Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 7.46185408937294e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM043261)
  • known disease mutation: rs8353 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:121973074T>CN/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.38T>C
cDNA.410T>C
g.70545T>C
AA changes L13P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 13
frameshift no
known variant Reference ID: rs104893717
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs8353 (pathogenic for Hypocalciuric hypercalcemia, familial, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM043261)

known disease mutation at this position, please check HGMD for details (HGMD ID CM043261)
known disease mutation at this position, please check HGMD for details (HGMD ID CM043261)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9190.018
1.4590.027
(flanking)-0.7460
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased70540wt: 0.57 / mu: 0.71wt: AGCTGCTGCTGGGTCCTCTTGGCACTCACCTGGCACACCTC
mu: AGCTGCTGCTGGGTCCTCTTGGCACCCACCTGGCACACCTC		 cttg|GCAC
Acc increased70539wt: 0.38 / mu: 0.47wt: TAGCTGCTGCTGGGTCCTCTTGGCACTCACCTGGCACACCT
mu: TAGCTGCTGCTGGGTCCTCTTGGCACCCACCTGGCACACCT		 tctt|GGCA
distance from splice site 148
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      13AFYSCCWVLLALTWHTSAYGPDQR
mutated  not conserved    13AFYSCCWVLLAPTWHTSAYGPDQ
Ptroglodytes  all identical  ENSPTRG00000015289  13AFYSCCWVLLALTWHTSAYGPDQ
Mmulatta  all identical  ENSMMUG00000007886  13AFYCCFWVLLALTWHTSAYGPDQ
Fcatus  all conserved  ENSFCAG00000008717  13AFYSCCLILLAITWCTSAYGPDQ
Mmusculus  all identical  ENSMUSG00000051980  13AWFGYCLALLALTWHSSAYGPDQ
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000016870  14ILLGSGYVISTYGPNQ
Drerio  not conserved  ENSDARG00000013649  13KFYLHYLVLLGSSCVISTYGPNQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011400  13LLCLVPHGSAYGPDK
protein features
start (aa)end (aa)featuredetails 
119SIGNALPotential.lost
20612TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
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 38
cDNA position
(for ins/del: last normal base / first normal base)		 410
gDNA position
(for ins/del: last normal base / first normal base)		 70545
chromosomal position
(for ins/del: last normal base / first normal base)		 121973074
original gDNA sequence snippet CTGCTGGGTCCTCTTGGCACTCACCTGGCACACCTCTGCCT
altered gDNA sequence snippet CTGCTGGGTCCTCTTGGCACCCACCTGGCACACCTCTGCCT
original cDNA sequence snippet CTGCTGGGTCCTCTTGGCACTCACCTGGCACACCTCTGCCT
altered cDNA sequence snippet CTGCTGGGTCCTCTTGGCACCCACCTGGCACACCTCTGCCT
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 LAPTWHTSAY 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*
speed 0.97 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