAGGTAAGAAGAGG
mu: TCATGTAAGAAGAGG		 AGGT|aaga
Donor increased70687wt: 0.22 / mu: 0.28wt: GAATGTATCAGGTAA
mu: GAATGTATCATGTAA		 ATGT|atca
Donor marginally increased70696wt: 0.9935 / mu: 0.9943 (marginal change - not scored)wt: AGGTAAGAAGAGGGG
mu: ATGTAAGAAGAGGGG		 GTAA|gaag
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      62LKSRPESVECIRYNFRGFRWLQAM
mutated  not conserved    62IMYNFRGFRWLQA
Ptroglodytes  all identical  ENSPTRG00000015289  62IRYNFRGFRWLQA
Mmulatta  all identical  ENSMMUG00000007886  62IRYNFRGFRWLQA
Fcatus  all identical  ENSFCAG00000008717  62IRYNFRGFRWLQA
Mmusculus  all identical  ENSMUSG00000051980  62IRYNFRGFRWLQA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016870  63LAARPESTKCVRFNFRGF
Drerio  all identical  ENSDARG00000013649  62VRYNFRGFRWLQS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011400  62LESRPESLECVRYNFRGFR
protein features
start (aa)end (aa)featuredetails 
20612TOPO_DOMExtracellular (Potential).lost
9090CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
130130CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
261261CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
287287CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
386386CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
400400CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
446446CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
468468CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
488488CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
541541CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
594594CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
613635TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
636649TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
650670TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
671681TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
682700TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
701724TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
725745TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
746769TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
770792TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
793805TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
806828TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
829836TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
837862TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
857857CONFLICTI -> T (in Ref. 3; BAA09453).might get lost (downstream of altered splice site)
8631078TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
878878CONFLICTA -> R (in Ref. 3; BAA09453).might get lost (downstream of altered splice site)
880900REGIONInteraction with RNF19A.might get lost (downstream of altered splice site)
926926CONFLICTQ -> R (in Ref. 2; AAA86503).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3267 / 3267
position (AA) of stopcodon in wt / mu AA sequence 1089 / 1089
position of stopcodon in wt / mu cDNA 3705 / 3705
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 439 / 439
chromosome 3
strand 1
last intron/exon boundary 2201
theoretical NMD boundary in CDS 1712
length of CDS 3267
coding sequence (CDS) position 185
cDNA position
(for ins/del: last normal base / first normal base)		 623
gDNA position
(for ins/del: last normal base / first normal base)		 70692
chromosomal position
(for ins/del: last normal base / first normal base)		 121973221
original gDNA sequence snippet GGAGTCTGTGGAATGTATCAGGTAAGAAGAGGGGCCTAATC
altered gDNA sequence snippet GGAGTCTGTGGAATGTATCATGTAAGAAGAGGGGCCTAATC
original cDNA sequence snippet GGAGTCTGTGGAATGTATCAGGTATAATTTCCGTGGGTTTC
altered cDNA sequence snippet GGAGTCTGTGGAATGTATCATGTATAATTTCCGTGGGTTTC
wildtype AA sequence MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC
IRYNFRGFRW LQAMIFAIEE INSSPALLPN LTLGYRIFDT CNTVSKALEA TLSFVAQNKI
DSLNLDEFCN CSEHIPSTIA VVGATGSGVS TAVANLLGLF YIPQVSYASS SRLLSNKNQF
KSFLRTIPND EHQATAMADI IEYFRWNWVG TIAADDDYGR PGIEKFREEA EERDICIDFS
ELISQYSDEE EIQHVVEVIQ NSTAKVIVVF SSGPDLEPLI KEIVRRNITG KIWLASEAWA
SSSLIAMPQY FHVVGGTIGF ALKAGQIPGF REFLKKVHPR KSVHNGFAKE FWEETFNCHL
QEGAKGPLPV DTFLRGHEES GDRFSNSSTA FRPLCTGDEN ISSVETPYID YTHLRISYNV
YLAVYSIAHA LQDIYTCLPG RGLFTNGSCA DIKKVEAWQV LKHLRHLNFT NNMGEQVTFD
ECGDLVGNYS IINWHLSPED GSIVFKEVGY YNVYAKKGER LFINEEKILW SGFSREPLTF
VLSVLQVPFS NCSRDCLAGT RKGIIEGEPT CCFECVECPD GEYSDETDAS ACNKCPDDFW
SNENHTSCIA KEIEFLSWTE PFGIALTLFA VLGIFLTAFV LGVFIKFRNT PIVKATNREL
SYLLLFSLLC CFSSSLFFIG EPQDWTCRLR QPAFGISFVL CISCILVKTN RVLLVFEAKI
PTSFHRKWWG LNLQFLLVFL CTFMQIVICV IWLYTAPPSS YRNQELEDEI IFITCHEGSL
MALGFLIGYT CLLAAICFFF AFKSRKLPEN FNEAKFITFS MLIFFIVWIS FIPAYASTYG
KFVSAVEVIA ILAASFGLLA CIFFNKIYII LFKPSRNTIE EVRCSTAAHA FKVAARATLR
RSNVSRKRSS SLGGSTGSTP SSSISSKSNS EDPFPQPERQ KQQQPLALTQ QEQQQQPLTL
PQQQRSQQQP RCKQKVIFGS GTVTFSLSFD EPQKNAMAHR NSTHQNSLEA QKSSDTLTRH
EPLLPLQCGE TDLDLTVQET GLQGPVGGDQ RPEVEDPEEL SPALVVSSSQ SFVISGGGST
VTENVVNS*
mutated AA sequence MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC
IMYNFRGFRW LQAMIFAIEE INSSPALLPN LTLGYRIFDT CNTVSKALEA TLSFVAQNKI
DSLNLDEFCN CSEHIPSTIA VVGATGSGVS TAVANLLGLF YIPQVSYASS SRLLSNKNQF
KSFLRTIPND EHQATAMADI IEYFRWNWVG TIAADDDYGR PGIEKFREEA EERDICIDFS
ELISQYSDEE EIQHVVEVIQ NSTAKVIVVF SSGPDLEPLI KEIVRRNITG KIWLASEAWA
SSSLIAMPQY FHVVGGTIGF ALKAGQIPGF REFLKKVHPR KSVHNGFAKE FWEETFNCHL
QEGAKGPLPV DTFLRGHEES GDRFSNSSTA FRPLCTGDEN ISSVETPYID YTHLRISYNV
YLAVYSIAHA LQDIYTCLPG RGLFTNGSCA DIKKVEAWQV LKHLRHLNFT NNMGEQVTFD
ECGDLVGNYS IINWHLSPED GSIVFKEVGY YNVYAKKGER LFINEEKILW SGFSREPLTF
VLSVLQVPFS NCSRDCLAGT RKGIIEGEPT CCFECVECPD GEYSDETDAS ACNKCPDDFW
SNENHTSCIA KEIEFLSWTE PFGIALTLFA VLGIFLTAFV LGVFIKFRNT PIVKATNREL
SYLLLFSLLC CFSSSLFFIG EPQDWTCRLR QPAFGISFVL CISCILVKTN RVLLVFEAKI
PTSFHRKWWG LNLQFLLVFL CTFMQIVICV IWLYTAPPSS YRNQELEDEI IFITCHEGSL
MALGFLIGYT CLLAAICFFF AFKSRKLPEN FNEAKFITFS MLIFFIVWIS FIPAYASTYG
KFVSAVEVIA ILAASFGLLA CIFFNKIYII LFKPSRNTIE EVRCSTAAHA FKVAARATLR
RSNVSRKRSS SLGGSTGSTP SSSISSKSNS EDPFPQPERQ KQQQPLALTQ QEQQQQPLTL
PQQQRSQQQP RCKQKVIFGS GTVTFSLSFD EPQKNAMAHR NSTHQNSLEA QKSSDTLTRH
EPLLPLQCGE TDLDLTVQET GLQGPVGGDQ RPEVEDPEEL SPALVVSSSQ SFVISGGGST
VTENVVNS*
speed 0.32 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

disease causing

 Model: simple_aae, prob: 0.999999999784697 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950199)
  • known disease mutation: rs8334 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:121973221G>TN/A show variant in all transcripts   IGV
HGNC symbol CASR
Ensembl transcript ID ENST00000296154
Genbank transcript ID N/A
UniProt peptide P41180
alteration type single base exchange
alteration region CDS
DNA changes c.185G>T
cDNA.213G>T
g.70692G>T
AA changes R62M Score: 91 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 62
frameshift no
known variant Reference ID: rs121909265
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8334 (pathogenic for Hypocalciuric hypercalcemia, familial, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950199)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2131
5.9181
(flanking)5.9181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost70691sequence motif lost- wt: TCAG|gtaa
 mu: TCAT.gtaa
Donor marginally decreased70691wt: 0.9981 / mu: 0.9199 (marginal change - not scored)wt: GTATCAGGTAAGAAG
mu: GTATCATGTAAGAAG		 ATCA|ggta
Donor marginally increased70694wt: 0.8205 / mu: 0.8923 (marginal change - not scored)wt: TCAGGTAAGAAGAGG
mu: TCATGTAAGAAGAGG		 AGGT|aaga
Donor increased70687wt: 0.22 / mu: 0.28wt: GAATGTATCAGGTAA
mu: GAATGTATCATGTAA		 ATGT|atca
Donor marginally increased70696wt: 0.9935 / mu: 0.9943 (marginal change - not scored)wt: AGGTAAGAAGAGGGG
mu: ATGTAAGAAGAGGGG		 GTAA|gaag
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      62LKSRPESVECIRYNFRGFRWLQAM
mutated  not conserved    62IMYNFRGFRWLQA
Ptroglodytes  all identical  ENSPTRG00000015289  62IRYNFRGFRWLQA
Mmulatta  all identical  ENSMMUG00000007886  62IRYNFRGFRWLQA
Fcatus  all identical  ENSFCAG00000008717  62IRYNFRGFRWLQA
Mmusculus  all identical  ENSMUSG00000051980  62IRYNFRGFRWLQA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016870  63LAARPESTKCVRFNFRGF
Drerio  all identical  ENSDARG00000013649  62VRYNFRGFRWLQS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011400  62LESRPESLECVRYNFRGFR
protein features
start (aa)end (aa)featuredetails 
20612TOPO_DOMExtracellular (Potential).lost
9090CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
130130CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
261261CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
287287CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
386386CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
400400CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
446446CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
468468CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
488488CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
541541CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
594594CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
613635TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
636649TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
650670TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
671681TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
682700TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
701724TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
725745TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
746769TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
770792TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
793805TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
806828TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
829836TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
837862TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
857857CONFLICTI -> T (in Ref. 3; BAA09453).might get lost (downstream of altered splice site)
8631078TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
878878CONFLICTA -> R (in Ref. 3; BAA09453).might get lost (downstream of altered splice site)
880900REGIONInteraction with RNF19A.might get lost (downstream of altered splice site)
926926CONFLICTQ -> R (in Ref. 2; AAA86503).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3237 / 3237
position (AA) of stopcodon in wt / mu AA sequence 1079 / 1079
position of stopcodon in wt / mu cDNA 3265 / 3265
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 29 / 29
chromosome 3
strand 1
last intron/exon boundary 1761
theoretical NMD boundary in CDS 1682
length of CDS 3237
coding sequence (CDS) position 185
cDNA position
(for ins/del: last normal base / first normal base)		 213
gDNA position
(for ins/del: last normal base / first normal base)		 70692
chromosomal position
(for ins/del: last normal base / first normal base)		 121973221
original gDNA sequence snippet GGAGTCTGTGGAATGTATCAGGTAAGAAGAGGGGCCTAATC
altered gDNA sequence snippet GGAGTCTGTGGAATGTATCATGTAAGAAGAGGGGCCTAATC
original cDNA sequence snippet GGAGTCTGTGGAATGTATCAGGTATAATTTCCGTGGGTTTC
altered cDNA sequence snippet GGAGTCTGTGGAATGTATCATGTATAATTTCCGTGGGTTTC
wildtype AA sequence MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC
IRYNFRGFRW LQAMIFAIEE INSSPALLPN LTLGYRIFDT CNTVSKALEA TLSFVAQNKI
DSLNLDEFCN CSEHIPSTIA VVGATGSGVS TAVANLLGLF YIPQVSYASS SRLLSNKNQF
KSFLRTIPND EHQATAMADI IEYFRWNWVG TIAADDDYGR PGIEKFREEA EERDICIDFS
ELISQYSDEE EIQHVVEVIQ NSTAKVIVVF SSGPDLEPLI KEIVRRNITG KIWLASEAWA
SSSLIAMPQY FHVVGGTIGF ALKAGQIPGF REFLKKVHPR KSVHNGFAKE FWEETFNCHL
QEGAKGPLPV DTFLRGHEES GDRFSNSSTA FRPLCTGDEN ISSVETPYID YTHLRISYNV
YLAVYSIAHA LQDIYTCLPG RGLFTNGSCA DIKKVEAWQV LKHLRHLNFT NNMGEQVTFD
ECGDLVGNYS IINWHLSPED GSIVFKEVGY YNVYAKKGER LFINEEKILW SGFSREVPFS
NCSRDCLAGT RKGIIEGEPT CCFECVECPD GEYSDETDAS ACNKCPDDFW SNENHTSCIA
KEIEFLSWTE PFGIALTLFA VLGIFLTAFV LGVFIKFRNT PIVKATNREL SYLLLFSLLC
CFSSSLFFIG EPQDWTCRLR QPAFGISFVL CISCILVKTN RVLLVFEAKI PTSFHRKWWG
LNLQFLLVFL CTFMQIVICV IWLYTAPPSS YRNQELEDEI IFITCHEGSL MALGFLIGYT
CLLAAICFFF AFKSRKLPEN FNEAKFITFS MLIFFIVWIS FIPAYASTYG KFVSAVEVIA
ILAASFGLLA CIFFNKIYII LFKPSRNTIE EVRCSTAAHA FKVAARATLR RSNVSRKRSS
SLGGSTGSTP SSSISSKSNS EDPFPQPERQ KQQQPLALTQ QEQQQQPLTL PQQQRSQQQP
RCKQKVIFGS GTVTFSLSFD EPQKNAMAHR NSTHQNSLEA QKSSDTLTRH EPLLPLQCGE
TDLDLTVQET GLQGPVGGDQ RPEVEDPEEL SPALVVSSSQ SFVISGGGST VTENVVNS*
mutated AA sequence MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC
IMYNFRGFRW LQAMIFAIEE INSSPALLPN LTLGYRIFDT CNTVSKALEA TLSFVAQNKI
DSLNLDEFCN CSEHIPSTIA VVGATGSGVS TAVANLLGLF YIPQVSYASS SRLLSNKNQF
KSFLRTIPND EHQATAMADI IEYFRWNWVG TIAADDDYGR PGIEKFREEA EERDICIDFS
ELISQYSDEE EIQHVVEVIQ NSTAKVIVVF SSGPDLEPLI KEIVRRNITG KIWLASEAWA
SSSLIAMPQY FHVVGGTIGF ALKAGQIPGF REFLKKVHPR KSVHNGFAKE FWEETFNCHL
QEGAKGPLPV DTFLRGHEES GDRFSNSSTA FRPLCTGDEN ISSVETPYID YTHLRISYNV
YLAVYSIAHA LQDIYTCLPG RGLFTNGSCA DIKKVEAWQV LKHLRHLNFT NNMGEQVTFD
ECGDLVGNYS IINWHLSPED GSIVFKEVGY YNVYAKKGER LFINEEKILW SGFSREVPFS
NCSRDCLAGT RKGIIEGEPT CCFECVECPD GEYSDETDAS ACNKCPDDFW SNENHTSCIA
KEIEFLSWTE PFGIALTLFA VLGIFLTAFV LGVFIKFRNT PIVKATNREL SYLLLFSLLC
CFSSSLFFIG EPQDWTCRLR QPAFGISFVL CISCILVKTN RVLLVFEAKI PTSFHRKWWG
LNLQFLLVFL CTFMQIVICV IWLYTAPPSS YRNQELEDEI IFITCHEGSL MALGFLIGYT
CLLAAICFFF AFKSRKLPEN FNEAKFITFS MLIFFIVWIS FIPAYASTYG KFVSAVEVIA
ILAASFGLLA CIFFNKIYII LFKPSRNTIE EVRCSTAAHA FKVAARATLR RSNVSRKRSS
SLGGSTGSTP SSSISSKSNS EDPFPQPERQ KQQQPLALTQ QEQQQQPLTL PQQQRSQQQP
RCKQKVIFGS GTVTFSLSFD EPQKNAMAHR NSTHQNSLEA QKSSDTLTRH EPLLPLQCGE
TDLDLTVQET GLQGPVGGDQ RPEVEDPEEL SPALVVSSSQ SFVISGGGST VTENVVNS*
speed 0.32 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