Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999961485513863 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040381)
  • known disease mutation: rs4543 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:62469971T>CN/A show variant in all transcripts   IGV
HGNC symbol BSCL2
Ensembl transcript ID ENST00000405837
Genbank transcript ID N/A
UniProt peptide Q96G97
alteration type single base exchange
alteration region CDS
DNA changes c.455A>G
cDNA.952A>G
g.7347A>G
AA changes N152S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 152
frameshift no
known variant Reference ID: rs137852972
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs4543 (pathogenic for Spastic paraplegia 17|Distal hereditary motor neuronopathy type 5|Charcot-Marie-Tooth disease, type 2|not specified|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 CM040381)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040381)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040381)
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)0.5321
4.1131
(flanking)4.1131
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 increased7339wt: 0.9823 / mu: 0.9923 (marginal change - not scored)wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC
mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC		 ccct|GTTG
Acc marginally increased7340wt: 0.9418 / mu: 0.9656 (marginal change - not scored)wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT
mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT		 cctg|TTGC
Acc marginally increased7337wt: 0.9416 / mu: 0.9448 (marginal change - not scored)wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG
mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG		 ttcc|CTGT
Acc marginally increased7341wt: 0.8919 / mu: 0.9018 (marginal change - not scored)wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA
mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA		 ctgt|TGCC
Acc marginally increased7348wt: 0.3058 / mu: 0.3070 (marginal change - not scored)wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG
mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG		 caat|GTCT
Acc marginally increased7338wt: 0.9229 / mu: 0.9398 (marginal change - not scored)wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA
mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA		 tccc|TGTT
Acc marginally increased7343wt: 0.9563 / mu: 0.9756 (marginal change - not scored)wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG
mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG		 gttg|CCAA
Acc marginally increased7344wt: 0.6579 / mu: 0.6771 (marginal change - not scored)wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG
mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG		 ttgc|CAAT
Acc marginally increased7346wt: 0.9838 / mu: 0.9901 (marginal change - not scored)wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT
mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT		 gcca|ATGT
distance from splice site 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      152STTSLCSFPVANVSLTKGGRDRVL
mutated  all conserved    152STTSLCSFPVASVSLTKGGRDRV
Ptroglodytes  all identical  ENSPTRG00000003784  152STTSLCSFPVANVSLTKGGRDRV
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000018428  82STSLLCSFPVANVSLAKGGRDRV
Mmusculus  all identical  ENSMUSG00000071657  148STASLCSFPVANVSLAKSGRDRV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000037008  123DAVLCSFPMANVSLLKNGRDQV
Dmelanogaster  all conserved  FBgn0040336  110CTFPHAHVSLTK--KQQL
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000006021  73PPGILCSFPMSNVSLLRNNRDRV
protein features
start (aa)end (aa)featuredetails 
48242TOPO_DOMLumenal (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1395 / 1395
position (AA) of stopcodon in wt / mu AA sequence 465 / 465
position of stopcodon in wt / mu cDNA 1892 / 1892
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 498 / 498
chromosome 11
strand -1
last intron/exon boundary 1738
theoretical NMD boundary in CDS 1190
length of CDS 1395
coding sequence (CDS) position 455
cDNA position
(for ins/del: last normal base / first normal base)		 952
gDNA position
(for ins/del: last normal base / first normal base)		 7347
chromosomal position
(for ins/del: last normal base / first normal base)		 62469971
original gDNA sequence snippet CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG
altered gDNA sequence snippet CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG
original cDNA sequence snippet CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG
altered cDNA sequence snippet CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG
wildtype AA sequence MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ANVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGAG
PEGQEESTPQ SDVTEDGESP EDPSGTEGQL SEEEKPDQQP LSGEEELEPE ASDGSGSWED
AALLTEANLP APAPASASAP VLETLGSSEP AGGALRQRPT CSSS*
mutated AA sequence MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ASVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGAG
PEGQEESTPQ SDVTEDGESP EDPSGTEGQL SEEEKPDQQP LSGEEELEPE ASDGSGSWED
AALLTEANLP APAPASASAP VLETLGSSEP AGGALRQRPT CSSS*
speed 0.85 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