Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999633780756 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080377)
  • known disease mutation: rs16254 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:49217768G>TN/A show variant in all transcripts   IGV
HGNC symbol FSHR
Ensembl transcript ID ENST00000346173
Genbank transcript ID N/A
UniProt peptide P23945
alteration type single base exchange
alteration region CDS
DNA changes c.383C>A
cDNA.493C>A
g.163909C>A
AA changes S128Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 128
frameshift no
known variant Reference ID: rs121909665
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16254 (pathogenic for Ovarian hyperstimulation syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080377)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080377)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080377)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0540.998
3.7751
(flanking)3.1511
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 increased163904wt: 0.6695 / mu: 0.6843 (marginal change - not scored)wt: ATTTTGTTTCTCTCTAGGTTAATATCCAACACAGGTATTAA
mu: ATTTTGTTTCTCTCTAGGTTAATATACAACACAGGTATTAA		 gtta|ATAT
Acc marginally increased163899wt: 0.9952 / mu: 0.9955 (marginal change - not scored)wt: CTCTCATTTTGTTTCTCTCTAGGTTAATATCCAACACAGGT
mu: CTCTCATTTTGTTTCTCTCTAGGTTAATATACAACACAGGT		 tcta|GGTT
Donor marginally increased163912wt: 0.9629 / mu: 0.9662 (marginal change - not scored)wt: ATCCAACACAGGTAT
mu: ATACAACACAGGTAT		 CCAA|caca
Acc gained1639080.44mu: TGTTTCTCTCTAGGTTAATATACAACACAGGTATTAAGCAC atat|ACAA
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      128QNLPNLQYLLISNTGIKHLPDVHK
mutated  not conserved    128NLQYLLIYNTGIKHLPDVH
Ptroglodytes  all identical  ENSPTRG00000011914  128NLQYLLISNTGIKHLPDVH
Mmulatta  all identical  ENSMMUG00000017196  128NLRYLLISNTGIKHLPDVH
Fcatus  not conserved  ENSFCAG00000001215  128NLRYXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000032937  128SLRYLLISNTGIKHLPAFH
Ggallus  all identical  ENSGALG00000009100  128SLRYLLISNTGLSFLPVVH
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000071494  135WRLPKLRYLTISNTGLKILPDFS
Dmelanogaster  not conserved  FBgn0016650  334-GLQNIEALYIQNTHTLKTIPSIY
Celegans  all identical  C50H2.1  264KNMAGLQTLDLSHTSIDT
Xtropicalis  all identical  ENSXETG00000025827  28QNLPKLKYLLISNTGIHFIPVVS
protein features
start (aa)end (aa)featuredetails 
18366TOPO_DOMExtracellular (Potential).lost
119143REPEATLRR 4.lost
124130STRANDlost
143145STRANDmight get lost (downstream of altered splice site)
144169REPEATLRR 5.might get lost (downstream of altered splice site)
147153STRANDmight get lost (downstream of altered splice site)
168171STRANDmight get lost (downstream of altered splice site)
170192REPEATLRR 6.might get lost (downstream of altered splice site)
173176STRANDmight get lost (downstream of altered splice site)
187192TURNmight get lost (downstream of altered splice site)
191191CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
193199STRANDmight get lost (downstream of altered splice site)
193216REPEATLRR 7.might get lost (downstream of altered splice site)
197198CONFLICTEL -> AV (in Ref. 1; AAA52477).might get lost (downstream of altered splice site)
199199CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
211216TURNmight get lost (downstream of altered splice site)
217240REPEATLRR 8.might get lost (downstream of altered splice site)
221224STRANDmight get lost (downstream of altered splice site)
235237STRANDmight get lost (downstream of altered splice site)
241259REPEATLRR 9.might get lost (downstream of altered splice site)
243245STRANDmight get lost (downstream of altered splice site)
258260TURNmight get lost (downstream of altered splice site)
266268STRANDmight get lost (downstream of altered splice site)
272280HELIXmight get lost (downstream of altered splice site)
293293CARBOHYDN-linked (GlcNAc...) (By similarity).might get lost (downstream of altered splice site)
295295CONFLICTS -> P (in Ref. 8; CAA48179).might get lost (downstream of altered splice site)
318318CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
345348STRANDmight get lost (downstream of altered splice site)
367387TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
388398TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
399421TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
422443TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
442442DISULFIDBy similarity.might get lost (downstream of altered splice site)
444465TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
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 1902 / 1902
position (AA) of stopcodon in wt / mu AA sequence 634 / 634
position of stopcodon in wt / mu cDNA 2012 / 2012
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 111 / 111
chromosome 2
strand -1
last intron/exon boundary 779
theoretical NMD boundary in CDS 618
length of CDS 1902
coding sequence (CDS) position 383
cDNA position
(for ins/del: last normal base / first normal base)		 493
gDNA position
(for ins/del: last normal base / first normal base)		 163909
chromosomal position
(for ins/del: last normal base / first normal base)		 49217768
original gDNA sequence snippet GTTTCTCTCTAGGTTAATATCCAACACAGGTATTAAGCACC
altered gDNA sequence snippet GTTTCTCTCTAGGTTAATATACAACACAGGTATTAAGCACC
original cDNA sequence snippet CCTTCAATATCTGTTAATATCCAACACAGGTATTAAGCACC
altered cDNA sequence snippet CCTTCAATATCTGTTAATATACAACACAGGTATTAAGCACC
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 VILSELHPIC NKSILRQEVD
YMTQARGQRS SLAEDNESSY SRGFDMTYTE FDYDLCNEVV DVTCSPKPDA FNPCEDIMGY
NILRVLIWFI SILAITGNII VLVILTTSQY KLTVPRFLMC NLAFADLCIG IYLLLIASVD
IHTKSQYHNY AIDWQTGAGC DAAGFFTVFA SELSVYTLTA ITLERWHTIT HAMQLDCKVQ
LRHAASVMVM GWIFAFAAAL FPIFGISSYM KVSICLPMDI DSPLSQLYVM SLLVLNVLAF
VVICGCYIHI YLTVRNPNIV SSSSDTRIAK RMAMLIFTDF LCMAPISFFA ISASLKVPLI
TVSKAKILLV LFHPINSCAN PFLYAIFTKN FRRDFFILLS KCGCYEMQAQ IYRTETSSTV
HNTHPRNGHC SSAPRVTSGS TYILVPLSHL AQN*
mutated AA sequence MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLIYNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCAF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILSELHPIC NKSILRQEVD
YMTQARGQRS SLAEDNESSY SRGFDMTYTE FDYDLCNEVV DVTCSPKPDA FNPCEDIMGY
NILRVLIWFI SILAITGNII VLVILTTSQY KLTVPRFLMC NLAFADLCIG IYLLLIASVD
IHTKSQYHNY AIDWQTGAGC DAAGFFTVFA SELSVYTLTA ITLERWHTIT HAMQLDCKVQ
LRHAASVMVM GWIFAFAAAL FPIFGISSYM KVSICLPMDI DSPLSQLYVM SLLVLNVLAF
VVICGCYIHI YLTVRNPNIV SSSSDTRIAK RMAMLIFTDF LCMAPISFFA ISASLKVPLI
TVSKAKILLV LFHPINSCAN PFLYAIFTKN FRRDFFILLS KCGCYEMQAQ IYRTETSSTV
HNTHPRNGHC SSAPRVTSGS TYILVPLSHL AQN*
speed 0.41 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