Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999976964 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM031991)
  • known disease mutation: rs16250 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:49190261C>TN/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.1621G>A
cDNA.1685G>A
g.191416G>A
AA changes D541N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 541
frameshift no
known variant Reference ID: rs28928871
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16250 (pathogenic for Ovarian hyperstimulation syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031991)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031991)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031991)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8871
5.9131
(flanking)-0.1690.886
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 increased191414wt: 0.8955 / mu: 0.8982 (marginal change - not scored)wt: CAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAGC
mu: CAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAGC		 ctag|TGAC
Acc marginally increased191413wt: 0.9554 / mu: 0.9588 (marginal change - not scored)wt: CCAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAG
mu: CCAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAG		 tcta|GTGA
Donor marginally increased191413wt: 0.9668 / mu: 0.9696 (marginal change - not scored)wt: CCTCTAGTGACACCA
mu: CCTCTAGTAACACCA		 TCTA|gtga
distance from splice site 492
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      541VRNPNIVSSSSDTRIAKRMAMLIF
mutated  all conserved    541NTRIAKRMAMLI
Ptroglodytes  all identical  ENSPTRG00000011914  567VRNPNIVSSSSDTRIAKRMAMLI
Mmulatta  all identical  ENSMMUG00000017196  567VRNPNIVSSSSDTRIAKRMAMLI
Fcatus  all identical  ENSFCAG00000001215  567VRNPNIVSSSSDTKIAKRMAMLI
Mmusculus  all identical  ENSMUSG00000032937  566VRNPNIVSSSRDTKIAKRMATLI
Ggallus  all identical  ENSGALG00000009100  567VRNPNVISSNSDTKIAKRMAILI
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000071494  548ANADMRIAKRMAVLI
Dmelanogaster  all conserved  FBgn0016650  694LGRETRQAHQNSPGELSVAKKMA
Celegans  all identical  C50H2.1  634LKENE--TREEDRALITKMTVLV
Xtropicalis  all identical  ENSXETG00000025827  469VRNPDVISSNSDTKIAKRMAILI
protein features
start (aa)end (aa)featuredetails 
529550TRANSMEMHelical; Name=5; (Potential).lost
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 1621
cDNA position
(for ins/del: last normal base / first normal base)		 1685
gDNA position
(for ins/del: last normal base / first normal base)		 191416
chromosomal position
(for ins/del: last normal base / first normal base)		 49190261
original gDNA sequence snippet ACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAGCGC
altered gDNA sequence snippet ACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAGCGC
original cDNA sequence snippet ACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAGCGC
altered cDNA sequence snippet ACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAGCGC
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 LNVLAFVVIC GCYIHIYLTV RNPNIVSSSS
NTRIAKRMAM LIFTDFLCMA PISFFAISAS LKVPLITVSK AKILLVLFHP INSCANPFLY
AIFTKNFRRD FFILLSKCGC YEMQAQIYRT ETSSTVHNTH PRNGHCSSAP RVTSGSTYIL
VPLSHLAQN*
speed 1.06 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