Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999707753 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:44943757A>GN/A show variant in all transcripts   IGV
HGNC symbol SPG11
Ensembl transcript ID ENST00000559193
Genbank transcript ID N/A
UniProt peptide Q96JI7
alteration type single base exchange
alteration region CDS
DNA changes c.1388T>C
cDNA.1399T>C
g.12120T>C
AA changes F463S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 463
frameshift no
known variant Reference ID: rs3759871
databasehomozygous (G/G)heterozygousallele carriers
1000G56212541816
ExAC13393598119374
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3030.004
0.690.009
(flanking)0.2670.012
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 increased12127wt: 0.8616 / mu: 0.8772 (marginal change - not scored)wt: GGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTATTCCTGT
mu: GGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTATTCCTGT		 cctt|GGCA
Donor increased12111wt: 0.65 / mu: 0.76wt: GGGCATGCAGTGTTT
mu: GGGCATGCAGTGTTC		 GCAT|gcag
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      463LWDLETQGMQCFSLGTKCIPVDSS
mutated  not conserved    463LWDLETQGMQCSSLGTKCIPVDS
Ptroglodytes  all identical  ENSPTRG00000007016  463LWDLETQGMQCFSLGTKCIPVDS
Mmulatta  all identical  ENSMMUG00000014291  460LWDLENQGMQCFSLGRKCIPVDS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000033396  456LWDLETQSMQCFSLSQKCTPVDI
Ggallus  all conserved  ENSGALG00000008180  471LWDFESQDVAHYQFGKNSVYVDC
Trubripes  not conserved  ENSTRUG00000014452  394SGRVSYHQTCGEAAPVQR
Drerio  no alignment  ENSDARG00000045968  n/a
Dmelanogaster  no alignment  FBgn0034786  n/a
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000025297  341QWDMQSKEISSYPLGKAHFVHCS
protein features
start (aa)end (aa)featuredetails 
11237TOPO_DOMExtracellular (Potential).lost
612612CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
10461046CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
12051205CONFLICTN -> K (in Ref. 5; CAH10686).might get lost (downstream of altered splice site)
12381258TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
12591471TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
14721492TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
14932443TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
16741674CONFLICTR -> G (in Ref. 6; BAC03600).might get lost (downstream of altered splice site)
19551955MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
19581958MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
19611961MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
22532253CONFLICTD -> G (in Ref. 4; AAH94704).might get lost (downstream of altered splice site)
23782378CONFLICTF -> L (in Ref. 6; BAB15065).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2340 / 2340
position (AA) of stopcodon in wt / mu AA sequence 780 / 780
position of stopcodon in wt / mu cDNA 2351 / 2351
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 12 / 12
chromosome 15
strand -1
last intron/exon boundary 2256
theoretical NMD boundary in CDS 2194
length of CDS 2340
coding sequence (CDS) position 1388
cDNA position
(for ins/del: last normal base / first normal base)		 1399
gDNA position
(for ins/del: last normal base / first normal base)		 12120
chromosomal position
(for ins/del: last normal base / first normal base)		 44943757
original gDNA sequence snippet GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA
altered gDNA sequence snippet GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA
original cDNA sequence snippet GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA
altered cDNA sequence snippet GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA
wildtype AA sequence MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVGKGETT*
mutated AA sequence MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCSSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVGKGETT*
speed 0.72 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