Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.000916477430865964 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1612506)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:108307727T>AN/A show variant in all transcripts   IGV
HGNC symbol VAV3
Ensembl transcript ID ENST00000371846
Genbank transcript ID N/A
UniProt peptide Q9UKW4
alteration type single base exchange
alteration region CDS
DNA changes c.697A>T
cDNA.876A>T
g.200040A>T
AA changes T233S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 233
frameshift no
known variant Reference ID: rs7528153
databasehomozygous (A/A)heterozygousallele carriers
1000G70111411842
ExAC22304-1184110463

known disease mutation at this position, please check HGMD for details (HGMD ID CM1612506)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2881
1.3591
(flanking)2.2191
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased200038wt: 0.39 / mu: 0.73wt: TAGTTTAGACTACATTTCTAAGACAAAAGAAGATGTCAAAC
mu: TAGTTTAGACTACATTTCTAAGTCAAAAGAAGATGTCAAAC		 ctaa|GACA
Acc increased200037wt: 0.24 / mu: 0.28wt: CTAGTTTAGACTACATTTCTAAGACAAAAGAAGATGTCAAA
mu: CTAGTTTAGACTACATTTCTAAGTCAAAAGAAGATGTCAAA		 tcta|AGAC
Donor increased200033wt: 0.48 / mu: 0.93wt: TACATTTCTAAGACA
mu: TACATTTCTAAGTCA		 CATT|tcta
Donor marginally increased200043wt: 0.9945 / mu: 0.9953 (marginal change - not scored)wt: AGACAAAAGAAGATG
mu: AGTCAAAAGAAGATG		 ACAA|aaga
Donor marginally increased200038wt: 0.9667 / mu: 0.9731 (marginal change - not scored)wt: TTCTAAGACAAAAGA
mu: TTCTAAGTCAAAAGA		 CTAA|gaca
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      233SAISSLDYISKTKEDVKLKLEECS
mutated  all conserved    233SAISSLDYISKSKEDVKLK
Ptroglodytes  all identical  ENSPTRG00000001024  298SAISSLDYISKTKEDVKLK
Mmulatta  all identical  ENSMMUG00000019714  298SAISSLDYISKTKEDVKLK
Fcatus  all identical  ENSFCAG00000001191  272LAISSLDNISKTKEDVKLK
Mmusculus  all identical  ENSMUSG00000033721  298SAISNLDYISKTKEDVKLK
Ggallus  all identical  ENSGALG00000001915  230TAISCLDNISKTKEDVKLKLEE
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0040068  530GAIDYLADVCKKNQIIDQLVQKC
Celegans  all identical  C35B8.2  364DSRKLSNELLKTNEFISRNINEL
Xtropicalis  all identical  ENSXETG00000009944  298LAISVLDNISKTREDVRLK
protein features
start (aa)end (aa)featuredetails 
192371DOMAINDH.lost
400502DOMAINPH.might get lost (downstream of altered splice site)
429429CONFLICTV -> A (in Ref. 2; AAD20348).might get lost (downstream of altered splice site)
513562ZN_FINGPhorbol-ester/DAG-type.might get lost (downstream of altered splice site)
560847REGIONSufficient for interaction with ROS1.might get lost (downstream of altered splice site)
592660DOMAINSH3 1.might get lost (downstream of altered splice site)
672766DOMAINSH2.might get lost (downstream of altered splice site)
786786MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
788847DOMAINSH3 2.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1671 / 1671
position (AA) of stopcodon in wt / mu AA sequence 557 / 557
position of stopcodon in wt / mu cDNA 1850 / 1850
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 180 / 180
chromosome 1
strand -1
last intron/exon boundary 1762
theoretical NMD boundary in CDS 1532
length of CDS 1671
coding sequence (CDS) position 697
cDNA position
(for ins/del: last normal base / first normal base)		 876
gDNA position
(for ins/del: last normal base / first normal base)		 200040
chromosomal position
(for ins/del: last normal base / first normal base)		 108307727
original gDNA sequence snippet GTTTAGACTACATTTCTAAGACAAAAGAAGATGTCAAACTG
altered gDNA sequence snippet GTTTAGACTACATTTCTAAGTCAAAAGAAGATGTCAAACTG
original cDNA sequence snippet GTTTAGACTACATTTCTAAGACAAAAGAAGATGTCAAACTG
altered cDNA sequence snippet GTTTAGACTACATTTCTAAGTCAAAAGAAGATGTCAAACTG
wildtype AA sequence MSQFLCLKNI RTFLTACCET FGMRKSELFE AFDLFDVRDF GKVIETLSRL SRTPIALATG
IRPFPTEESI NDEDIYKGLP DLIDETLVED EEDLYDCVYG EDEGGEVYED LMKAEEAHQP
KCPENDIRSC CLAEIKQTEE KYTETLESIE KYFMAPLKRF LTAAEFDSVF INIPELVKLH
RNLMQEIHDS IVNKNDQNLY QVFINYKERL VIYGQYCSGV ESAISSLDYI SKTKEDVKLK
LEECSKRANN GKFTLRDLLV VPMQRVLKYH LLLQELVKHT TDPTEKANLK LALDAMKDLA
QYVNEVKRDN ETLREIKQFQ LSIENLNQPV LLFGRPQGDG EIRITTLDKH TKQERHIFLF
DLAVIVCKRK GDNYEMKEII DLQQYKIANN PTTDKENKKW SYGFYLIHTQ GQNGLEFYCK
TKDLKKKWLE QFEMALSNIR PDYADSNFHD FKMHTFTRVT SCKVCQMLLR GTFYQGYLCF
KCGARAHKEC LGRVDNCGRV NSGEQGTLKL PEKRTNGLRR TPKQVDPDVP CLLHFFISMA
PATRSIVKSQ KKNKKF*
mutated AA sequence MSQFLCLKNI RTFLTACCET FGMRKSELFE AFDLFDVRDF GKVIETLSRL SRTPIALATG
IRPFPTEESI NDEDIYKGLP DLIDETLVED EEDLYDCVYG EDEGGEVYED LMKAEEAHQP
KCPENDIRSC CLAEIKQTEE KYTETLESIE KYFMAPLKRF LTAAEFDSVF INIPELVKLH
RNLMQEIHDS IVNKNDQNLY QVFINYKERL VIYGQYCSGV ESAISSLDYI SKSKEDVKLK
LEECSKRANN GKFTLRDLLV VPMQRVLKYH LLLQELVKHT TDPTEKANLK LALDAMKDLA
QYVNEVKRDN ETLREIKQFQ LSIENLNQPV LLFGRPQGDG EIRITTLDKH TKQERHIFLF
DLAVIVCKRK GDNYEMKEII DLQQYKIANN PTTDKENKKW SYGFYLIHTQ GQNGLEFYCK
TKDLKKKWLE QFEMALSNIR PDYADSNFHD FKMHTFTRVT SCKVCQMLLR GTFYQGYLCF
KCGARAHKEC LGRVDNCGRV NSGEQGTLKL PEKRTNGLRR TPKQVDPDVP CLLHFFISMA
PATRSIVKSQ KKNKKF*
speed 0.33 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