Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999987 (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) chr5:35692775T>AN/A show variant in all transcripts   IGV
HGNC symbol SPEF2
Ensembl transcript ID ENST00000509059
Genbank transcript ID N/A
UniProt peptide Q9C093
alteration type single base exchange
alteration region CDS
DNA changes c.1848T>A
cDNA.2002T>A
g.74830T>A
AA changes N616K Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 616
frameshift no
known variant Reference ID: rs7710284
databasehomozygous (A/A)heterozygousallele carriers
1000G4069761382
ExAC39651883822803
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1310.001
-0.7380
(flanking)-0.5780
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased74834wt: 0.8426 / mu: 0.8894 (marginal change - not scored)wt: ATGATGAAGAAGATG
mu: AAGATGAAGAAGATG		 GATG|aaga
Donor increased74830wt: 0.40 / mu: 0.85wt: AAAAATGATGAAGAA
mu: AAAAAAGATGAAGAA		 AAAT|gatg
Donor increased74825wt: 0.22 / mu: 0.86wt: TTCAGAAAAATGATG
mu: TTCAGAAAAAAGATG		 CAGA|aaaa
Donor marginally increased74831wt: 0.9677 / mu: 0.9867 (marginal change - not scored)wt: AAAATGATGAAGAAG
mu: AAAAAGATGAAGAAG		 AATG|atga
Donor gained748240.32mu: ATTCAGAAAAAAGAT TCAG|aaaa
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      616EKVSEVLPIQKNDEEDALPVLQEE
mutated  not conserved    616EKVSEVLPIQKKDEEDALPVLQE
Ptroglodytes  not conserved  ENSPTRG00000016788  616EKVSEVLPIQKKDEEDALPVLQE
Mmulatta  not conserved  ENSMMUG00000018739  616EKVSEVLPIQKKDEENALPVLQE
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000072663  559QKSGKTPPTQEDDKRDPV-VNQE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000042913  615KQAASESQNEKSLEKNVSQTEHTTEQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
732758COILEDPotential.might get lost (downstream of altered splice site)
871909COILEDPotential.might get lost (downstream of altered splice site)
982982CROSSLNKGlycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin).might get lost (downstream of altered splice site)
16861712COILEDPotential.might get lost (downstream of altered splice site)
16981698CONFLICTD -> G (in Ref. 1; BAB15563).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2832 / 2832
position (AA) of stopcodon in wt / mu AA sequence 944 / 944
position of stopcodon in wt / mu cDNA 2986 / 2986
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 155 / 155
chromosome 5
strand 1
last intron/exon boundary 2805
theoretical NMD boundary in CDS 2600
length of CDS 2832
coding sequence (CDS) position 1848
cDNA position
(for ins/del: last normal base / first normal base)		 2002
gDNA position
(for ins/del: last normal base / first normal base)		 74830
chromosomal position
(for ins/del: last normal base / first normal base)		 35692775
original gDNA sequence snippet GTTCTACCAATTCAGAAAAATGATGAAGAAGATGCTCTACC
altered gDNA sequence snippet GTTCTACCAATTCAGAAAAAAGATGAAGAAGATGCTCTACC
original cDNA sequence snippet GTTCTACCAATTCAGAAAAATGATGAAGAAGATGCTCTACC
altered cDNA sequence snippet GTTCTACCAATTCAGAAAAAAGATGAAGAAGATGCTCTACC
wildtype AA sequence MSEILCQWLN KELKVSRTVS PKSFAKAFSS GYLLGEVLHK FELQDDFSEF LDSRVSSAKL
NNFSRLEPTL NLLGVQFDQN VAHGIITEKP GVATKLLYQL YIALQKKKKS GLTGVEMQTM
QRLTNLRLQN MKSDTFQERL RHMIPRQTDF NLMRITYRFQ EKYKHVKEDL AHLHFEKLER
FQKLKEEQRC FDIEKQYLNR RRQNEIMAKI QAAIIQIPKP ASNRTLKALE AQKMMKKKKE
AEDVADEIKK FEALIKKDLQ AKESASKTSL DTAGQTTTDL LNTYSDDEYI KKIQKRLEED
AFAREQREKR RRKLLMDQLI AHEAQEEAYR EEQLINRLMR QSQQERRIAV QLMHVRHEKE
VLWQNRIFRE KQHEERRLKD FQDALDREAA LAKQAKIDFE EQFLKEKRFH DQIAVERAQA
RYEKHYSVCA EILDQIVDLS TKVADYRMLT NNLIPYKLMH DWKELFFNAK PIYEQASVKT
LPANPSREQL TELEKRDLLD TNDYEEYKNM VGEWALPEEM VDNLPPSNNC ILGHILHRLA
EKSLPPRAES TTPELPSFAV KGCLLGKTLS GKTTILRSLQ KDFPIQILSI DTLVQEAIQA
FHDNEKVSEV LPIQKNDEED ALPVLQEEIK ESQDPQHVFS AGPVSDEVLP ETEGANADKT
PKAEEVKSSD SFLKLTTRAQ LGAKSEQLLK KGKSIPDVLL VDIIVNAINE IPVNQDCILD
GFPMTLNQAQ LLEEALTGCN RNLTEVERKK AQKSTLAIDP ATSKEIPLPS PAFDFVILLD
VSDTSSMSRM NDIIAEELSY KTAHEDISQR VAAENQDKDG DQNLRDQIQH RIIGFLDNWP
LLEQWFSEPE NILIKINAEI DKESLCEKVK EILTTEIAKK KNKVEKKLEE KEAEKKAAAS
LAELPLPTPP PAPPPEPEKE KEIHQSHVAS KTPTAKGKPQ SGD*
mutated AA sequence MSEILCQWLN KELKVSRTVS PKSFAKAFSS GYLLGEVLHK FELQDDFSEF LDSRVSSAKL
NNFSRLEPTL NLLGVQFDQN VAHGIITEKP GVATKLLYQL YIALQKKKKS GLTGVEMQTM
QRLTNLRLQN MKSDTFQERL RHMIPRQTDF NLMRITYRFQ EKYKHVKEDL AHLHFEKLER
FQKLKEEQRC FDIEKQYLNR RRQNEIMAKI QAAIIQIPKP ASNRTLKALE AQKMMKKKKE
AEDVADEIKK FEALIKKDLQ AKESASKTSL DTAGQTTTDL LNTYSDDEYI KKIQKRLEED
AFAREQREKR RRKLLMDQLI AHEAQEEAYR EEQLINRLMR QSQQERRIAV QLMHVRHEKE
VLWQNRIFRE KQHEERRLKD FQDALDREAA LAKQAKIDFE EQFLKEKRFH DQIAVERAQA
RYEKHYSVCA EILDQIVDLS TKVADYRMLT NNLIPYKLMH DWKELFFNAK PIYEQASVKT
LPANPSREQL TELEKRDLLD TNDYEEYKNM VGEWALPEEM VDNLPPSNNC ILGHILHRLA
EKSLPPRAES TTPELPSFAV KGCLLGKTLS GKTTILRSLQ KDFPIQILSI DTLVQEAIQA
FHDNEKVSEV LPIQKKDEED ALPVLQEEIK ESQDPQHVFS AGPVSDEVLP ETEGANADKT
PKAEEVKSSD SFLKLTTRAQ LGAKSEQLLK KGKSIPDVLL VDIIVNAINE IPVNQDCILD
GFPMTLNQAQ LLEEALTGCN RNLTEVERKK AQKSTLAIDP ATSKEIPLPS PAFDFVILLD
VSDTSSMSRM NDIIAEELSY KTAHEDISQR VAAENQDKDG DQNLRDQIQH RIIGFLDNWP
LLEQWFSEPE NILIKINAEI DKESLCEKVK EILTTEIAKK KNKVEKKLEE KEAEKKAAAS
LAELPLPTPP PAPPPEPEKE KEIHQSHVAS KTPTAKGKPQ SGD*
speed 1.12 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