Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999967367666 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM991256)
  • known disease mutation: rs6372 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:77425043A>CN/A show variant in all transcripts   IGV
HGNC symbol AP3B1
Ensembl transcript ID ENST00000519295
Genbank transcript ID N/A
UniProt peptide O00203
alteration type single base exchange
alteration region CDS
DNA changes c.1592T>G
cDNA.1864T>G
g.165537T>G
AA changes L531R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 531
frameshift no
known variant Reference ID: rs121908904
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6372 (pathogenic for Hermansky-Pudlak syndrome 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM991256)

known disease mutation at this position, please check HGMD for details (HGMD ID CM991256)
known disease mutation at this position, please check HGMD for details (HGMD ID CM991256)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.371
5.0761
(flanking)4.461
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased165531wt: 0.46 / mu: 0.99wt: TATTAGGCAGCTTAT
mu: TATTAGGCAGCGTAT		 TTAG|gcag
Donor increased165534wt: 0.23 / mu: 0.28wt: TAGGCAGCTTATTGT
mu: TAGGCAGCGTATTGT		 GGCA|gctt
distance from splice site 89
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      531DIRDRTRFIRQLIVPNVKSGALSK
mutated  not conserved    531DIRDRTRFIRQRIVPNVKSGA
Ptroglodytes  all identical  ENSPTRG00000017015  580DIRDRTRFIRQLIVPNEKSGA
Mmulatta  all identical  ENSMMUG00000001360  540DIRDRTRFIRQLIVP
Fcatus  no alignment  ENSFCAG00000007759  n/a
Mmusculus  all identical  ENSMUSG00000021686  581DIRDRTRFIRQLIVPNEKSG
Ggallus  all identical  ENSGALG00000004390  583DIRDRTRFIRQLIVPNEKS
Trubripes  all identical  ENSTRUG00000018286  583DIRDRTRFIRQLIVPNEK
Drerio  no alignment  ENSDARG00000089282  n/a
Dmelanogaster  all conserved  FBgn0003210  616DVRDRARFLRQIIFPASGTSSVLS
Celegans  all identical  R11A5.1  541LMF---NTEILS
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
592592MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
609609MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
661661MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
677802COMPBIASGlu/Ser-rich.might get lost (downstream of altered splice site)
804804CONFLICTMissing (in Ref. 1; AAD03778).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3138 / 3138
position (AA) of stopcodon in wt / mu AA sequence 1046 / 1046
position of stopcodon in wt / mu cDNA 3410 / 3410
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 273 / 273
chromosome 5
strand -1
last intron/exon boundary 3257
theoretical NMD boundary in CDS 2934
length of CDS 3138
coding sequence (CDS) position 1592
cDNA position
(for ins/del: last normal base / first normal base)		 1864
gDNA position
(for ins/del: last normal base / first normal base)		 165537
chromosomal position
(for ins/del: last normal base / first normal base)		 77425043
original gDNA sequence snippet TACAAGATTTATTAGGCAGCTTATTGTTCCGAATGTAAAGA
altered gDNA sequence snippet TACAAGATTTATTAGGCAGCGTATTGTTCCGAATGTAAAGA
original cDNA sequence snippet TACAAGATTTATTAGGCAGCTTATTGTTCCGAATGTAAAGA
altered cDNA sequence snippet TACAAGATTTATTAGGCAGCGTATTGTTCCGAATGTAAAGA
wildtype AA sequence MLESNKDSAK LDAMKRIVGM IAKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ
QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS ADLSPYVRKN
AAHAIQKLYS LDPEQKEMLI EVIEKLLKDK STLVAGSVVM AFEEVCPDRI DLIHKNYRKL
CNLLVDVEEW GQVVIIHMLT RYARTQFVSP WKEGDELEDN GKNFYESDDD QKEKTDKKKK
PYTMDPDHRL LIRNTKPLLQ SRNAAVVMAV AQLYWHISPK SEAGIISKSL VRLLRSNREV
QYIVLQNIAT MSIQRKGMFE PYLKSFYVRS TDPTMIKTLK LEILTNLANE ANISTLLREF
QTYVKSQDKQ FAAATIQTIG RCATNILEVT DTCLNGLVCL LSNRDEIVVA ESVVVIKKLL
QMQPAQHGEI IKHMAKLLDS ITVPVARASI LWLIGENCER VPKIAPDVLR KMAKSFTSED
DLVKLQILNL GAKLYLTNSK QTKLLTQYIL NLGKYDQNYD IRDRTRFIRQ LIVPNVKSGA
LSKYAKKIFL AQKPAPLLES PFKDRDHFQL GTLSHTLNIK ATGYLELSNW PEVAPDPSVR
NVEVIELAKE WTPAGKAKQE NSAKKFYSES EEEEDSSDSS SDSESESGSE SGEQGESGEE
GDSNEDSSED SSSEQDSESG RESGLENKRT AKRNSKAKGK SDSEDGEKEN EKSKTSDSSN
DESSSIEDSS SDSESESEPE SESESRRVTK EKEKKTKQDR TPLTKDVSLL DLDDFNPVST
PVALPTPALS PSLMADLEGL HLSTSSSVIS VSTPAFVPTK THVLLHRMSG KGLAAHYFFP
RQPCIFGDKM VSIQITLNNT TDRKIENIHI GEKKLPIGMK MHVFNPIDSL EPEGSITVSM
GIDFCDSTQT ASFQLCTKDD CFNVNIQPPV GELLLPVAMS EKDFKKEQGV LTGMNETSAV
IIAAPQNFTP SVIFQKVVNV ANVGAVPSGQ DNIHRFAAKT VHSGSLMLVT VELKEGSTAQ
LIINTEKTVI GSVLLRELKP VLSQG*
mutated AA sequence MLESNKDSAK LDAMKRIVGM IAKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ
QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS ADLSPYVRKN
AAHAIQKLYS LDPEQKEMLI EVIEKLLKDK STLVAGSVVM AFEEVCPDRI DLIHKNYRKL
CNLLVDVEEW GQVVIIHMLT RYARTQFVSP WKEGDELEDN GKNFYESDDD QKEKTDKKKK
PYTMDPDHRL LIRNTKPLLQ SRNAAVVMAV AQLYWHISPK SEAGIISKSL VRLLRSNREV
QYIVLQNIAT MSIQRKGMFE PYLKSFYVRS TDPTMIKTLK LEILTNLANE ANISTLLREF
QTYVKSQDKQ FAAATIQTIG RCATNILEVT DTCLNGLVCL LSNRDEIVVA ESVVVIKKLL
QMQPAQHGEI IKHMAKLLDS ITVPVARASI LWLIGENCER VPKIAPDVLR KMAKSFTSED
DLVKLQILNL GAKLYLTNSK QTKLLTQYIL NLGKYDQNYD IRDRTRFIRQ RIVPNVKSGA
LSKYAKKIFL AQKPAPLLES PFKDRDHFQL GTLSHTLNIK ATGYLELSNW PEVAPDPSVR
NVEVIELAKE WTPAGKAKQE NSAKKFYSES EEEEDSSDSS SDSESESGSE SGEQGESGEE
GDSNEDSSED SSSEQDSESG RESGLENKRT AKRNSKAKGK SDSEDGEKEN EKSKTSDSSN
DESSSIEDSS SDSESESEPE SESESRRVTK EKEKKTKQDR TPLTKDVSLL DLDDFNPVST
PVALPTPALS PSLMADLEGL HLSTSSSVIS VSTPAFVPTK THVLLHRMSG KGLAAHYFFP
RQPCIFGDKM VSIQITLNNT TDRKIENIHI GEKKLPIGMK MHVFNPIDSL EPEGSITVSM
GIDFCDSTQT ASFQLCTKDD CFNVNIQPPV GELLLPVAMS EKDFKKEQGV LTGMNETSAV
IIAAPQNFTP SVIFQKVVNV ANVGAVPSGQ DNIHRFAAKT VHSGSLMLVT VELKEGSTAQ
LIINTEKTVI GSVLLRELKP VLSQG*
speed 1.50 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