Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.867507701585762 (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) chr1:38397369C>TN/A show variant in all transcripts   IGV
HGNC symbol INPP5B
Ensembl transcript ID ENST00000373023
Genbank transcript ID N/A
UniProt peptide P32019
alteration type single base exchange
alteration region CDS
DNA changes c.748G>A
cDNA.842G>A
g.15361G>A
AA changes G250S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 250
frameshift no
known variant Reference ID: rs35267671
databasehomozygous (T/T)heterozygousallele carriers
1000G3979851382
ExAC371862589976
regulatory features Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Egr1, Transcription Factor, Egr1 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Pbx3, Transcription Factor, Pbx3 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SP1, Transcription Factor, SP1 Transcription Factor Binding
SP2, Transcription Factor, SP2 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)3.6040.999
-0.1830.953
(flanking)1.1930.957
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 increased15361wt: 0.6960 / mu: 0.7328 (marginal change - not scored)wt: GGGAAATGTCTGCCGCCGCCGGCTCTCGGGAGCGCAACACT
mu: GGGAAATGTCTGCCGCCGCCAGCTCTCGGGAGCGCAACACT		 gccg|GCTC
Donor increased15366wt: 0.32 / mu: 0.53wt: GGCTCTCGGGAGCGC
mu: AGCTCTCGGGAGCGC		 CTCT|cggg
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      250EEAGREMSAAAGSRERNTAGGSNF
mutated  not conserved    250AGREMSAAASSRERNTAGGSN
Ptroglodytes  all identical  ENSPTRG00000030681  250AGREMSAAAGSRERNTAGGSN
Mmulatta  no alignment  ENSMMUG00000023277  n/a
Fcatus  all identical  ENSFCAG00000011021  198EETGWEMSAASGSRECDSA
Mmusculus  all identical  ENSMUSG00000028894  250ADWEMSAGGGSRERDCAGVSN
Ggallus  no alignment  ENSGALG00000001606  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000042111  n/a
Dmelanogaster  no alignment  FBgn0023508  n/a
Celegans  no alignment  C16C2.3  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
340353STRANDmight get lost (downstream of altered splice site)
342668REGION5-phosphatase (By similarity).might get lost (downstream of altered splice site)
355355METALMagnesium.might get lost (downstream of altered splice site)
364367HELIXmight get lost (downstream of altered splice site)
368370STRANDmight get lost (downstream of altered splice site)
375382STRANDmight get lost (downstream of altered splice site)
383383BINDINGSubstrate.might get lost (downstream of altered splice site)
383383METALMagnesium.might get lost (downstream of altered splice site)
388391HELIXmight get lost (downstream of altered splice site)
398409HELIXmight get lost (downstream of altered splice site)
416424STRANDmight get lost (downstream of altered splice site)
427434STRANDmight get lost (downstream of altered splice site)
435440HELIXmight get lost (downstream of altered splice site)
441450STRANDmight get lost (downstream of altered splice site)
453455HELIXmight get lost (downstream of altered splice site)
459460REGIONSubstrate binding.might get lost (downstream of altered splice site)
460469STRANDmight get lost (downstream of altered splice site)
472480STRANDmight get lost (downstream of altered splice site)
485487HELIXmight get lost (downstream of altered splice site)
488501HELIXmight get lost (downstream of altered splice site)
509511STRANDmight get lost (downstream of altered splice site)
518527STRANDmight get lost (downstream of altered splice site)
537545HELIXmight get lost (downstream of altered splice site)
549553HELIXmight get lost (downstream of altered splice site)
557563HELIXmight get lost (downstream of altered splice site)
582583REGIONSubstrate binding.might get lost (downstream of altered splice site)
587606CONFLICTGSDDWDTSEKCRAPAWCDRI -> RALTTGIPVRSAVLLPG VIGF (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
588591STRANDmight get lost (downstream of altered splice site)
596598REGIONSubstrate binding.might get lost (downstream of altered splice site)
604620STRANDmight get lost (downstream of altered splice site)
626629STRANDmight get lost (downstream of altered splice site)
632643STRANDmight get lost (downstream of altered splice site)
669782REGIONASH (By similarity).might get lost (downstream of altered splice site)
821993DOMAINRho-GAP.might get lost (downstream of altered splice site)
911911CONFLICTG -> P (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
990990MUTAGENC->S: Loss of prenylation and membrane localization.might get lost (downstream of altered splice site)
990990LIPIDS-farnesyl cysteine (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2982 / 2982
position (AA) of stopcodon in wt / mu AA sequence 994 / 994
position of stopcodon in wt / mu cDNA 3076 / 3076
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 95 / 95
chromosome 1
strand -1
last intron/exon boundary 2961
theoretical NMD boundary in CDS 2816
length of CDS 2982
coding sequence (CDS) position 748
cDNA position
(for ins/del: last normal base / first normal base)		 842
gDNA position
(for ins/del: last normal base / first normal base)		 15361
chromosomal position
(for ins/del: last normal base / first normal base)		 38397369
original gDNA sequence snippet GGGAAATGTCTGCCGCCGCCGGCTCTCGGGAGCGCAACACT
altered gDNA sequence snippet GGGAAATGTCTGCCGCCGCCAGCTCTCGGGAGCGCAACACT
original cDNA sequence snippet GGGAAATGTCTGCCGCCGCCGGCTCTCGGGAGCGCAACACT
altered cDNA sequence snippet GGGAAATGTCTGCCGCCGCCAGCTCTCGGGAGCGCAACACT
wildtype AA sequence MDQSVAIQET LAEGEYCVIA VQGVLCEGDS RQSRLLGLVR YRLEHGGQEH ALFLYTHRRM
AITGDDVSLD QIVPVSRDFT LEEVSPDGEL YILGSDVTVQ LDTAELSLVF QLPFGSQTRM
FLHEVARACP GFDSATRDPE FLWLSRYRCA ELELEMPTPR GCNSALVTWP GYATIGGGRY
PSRKKRWGLE EARPQGAGSV LFWGGAMEKT GFRLMERAHG GGFVWGRSAR DGRRDEELEE
AGREMSAAAG SRERNTAGGS NFDGLRPNGK GVPMDQSSRG QDKPESLQPR QNKSKSEITD
MVRSSTITVS DKAHILSMQK FGLRDTIVKS HLLQKEEDYT YIQNFRFFAG TYNVNGQSPK
ECLRLWLSNG IQAPDVYCVG FQELDLSKEA FFFHDTPKEE EWFKAVSEGL HPDAKYAKVK
LIRLVGIMLL LYVKQEHAAY ISEVEAETVG TGIMGRMGNK GGVAIRFQFH NTSICVVNSH
LAAHIEEYER RNQDYKDICS RMQFCQPDPS LPPLTISNHD VILWLGDLNY RIEELDVEKV
KKLIEEKDFQ MLYAYDQLKI QVAAKTVFEG FTEGELTFQP TYKYDTGSDD WDTSEKCRAP
AWCDRILWKG KNITQLSYQS HMALKTSDHK PVSSVFDIGV RVVNDELYRK TLEEIVRSLD
KMENANIPSV SLSKREFCFQ NVKYMQLKVE SFTIHNGQVP CHFEFINKPD EESYCKQWLN
ANPSRGFLLP DSDVEIDLEL FVNKMTATKL NSGEDKIEDI LVLHLDRGKD YFLSVSGNYL
PSCFGSPIHT LCYMREPILD LPLETISELT LMPVWTGDDG SQLDSPMEIP KELWMMVDYL
YRNAVQQEDL FQQPGLRSEF EHIRDCLDTG MIDNLSASNH SVAEALLLFL ESLPEPVICY
STYHNCLECS GNYTASKQVI STLPIFHKNV FHYLMAFLRE LLKNSAKNHL DENILASIFG
SLLLRNPAGH QKLDMTEKKK AQEFIHQFLC NPL*
mutated AA sequence MDQSVAIQET LAEGEYCVIA VQGVLCEGDS RQSRLLGLVR YRLEHGGQEH ALFLYTHRRM
AITGDDVSLD QIVPVSRDFT LEEVSPDGEL YILGSDVTVQ LDTAELSLVF QLPFGSQTRM
FLHEVARACP GFDSATRDPE FLWLSRYRCA ELELEMPTPR GCNSALVTWP GYATIGGGRY
PSRKKRWGLE EARPQGAGSV LFWGGAMEKT GFRLMERAHG GGFVWGRSAR DGRRDEELEE
AGREMSAAAS SRERNTAGGS NFDGLRPNGK GVPMDQSSRG QDKPESLQPR QNKSKSEITD
MVRSSTITVS DKAHILSMQK FGLRDTIVKS HLLQKEEDYT YIQNFRFFAG TYNVNGQSPK
ECLRLWLSNG IQAPDVYCVG FQELDLSKEA FFFHDTPKEE EWFKAVSEGL HPDAKYAKVK
LIRLVGIMLL LYVKQEHAAY ISEVEAETVG TGIMGRMGNK GGVAIRFQFH NTSICVVNSH
LAAHIEEYER RNQDYKDICS RMQFCQPDPS LPPLTISNHD VILWLGDLNY RIEELDVEKV
KKLIEEKDFQ MLYAYDQLKI QVAAKTVFEG FTEGELTFQP TYKYDTGSDD WDTSEKCRAP
AWCDRILWKG KNITQLSYQS HMALKTSDHK PVSSVFDIGV RVVNDELYRK TLEEIVRSLD
KMENANIPSV SLSKREFCFQ NVKYMQLKVE SFTIHNGQVP CHFEFINKPD EESYCKQWLN
ANPSRGFLLP DSDVEIDLEL FVNKMTATKL NSGEDKIEDI LVLHLDRGKD YFLSVSGNYL
PSCFGSPIHT LCYMREPILD LPLETISELT LMPVWTGDDG SQLDSPMEIP KELWMMVDYL
YRNAVQQEDL FQQPGLRSEF EHIRDCLDTG MIDNLSASNH SVAEALLLFL ESLPEPVICY
STYHNCLECS GNYTASKQVI STLPIFHKNV FHYLMAFLRE LLKNSAKNHL DENILASIFG
SLLLRNPAGH QKLDMTEKKK AQEFIHQFLC NPL*
speed 1.18 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