Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997493906 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM031989)
  • known disease mutation at this position (HGMD CM1514360)
  • known disease mutation: rs16249 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:49190614G>AN/A show variant in all transcripts   IGV
HGNC symbol FSHR
Ensembl transcript ID ENST00000406846
Genbank transcript ID NM_000145
UniProt peptide P23945
alteration type single base exchange
alteration region CDS
DNA changes c.1346C>T
cDNA.1466C>T
g.191063C>T
AA changes T449I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 449
frameshift no
known variant Reference ID: rs28928870
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16249 (pathogenic for Ovarian hyperstimulation syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM1514360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1514360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031989)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1514360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031989)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031989)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.9920.076
5.9771
(flanking)2.2961
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased191069wt: 0.73 / mu: 0.82wt: TGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCT
mu: TGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCT		 tctt|TGCC
Acc marginally increased191070wt: 0.8597 / mu: 0.8632 (marginal change - not scored)wt: GCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTA
mu: GCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTA		 cttt|GCCA
Acc increased191062wt: 0.39 / mu: 0.45wt: GTGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTG
mu: GTGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTG		 ttca|CTGT
Acc marginally increased191071wt: 0.8714 / mu: 0.9260 (marginal change - not scored)wt: CTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTAC
mu: CTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTAC		 tttg|CCAG
Acc marginally increased191072wt: 0.9318 / mu: 0.9611 (marginal change - not scored)wt: TGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTACA
mu: TGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTACA		 ttgc|CAGT
Acc marginally increased191068wt: 0.9908 / mu: 0.9944 (marginal change - not scored)wt: CTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTC
mu: CTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTC		 gtct|TTGC
Acc increased191065wt: 0.63 / mu: 0.78wt: ATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCA
mu: ATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCA		 actg|TCTT
Acc marginally increased191074wt: 0.9925 / mu: 0.9948 (marginal change - not scored)wt: GCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTACACT
mu: GCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTACACT		 gcca|GTGA
Acc marginally increased191061wt: 0.8817 / mu: 0.9376 (marginal change - not scored)wt: TGTGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCT
mu: TGTGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCT		 tttc|ACTG
Acc marginally increased191066wt: 0.7906 / mu: 0.8393 (marginal change - not scored)wt: TGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAG
mu: TGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAG		 ctgt|CTTT
distance from splice site 492
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      449TGAGCDAAGFFTVFASELSVYTLT
mutated  not conserved    449TGAGCDAAGFFIVFASELSVYTL
Ptroglodytes  all identical  ENSPTRG00000011914  449TGAGCDAAGFFTVFASELSVYTL
Mmulatta  all identical  ENSMMUG00000017196  449TGAGCDAAGFFTVFASELSVYTL
Fcatus  all identical  ENSFCAG00000001215  449TGAGCDAAGFFTVFASELSVYTL
Mmusculus  all identical  ENSMUSG00000032937  448TGAGCDAAGFFTVFASELSVYTL
Ggallus  all identical  ENSGALG00000009100  449TGAGCNAAGFFTVFASELSVYTL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000071494  430VAGFFTVFSSELSVYTL
Dmelanogaster  all identical  FBgn0016650  576YGLGCKVAGFLTVFAS
Celegans  not conserved  C50H2.1  517TGWGCRAAGFLAVFASELGIISM
Xtropicalis  all identical  ENSXETG00000025827  351TGAGCHAAGFFTVFASELSVF
protein features
start (aa)end (aa)featuredetails 
444465TRANSMEMHelical; Name=3; (Potential).lost
466485TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
486508TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
509528TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
517517DISULFIDBy similarity.might get lost (downstream of altered splice site)
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 2088 / 2088
position (AA) of stopcodon in wt / mu AA sequence 696 / 696
position of stopcodon in wt / mu cDNA 2208 / 2208
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 121 / 121
chromosome 2
strand -1
last intron/exon boundary 975
theoretical NMD boundary in CDS 804
length of CDS 2088
coding sequence (CDS) position 1346
cDNA position
(for ins/del: last normal base / first normal base)		 1466
gDNA position
(for ins/del: last normal base / first normal base)		 191063
chromosomal position
(for ins/del: last normal base / first normal base)		 49190614
original gDNA sequence snippet TGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGT
altered gDNA sequence snippet TGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGT
original cDNA sequence snippet TGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGT
altered cDNA sequence snippet TGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGT
wildtype AA sequence MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCAF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILDISRTRI HSLPSYGLEN
LKKLRARSTY NLKKLPTLEK LVALMEASLT YPSHCCAFAN WRRQISELHP ICNKSILRQE
VDYMTQARGQ RSSLAEDNES SYSRGFDMTY TEFDYDLCNE VVDVTCSPKP DAFNPCEDIM
GYNILRVLIW FISILAITGN IIVLVILTTS QYKLTVPRFL MCNLAFADLC IGIYLLLIAS
VDIHTKSQYH NYAIDWQTGA GCDAAGFFTV FASELSVYTL TAITLERWHT ITHAMQLDCK
VQLRHAASVM VMGWIFAFAA ALFPIFGISS YMKVSICLPM DIDSPLSQLY VMSLLVLNVL
AFVVICGCYI HIYLTVRNPN IVSSSSDTRI AKRMAMLIFT DFLCMAPISF FAISASLKVP
LITVSKAKIL LVLFHPINSC ANPFLYAIFT KNFRRDFFIL LSKCGCYEMQ AQIYRTETSS
TVHNTHPRNG HCSSAPRVTS GSTYILVPLS HLAQN*
mutated AA sequence MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCAF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILDISRTRI HSLPSYGLEN
LKKLRARSTY NLKKLPTLEK LVALMEASLT YPSHCCAFAN WRRQISELHP ICNKSILRQE
VDYMTQARGQ RSSLAEDNES SYSRGFDMTY TEFDYDLCNE VVDVTCSPKP DAFNPCEDIM
GYNILRVLIW FISILAITGN IIVLVILTTS QYKLTVPRFL MCNLAFADLC IGIYLLLIAS
VDIHTKSQYH NYAIDWQTGA GCDAAGFFIV FASELSVYTL TAITLERWHT ITHAMQLDCK
VQLRHAASVM VMGWIFAFAA ALFPIFGISS YMKVSICLPM DIDSPLSQLY VMSLLVLNVL
AFVVICGCYI HIYLTVRNPN IVSSSSDTRI AKRMAMLIFT DFLCMAPISF FAISASLKVP
LITVSKAKIL LVLFHPINSC ANPFLYAIFT KNFRRDFFIL LSKCGCYEMQ AQIYRTETSS
TVHNTHPRNG HCSSAPRVTS GSTYILVPLS HLAQN*
speed 0.54 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