Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999717683985 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM067992)
  • known disease mutation: rs16253 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:49190326A>GN/A show variant in all transcripts   IGV
HGNC symbol FSHR
Ensembl transcript ID ENST00000304421
Genbank transcript ID NM_181446
UniProt peptide P23945
alteration type single base exchange
alteration region CDS
DNA changes c.1556T>C
cDNA.1620T>C
g.191351T>C
AA changes I519T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 519
frameshift no
known variant Reference ID: rs121909664
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16253 (pathogenic for Ovarian hyperstimulation syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM067992)

known disease mutation at this position, please check HGMD for details (HGMD ID CM067992)
known disease mutation at this position, please check HGMD for details (HGMD ID CM067992)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7841
4.8871
(flanking)2.4151
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 increased191347wt: 0.2976 / mu: 0.3252 (marginal change - not scored)wt: TCAATGTCCTGGCCTTTGTGGTCATCTGTGGCTGCTATATC
mu: TCAATGTCCTGGCCTTTGTGGTCACCTGTGGCTGCTATATC		 gtgg|TCAT
Acc marginally increased191345wt: 0.7249 / mu: 0.7872 (marginal change - not scored)wt: GCTCAATGTCCTGGCCTTTGTGGTCATCTGTGGCTGCTATA
mu: GCTCAATGTCCTGGCCTTTGTGGTCACCTGTGGCTGCTATA		 ttgt|GGTC
Acc marginally increased191343wt: 0.3631 / mu: 0.4300 (marginal change - not scored)wt: GTGCTCAATGTCCTGGCCTTTGTGGTCATCTGTGGCTGCTA
mu: GTGCTCAATGTCCTGGCCTTTGTGGTCACCTGTGGCTGCTA		 cttt|GTGG
Donor gained1913460.44mu: TTTGTGGTCACCTGT TGTG|gtca
distance from splice site 557
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      519LLVLNVLAFVVICGCYIHIYLTVR
mutated  not conserved    519LLVLNVLAFVVTCGCYIHIYLTV
Ptroglodytes  all identical  ENSPTRG00000011914  545AFVVICGCYIHMYLTV
Mmulatta  all identical  ENSMMUG00000017196  545AFVVICGCYTHIYLTV
Fcatus  all identical  ENSFCAG00000001215  545AFVVICCCYAHIYLTV
Mmusculus  all identical  ENSMUSG00000032937  544AFVVICGCYTHIYLTV
Ggallus  all identical  ENSGALG00000009100  545AFVIICICYICIYFTV
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000071494  526LLLLNAAAFLVVCVCYTLIYLTV
Dmelanogaster  all identical  FBgn0016650  672ILGSNGVAFSIIAVCYAQIYLSL
Celegans  all conserved  C50H2.1  612FNFLAFAAMALSYGFIVKML
Xtropicalis  all identical  ENSXETG00000025827  447LLVLNVLAFVVICTCYIGIYLTV
protein features
start (aa)end (aa)featuredetails 
509528TOPO_DOMExtracellular (Potential).lost
529550TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
551573TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
574597TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
598608TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
609630TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
631695TOPO_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 2010 / 2010
position (AA) of stopcodon in wt / mu AA sequence 670 / 670
position of stopcodon in wt / mu cDNA 2074 / 2074
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 65 / 65
chromosome 2
strand -1
last intron/exon boundary 841
theoretical NMD boundary in CDS 726
length of CDS 2010
coding sequence (CDS) position 1556
cDNA position
(for ins/del: last normal base / first normal base)		 1620
gDNA position
(for ins/del: last normal base / first normal base)		 191351
chromosomal position
(for ins/del: last normal base / first normal base)		 49190326
original gDNA sequence snippet TGTCCTGGCCTTTGTGGTCATCTGTGGCTGCTATATCCACA
altered gDNA sequence snippet TGTCCTGGCCTTTGTGGTCACCTGTGGCTGCTATATCCACA
original cDNA sequence snippet TGTCCTGGCCTTTGTGGTCATCTGTGGCTGCTATATCCACA
altered cDNA sequence snippet TGTCCTGGCCTTTGTGGTCACCTGTGGCTGCTATATCCACA
wildtype AA sequence MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLW LNKNGIQEIH NCAFNGTQLD ELNLSDNNNL
EELPNDVFHG ASGPVILDIS RTRIHSLPSY GLENLKKLRA RSTYNLKKLP TLEKLVALME
ASLTYPSHCC AFANWRRQIS ELHPICNKSI LRQEVDYMTQ ARGQRSSLAE DNESSYSRGF
DMTYTEFDYD LCNEVVDVTC SPKPDAFNPC EDIMGYNILR VLIWFISILA ITGNIIVLVI
LTTSQYKLTV PRFLMCNLAF ADLCIGIYLL LIASVDIHTK SQYHNYAIDW QTGAGCDAAG
FFTVFASELS VYTLTAITLE RWHTITHAMQ LDCKVQLRHA ASVMVMGWIF AFAAALFPIF
GISSYMKVSI CLPMDIDSPL SQLYVMSLLV LNVLAFVVIC GCYIHIYLTV RNPNIVSSSS
DTRIAKRMAM LIFTDFLCMA PISFFAISAS LKVPLITVSK AKILLVLFHP INSCANPFLY
AIFTKNFRRD FFILLSKCGC YEMQAQIYRT ETSSTVHNTH PRNGHCSSAP RVTSGSTYIL
VPLSHLAQN*
mutated AA sequence MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLW LNKNGIQEIH NCAFNGTQLD ELNLSDNNNL
EELPNDVFHG ASGPVILDIS RTRIHSLPSY GLENLKKLRA RSTYNLKKLP TLEKLVALME
ASLTYPSHCC AFANWRRQIS ELHPICNKSI LRQEVDYMTQ ARGQRSSLAE DNESSYSRGF
DMTYTEFDYD LCNEVVDVTC SPKPDAFNPC EDIMGYNILR VLIWFISILA ITGNIIVLVI
LTTSQYKLTV PRFLMCNLAF ADLCIGIYLL LIASVDIHTK SQYHNYAIDW QTGAGCDAAG
FFTVFASELS VYTLTAITLE RWHTITHAMQ LDCKVQLRHA ASVMVMGWIF AFAAALFPIF
GISSYMKVSI CLPMDIDSPL SQLYVMSLLV LNVLAFVVTC GCYIHIYLTV RNPNIVSSSS
DTRIAKRMAM LIFTDFLCMA PISFFAISAS LKVPLITVSK AKILLVLFHP INSCANPFLY
AIFTKNFRRD FFILLSKCGC YEMQAQIYRT ETSSTVHNTH PRNGHCSSAP RVTSGSTYIL
VPLSHLAQN*
speed 0.95 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