Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999697584 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM120703)
  • known disease mutation: rs100522 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:225368370T>CN/A show variant in all transcripts   IGV
HGNC symbol CUL3
Ensembl transcript ID ENST00000264414
Genbank transcript ID NM_001257198
UniProt peptide Q13618
alteration type single base exchange
alteration region CDS
DNA changes c.1376A>G
cDNA.1715A>G
g.81741A>G
AA changes K459R Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 459
frameshift no
known variant Reference ID: rs199469658
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs100522 (pathogenic for Pseudohypoaldosteronism type 2A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM120703)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.1741
5.0991
(flanking)5.0991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost81742sequence motif lost- wt: AAAG|gtaa
 mu: AAGG.gtaa
Donor marginally increased81735wt: 0.9795 / mu: 0.9990 (marginal change - not scored)wt: ATCTAAGTTAAAGGT
mu: ATCTAAGTTAAGGGT		 CTAA|gtta
Donor marginally decreased81742wt: 0.9961 / mu: 0.9937 (marginal change - not scored)wt: TTAAAGGTAAGGTGT
mu: TTAAGGGTAAGGTGT		 AAAG|gtaa
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      459DDSEKNMISKLKTECGCQFTSKLE
mutated  all conserved    459DDSEKNMISKLRTECGCQFTSKL
Ptroglodytes  all identical  ENSPTRG00000012986  459DDSEKNMISKLKTECGCQFTSKL
Mmulatta  all identical  ENSMMUG00000022259  459DDSEKNMISKLKTECGCQFTSKL
Fcatus  not conserved  ENSFCAG00000008145  371XXXXXXXXXXXTECGCQFTSKL
Mmusculus  all identical  ENSMUSG00000004364  459DDSEKNMISKLKTECGCQFTSKL
Ggallus  all identical  ENSGALG00000005108  437DDSEKNMISKLKTECGCQFTSKL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000038967  457DDSEKNMISKLKTECGCQFTSKL
Dmelanogaster  all identical  FBgn0261268  620DDFEKNMISKLKTECGCQFTSKL
Celegans  all identical  Y108G3AL.1  465DDVEKALLAKLKTECGCQFTQKL
Xtropicalis  all identical  ENSXETG00000008183  459DDSEKNMISKLKTECGCQFTSKL
protein features
start (aa)end (aa)featuredetails 
481481CONFLICTN -> T (in Ref. 4; AAQ01660).might get lost (downstream of altered splice site)
609609CONFLICTE -> G (in Ref. 8; AAH31844).might get lost (downstream of altered splice site)
666666CONFLICTT -> I (in Ref. 4; AAQ01660).might get lost (downstream of altered splice site)
712712CROSSLNKGlycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8) (By similarity).might get lost (downstream of altered splice site)
737737MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2307 / 2307
position (AA) of stopcodon in wt / mu AA sequence 769 / 769
position of stopcodon in wt / mu cDNA 2646 / 2646
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 340 / 340
chromosome 2
strand -1
last intron/exon boundary 2515
theoretical NMD boundary in CDS 2125
length of CDS 2307
coding sequence (CDS) position 1376
cDNA position
(for ins/del: last normal base / first normal base)		 1715
gDNA position
(for ins/del: last normal base / first normal base)		 81741
chromosomal position
(for ins/del: last normal base / first normal base)		 225368370
original gDNA sequence snippet AAACATGATATCTAAGTTAAAGGTAAGGTGTGTTTTAGATG
altered gDNA sequence snippet AAACATGATATCTAAGTTAAGGGTAAGGTGTGTTTTAGATG
original cDNA sequence snippet AAACATGATATCTAAGTTAAAGACTGAATGTGGATGTCAGT
altered cDNA sequence snippet AAACATGATATCTAAGTTAAGGACTGAATGTGGATGTCAGT
wildtype AA sequence MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN
AYTMVLHKHG EKLYTGLREV VTEHLINKVR EDVLNSLNNN FLQTLNQAWN DHQTAMVMIR
DILMYMDRVY VQQNNVENVY NLGLIIFRDQ VVRYGCIRDH LRQTLLDMIA RERKGEVVDR
GAIRNACQML MILGLEGRSV YEEDFEAPFL EMSAEFFQME SQKFLAENSA SVYIKKVEAR
INEEIERVMH CLDKSTEEPI VKVVERELIS KHMKTIVEME NSGLVHMLKN GKTEDLGCMY
KLFSRVPNGL KTMCECMSSY LREQGKALVS EEGEGKNPVD YIQGLLDLKS RFDRFLLESF
NNDRLFKQTI AGDFEYFLNL NSRSPEYLSL FIDDKLKKGV KGLTEQEVET ILDKAMVLFR
FMQEKDVFER YYKQHLARRL LTNKSVSDDS EKNMISKLKT ECGCQFTSKL EGMFRDMSIS
NTTMDEFRQH LQATGVSLGG VDLTVRVLTT GYWPTQSATP KCNIPPAPRH AFEIFRRFYL
AKHSGRQLTL QHHMGSADLN ATFYGPVKKE DGSEVGVGGA QVTGSNTRKH ILQVSTFQMT
ILMLFNNREK YTFEEIQQET DIPERELVRA LQSLACGKPT QRVLTKEPKS KEIENGHIFT
VNDQFTSKLH RVKIQTVAAK QGESDPERKE TRQKVDDDRK HEIEAAIVRI MKSRKKMQHN
VLVAEVTQQL KARFLPSPVV IKKRIEGLIE REYLARTPED RKVYTYVA*
mutated AA sequence MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN
AYTMVLHKHG EKLYTGLREV VTEHLINKVR EDVLNSLNNN FLQTLNQAWN DHQTAMVMIR
DILMYMDRVY VQQNNVENVY NLGLIIFRDQ VVRYGCIRDH LRQTLLDMIA RERKGEVVDR
GAIRNACQML MILGLEGRSV YEEDFEAPFL EMSAEFFQME SQKFLAENSA SVYIKKVEAR
INEEIERVMH CLDKSTEEPI VKVVERELIS KHMKTIVEME NSGLVHMLKN GKTEDLGCMY
KLFSRVPNGL KTMCECMSSY LREQGKALVS EEGEGKNPVD YIQGLLDLKS RFDRFLLESF
NNDRLFKQTI AGDFEYFLNL NSRSPEYLSL FIDDKLKKGV KGLTEQEVET ILDKAMVLFR
FMQEKDVFER YYKQHLARRL LTNKSVSDDS EKNMISKLRT ECGCQFTSKL EGMFRDMSIS
NTTMDEFRQH LQATGVSLGG VDLTVRVLTT GYWPTQSATP KCNIPPAPRH AFEIFRRFYL
AKHSGRQLTL QHHMGSADLN ATFYGPVKKE DGSEVGVGGA QVTGSNTRKH ILQVSTFQMT
ILMLFNNREK YTFEEIQQET DIPERELVRA LQSLACGKPT QRVLTKEPKS KEIENGHIFT
VNDQFTSKLH RVKIQTVAAK QGESDPERKE TRQKVDDDRK HEIEAAIVRI MKSRKKMQHN
VLVAEVTQQL KARFLPSPVV IKKRIEGLIE REYLARTPED RKVYTYVA*
speed 1.22 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