Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999983971 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM020708)
  • known disease mutation: rs16248 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:49190705C>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.1255G>A
cDNA.1375G>A
g.190972G>A
AA changes A419T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 419
frameshift no
known variant Reference ID: rs121909661
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16248 (pathogenic for Ovarian dysgenesis 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM020708)

known disease mutation at this position, please check HGMD for details (HGMD ID CM020708)
known disease mutation at this position, please check HGMD for details (HGMD ID CM020708)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)5.8771
5.8771
(flanking)-0.2970.95
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 increased190973wt: 0.8661 / mu: 0.8682 (marginal change - not scored)wt: AATCTACCTGCTGCTCATTGCATCAGTTGATATCCATACCA
mu: AATCTACCTGCTGCTCATTACATCAGTTGATATCCATACCA		 ttgc|ATCA
Acc marginally increased190977wt: 0.9373 / mu: 0.9378 (marginal change - not scored)wt: TACCTGCTGCTCATTGCATCAGTTGATATCCATACCAAGAG
mu: TACCTGCTGCTCATTACATCAGTTGATATCCATACCAAGAG		 atca|GTTG
Acc increased190975wt: 0.33 / mu: 0.59wt: TCTACCTGCTGCTCATTGCATCAGTTGATATCCATACCAAG
mu: TCTACCTGCTGCTCATTACATCAGTTGATATCCATACCAAG		 gcat|CAGT
Donor marginally increased190977wt: 0.6551 / mu: 0.7065 (marginal change - not scored)wt: GCATCAGTTGATATC
mu: ACATCAGTTGATATC		 ATCA|gttg
distance from splice site 401
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      419DLCIGIYLLLIASVDIHTKSQYHN
mutated  not conserved    419DLCIGIYLLLITSVDIHTKSQYH
Ptroglodytes  all identical  ENSPTRG00000011914  419DLCIGIYLLLIASVDIHTKSQYH
Mmulatta  all identical  ENSMMUG00000017196  419DLCIGIYLLLIASVDIHTKSQYH
Fcatus  all identical  ENSFCAG00000001215  419DLCIGIYLLLIASVDIYTKSQYH
Mmusculus  all identical  ENSMUSG00000032937  418DLCIGIYLLLIASVDIHTKSQYH
Ggallus  all identical  ENSGALG00000009100  419DLCIGIYLLFIASVDIQTKSRYY
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000071494  400DLCMGIYLLLIAAVDIHTQSRYY
Dmelanogaster  all identical  FBgn0016650  546DLCLGLYLLLVACIDAHSMGEYF
Celegans  all identical  C50H2.1  487YLAVLAIADAKMSDEYY
Xtropicalis  all identical  ENSXETG00000025827  321DLCMGVYLLLIAAVDIKTKSQYY
protein features
start (aa)end (aa)featuredetails 
399421TRANSMEMHelical; Name=2; (Potential).lost
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 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 1255
cDNA position
(for ins/del: last normal base / first normal base)		 1375
gDNA position
(for ins/del: last normal base / first normal base)		 190972
chromosomal position
(for ins/del: last normal base / first normal base)		 49190705
original gDNA sequence snippet GAATCTACCTGCTGCTCATTGCATCAGTTGATATCCATACC
altered gDNA sequence snippet GAATCTACCTGCTGCTCATTACATCAGTTGATATCCATACC
original cDNA sequence snippet GAATCTACCTGCTGCTCATTGCATCAGTTGATATCCATACC
altered cDNA sequence snippet GAATCTACCTGCTGCTCATTACATCAGTTGATATCCATACC
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 IGIYLLLITS
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*
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