Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000406846
Querying Taster for transcript #2: ENST00000304421
Querying Taster for transcript #3: ENST00000346173
Querying Taster for transcript #4: ENST00000541117
MT speed 0 s - this script 4.884152 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FSHRdisease_causing_automatic0.999999999594403simple_aae0D567Nsingle base exchangers28928871show file
FSHRdisease_causing_automatic0.999999999594403simple_aae0D303Nsingle base exchangers28928871show file
FSHRdisease_causing_automatic0.99999999976964simple_aae0D541Nsingle base exchangers28928871show file
FSHRdisease_causing_automatic0.99999999976964simple_aae0D505Nsingle base exchangers28928871show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999594403 (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 ENST00000406846
Genbank transcript ID NM_000145
UniProt peptide P23945
alteration type single base exchange
alteration region CDS
DNA changes c.1699G>A
cDNA.1819G>A
g.191416G>A
AA changes D567N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 567
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 increased191413wt: 0.9554 / mu: 0.9588 (marginal change - not scored)wt: CCAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAG
mu: CCAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAG		 tcta|GTGA
Acc marginally increased191414wt: 0.8955 / mu: 0.8982 (marginal change - not scored)wt: CAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAGC
mu: CAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAGC		 ctag|TGAC
Donor marginally increased191413wt: 0.9668 / mu: 0.9696 (marginal change - not scored)wt: CCTCTAGTGACACCA
mu: CCTCTAGTAACACCA		 TCTA|gtga
distance from splice site 845
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      567VRNPNIVSSSSDTRIAKRMAMLIF
mutated  all conserved    567VRNPNIVSSSSNTRIAKRMAMLI
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  694LGRETRQAHQNSPGELSV
Celegans  all identical  C50H2.1  634LKENE--TREEDRALITKMTVLV
Xtropicalis  all identical  ENSXETG00000025827  469VRNPDVISSNSDTKIAKRMAILI
protein features
start (aa)end (aa)featuredetails 
551573TOPO_DOMCytoplasmic (Potential).lost
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 1699
cDNA position
(for ins/del: last normal base / first normal base)		 1819
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 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 GCDAAGFFTV FASELSVYTL TAITLERWHT ITHAMQLDCK
VQLRHAASVM VMGWIFAFAA ALFPIFGISS YMKVSICLPM DIDSPLSQLY VMSLLVLNVL
AFVVICGCYI HIYLTVRNPN IVSSSSNTRI AKRMAMLIFT DFLCMAPISF FAISASLKVP
LITVSKAKIL LVLFHPINSC ANPFLYAIFT KNFRRDFFIL LSKCGCYEMQ AQIYRTETSS
TVHNTHPRNG HCSSAPRVTS GSTYILVPLS HLAQN*
speed 0.53 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999594403 (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 ENST00000541117
Genbank transcript ID N/A
UniProt peptide P23945
alteration type single base exchange
alteration region CDS
DNA changes c.907G>A
cDNA.1460G>A
g.191416G>A
AA changes D303N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 303
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 increased191413wt: 0.9554 / mu: 0.9588 (marginal change - not scored)wt: CCAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAG
mu: CCAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAG		 tcta|GTGA
Acc marginally increased191414wt: 0.8955 / mu: 0.8982 (marginal change - not scored)wt: CAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAGC
mu: CAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAGC		 ctag|TGAC
Donor marginally increased191413wt: 0.9668 / mu: 0.9696 (marginal change - not scored)wt: CCTCTAGTGACACCA
mu: CCTCTAGTAACACCA		 TCTA|gtga
distance from splice site 408
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      303VRNPNIVSSSSDTRIAKRMAMLIF
mutated  all conserved    303SSNTRIAKRMAMLI
Ptroglodytes  all identical  ENSPTRG00000011914  567SSDTRIAKRMAMLI
Mmulatta  all identical  ENSMMUG00000017196  567SSDTRIAKRMAMLI
Fcatus  all identical  ENSFCAG00000001215  567SSDTKIAKRMAMLI
Mmusculus  all identical  ENSMUSG00000032937  566SRDTKIAKRMATLI
Ggallus  all identical  ENSGALG00000009100  567NSDTKIAKRMAILI
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000071494  548ADMRIAKRMAVLI
Dmelanogaster  all conserved  FBgn0016650  694LGRETRQAHQNSPGELSVAKKMALL
Celegans  all identical  C50H2.1  634LKENE--TREEDRALITKMTVLV
Xtropicalis  all identical  ENSXETG00000025827  469SSNSDTKIAKRMAILI
protein features
start (aa)end (aa)featuredetails 
18366TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1296 / 1296
position (AA) of stopcodon in wt / mu AA sequence 432 / 432
position of stopcodon in wt / mu cDNA 1849 / 1849
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 554 / 554
chromosome 2
strand -1
last intron/exon boundary 616
theoretical NMD boundary in CDS 12
length of CDS 1296
coding sequence (CDS) position 907
cDNA position
(for ins/del: last normal base / first normal base)		 1460
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 MEASLTYPSH CCAFANWRRQ ISELHPICNK SILRQEVDYM TQARGQRSSL AEDNESSYSR
GFDMTYTEFD YDLCNEVVDV TCSPKPDAFN PCEDIMGYNI LRVLIWFISI LAITGNIIVL
VILTTSQYKL TVPRFLMCNL AFADLCIGIY LLLIASVDIH TKSQYHNYAI DWQTGAGCDA
AGFFTVFASE LSVYTLTAIT LERWHTITHA MQLDCKVQLR HAASVMVMGW IFAFAAALFP
IFGISSYMKV SICLPMDIDS PLSQLYVMSL LVLNVLAFVV ICGCYIHIYL TVRNPNIVSS
SSDTRIAKRM AMLIFTDFLC MAPISFFAIS ASLKVPLITV SKAKILLVLF HPINSCANPF
LYAIFTKNFR RDFFILLSKC GCYEMQAQIY RTETSSTVHN THPRNGHCSS APRVTSGSTY
ILVPLSHLAQ N*
mutated AA sequence MEASLTYPSH CCAFANWRRQ ISELHPICNK SILRQEVDYM TQARGQRSSL AEDNESSYSR
GFDMTYTEFD YDLCNEVVDV TCSPKPDAFN PCEDIMGYNI LRVLIWFISI LAITGNIIVL
VILTTSQYKL TVPRFLMCNL AFADLCIGIY LLLIASVDIH TKSQYHNYAI DWQTGAGCDA
AGFFTVFASE LSVYTLTAIT LERWHTITHA MQLDCKVQLR HAASVMVMGW IFAFAAALFP
IFGISSYMKV SICLPMDIDS PLSQLYVMSL LVLNVLAFVV ICGCYIHIYL TVRNPNIVSS
SSNTRIAKRM AMLIFTDFLC MAPISFFAIS ASLKVPLITV SKAKILLVLF HPINSCANPF
LYAIFTKNFR RDFFILLSKC GCYEMQAQIY RTETSSTVHN THPRNGHCSS APRVTSGSTY
ILVPLSHLAQ N*
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
back to results table
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 increased191413wt: 0.9554 / mu: 0.9588 (marginal change - not scored)wt: CCAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAG
mu: CCAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAG		 tcta|GTGA
Acc marginally increased191414wt: 0.8955 / mu: 0.8982 (marginal change - not scored)wt: CAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAGC
mu: CAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAGC		 ctag|TGAC
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 0.96 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
back to results table
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 ENST00000346173
Genbank transcript ID N/A
UniProt peptide P23945
alteration type single base exchange
alteration region CDS
DNA changes c.1513G>A
cDNA.1623G>A
g.191416G>A
AA changes D505N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 505
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 increased191413wt: 0.9554 / mu: 0.9588 (marginal change - not scored)wt: CCAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAG
mu: CCAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAG		 tcta|GTGA
Acc marginally increased191414wt: 0.8955 / mu: 0.8982 (marginal change - not scored)wt: CAACATCGTGTCCTCCTCTAGTGACACCAGGATCGCCAAGC
mu: CAACATCGTGTCCTCCTCTAGTAACACCAGGATCGCCAAGC		 ctag|TGAC
Donor marginally increased191413wt: 0.9668 / mu: 0.9696 (marginal change - not scored)wt: CCTCTAGTGACACCA
mu: CCTCTAGTAACACCA		 TCTA|gtga
distance from splice site 845
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      505VRNPNIVSSSSDTRIAKRMAMLIF
mutated  all conserved    505VRNPNIVSSSSNTRIAKRMAMLI
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  548VRNPAFVPANADMRIAKRMAVLI
Dmelanogaster  all conserved  FBgn0016650  696AHQNSPGELSVAKKMALLV
Celegans  all identical  C50H2.1  634LKENE--TREEDRALITKMTVLV
Xtropicalis  all identical  ENSXETG00000025827  469VRNPDVISSNSDTKIAKRMAIL
protein features
start (aa)end (aa)featuredetails 
486508TRANSMEMHelical; Name=4; (Potential).lost
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 1513
cDNA position
(for ins/del: last normal base / first normal base)		 1623
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 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
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 SSSSNTRIAK RMAMLIFTDF LCMAPISFFA ISASLKVPLI
TVSKAKILLV LFHPINSCAN PFLYAIFTKN FRRDFFILLS KCGCYEMQAQ IYRTETSSTV
HNTHPRNGHC SSAPRVTSGS TYILVPLSHL AQN*
speed 0.96 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
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Problems