Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999998323326317 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040382)
  • known disease mutation at this position (HGMD CM1210972)
  • known disease mutation: rs4544 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:62469965G>AN/A show variant in all transcripts   IGV
HGNC symbol BSCL2
Ensembl transcript ID ENST00000407022
Genbank transcript ID NM_032667
UniProt peptide Q96G97
alteration type single base exchange
alteration region CDS
DNA changes c.269C>T
cDNA.516C>T
g.7353C>T
AA changes S90L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 90
frameshift no
known variant Reference ID: rs137852973
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4544 (pathogenic for Spastic paraplegia 17|Distal hereditary motor neuronopathy type 5|Charcot-Marie-Tooth disease, type 2|NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE VC|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040382)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040382)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1210972)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040382)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1210972)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040382)
regulatory features BATF, Transcription Factor, BATF Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.4970.347
4.9610.999
(flanking)1.6981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased7361wt: 0.21 / mu: 0.38wt: TTGCCAATGTCTCGCTGACTAAGGGTGGACGTGATCGGGTG
mu: TTGCCAATGTCTTGCTGACTAAGGGTGGACGTGATCGGGTG		 acta|AGGG
Acc marginally increased7350wt: 0.9386 / mu: 0.9448 (marginal change - not scored)wt: CTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGGAC
mu: CTCCTTCCCTGTTGCCAATGTCTTGCTGACTAAGGGTGGAC		 atgt|CTCG
Acc increased7357wt: 0.46 / mu: 0.72wt: CCTGTTGCCAATGTCTCGCTGACTAAGGGTGGACGTGATCG
mu: CCTGTTGCCAATGTCTTGCTGACTAAGGGTGGACGTGATCG		 gctg|ACTA
Acc marginally increased7353wt: 0.3653 / mu: 0.3670 (marginal change - not scored)wt: CTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGGACGTG
mu: CTTCCCTGTTGCCAATGTCTTGCTGACTAAGGGTGGACGTG		 tctc|GCTG
Acc marginally increased7343wt: 0.9563 / mu: 0.9658 (marginal change - not scored)wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG
mu: CACTCTGCTCCTTCCCTGTTGCCAATGTCTTGCTGACTAAG		 gttg|CCAA
Acc marginally increased7344wt: 0.6579 / mu: 0.7032 (marginal change - not scored)wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG
mu: ACTCTGCTCCTTCCCTGTTGCCAATGTCTTGCTGACTAAGG		 ttgc|CAAT
Acc increased7362wt: 0.32 / mu: 0.42wt: TGCCAATGTCTCGCTGACTAAGGGTGGACGTGATCGGGTGA
mu: TGCCAATGTCTTGCTGACTAAGGGTGGACGTGATCGGGTGA		 ctaa|GGGT
Donor increased7358wt: 0.49 / mu: 0.57wt: CGCTGACTAAGGGTG
mu: TGCTGACTAAGGGTG		 CTGA|ctaa
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      90TSLCSFPVANVSLTKGGRDRVLMY
mutated  not conserved    90TSLCSFPVANVLLTKGGRDRVLM
Ptroglodytes  all identical  ENSPTRG00000003784  154TSLCSFPVANVSLTKGGRDRVLM
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000018428  84SLLCSFPVANVSLAKGGRDRVLM
Mmusculus  all identical  ENSMUSG00000071657  150ASLCSFPVANVSLAKSGRDRVLM
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000037008  125AVLCSFPMANVSLLKNGRDQVMM
Dmelanogaster  all identical  FBgn0040336  112CTFPHAHVSLTK--KQQLLM
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000006021  75GILCSFPMSNVSLLRNNRDRVLM
protein features
start (aa)end (aa)featuredetails 
48242TOPO_DOMLumenal (Potential).lost
242242CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
243263TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
264398TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1197 / 1197
position (AA) of stopcodon in wt / mu AA sequence 399 / 399
position of stopcodon in wt / mu cDNA 1444 / 1444
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 248 / 248
chromosome 11
strand -1
last intron/exon boundary 1290
theoretical NMD boundary in CDS 992
length of CDS 1197
coding sequence (CDS) position 269
cDNA position
(for ins/del: last normal base / first normal base)		 516
gDNA position
(for ins/del: last normal base / first normal base)		 7353
chromosomal position
(for ins/del: last normal base / first normal base)		 62469965
original gDNA sequence snippet CTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGGACGTG
altered gDNA sequence snippet CTTCCCTGTTGCCAATGTCTTGCTGACTAAGGGTGGACGTG
original cDNA sequence snippet CTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGGACGTG
altered cDNA sequence snippet CTTCCCTGTTGCCAATGTCTTGCTGACTAAGGGTGGACGTG
wildtype AA sequence MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVANVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*
mutated AA sequence MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVANVL LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*
speed 0.99 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