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MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000371265
MT speed 1.37 s - this script 4.777757 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BSNDdisease_causing_automatic0.999515149425995simple_aae0I12Tsingle base exchangers121908144show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999515149425995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM094871)
  • known disease mutation: rs4388 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:55464894T>CN/A show variant in all transcripts   IGV
HGNC symbol BSND
Ensembl transcript ID ENST00000371265
Genbank transcript ID NM_057176
UniProt peptide Q8WZ55
alteration type single base exchange
alteration region CDS
DNA changes c.35T>C
cDNA.289T>C
g.289T>C
AA changes I12T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
12
frameshift no
known variant Reference ID: rs121908144
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs4388 (pathogenic for Bartter disease type 4a|Autosomal recessive non-syndromic sensorineural deafness type DFNB|Sensorineural deafness with mild renal dysfunction|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM094871)

known disease mutation at this position, please check HGMD for details (HGMD ID CM094871)
known disease mutation at this position, please check HGMD for details (HGMD ID CM094871)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8311
3.8311
(flanking)0.0350.957
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 143
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      12MADEKTFRIGFIVLGLFLLALGTF
mutated  not conserved    12MADEKTFRIGFTVLGLFLLALGT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000005735  12MADEKTFRIGFIVLGLFLLALGT
Fcatus  no alignment  ENSFCAG00000008815  n/a
Mmusculus  all identical  ENSMUSG00000025418  12MADEKTFRIGFIVLGLFLLSLGT
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000086265  12MAENKPYRYGLIVLGMAFVALGM
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
626TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 963 / 963
position (AA) of stopcodon in wt / mu AA sequence 321 / 321
position of stopcodon in wt / mu cDNA 1217 / 1217
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 255 / 255
chromosome 1
strand 1
last intron/exon boundary 803
theoretical NMD boundary in CDS 498
length of CDS 963
coding sequence (CDS) position 35
cDNA position
(for ins/del: last normal base / first normal base)
289
gDNA position
(for ins/del: last normal base / first normal base)
289
chromosomal position
(for ins/del: last normal base / first normal base)
55464894
original gDNA sequence snippet GACCTTCCGGATCGGCTTCATTGTGCTGGGGCTTTTCCTGC
altered gDNA sequence snippet GACCTTCCGGATCGGCTTCACTGTGCTGGGGCTTTTCCTGC
original cDNA sequence snippet GACCTTCCGGATCGGCTTCATTGTGCTGGGGCTTTTCCTGC
altered cDNA sequence snippet GACCTTCCGGATCGGCTTCACTGTGCTGGGGCTTTTCCTGC
wildtype AA sequence MADEKTFRIG FIVLGLFLLA LGTFLMSHDR PQVYGTFYAM GSVMVIGGII WSMCQCYPKI
TFVPADSDFQ GILSPKAMGL LENGLAAEMK SPSPQPPYVR LWEEAAYDQS LPDFSHIQMK
VMSYSEDHRS LLAPEMGQPK LGTSDGGEGG PGDVQAWMEA AVVIHKGSDE SEGERRLTQS
WPGPLACPQG PAPLASFQDD LDMDSSEGSS PNASPHDREE ACSPQQEPQG CRCPLDRFQD
FALIDAPTLE DEPQEGQQWE IALPNNWQRY PRTKVEEKEA SDTGGEEPEK EEEDLYYGLP
DGAGDLLPDK ELGFEPDTQG *
mutated AA sequence MADEKTFRIG FTVLGLFLLA LGTFLMSHDR PQVYGTFYAM GSVMVIGGII WSMCQCYPKI
TFVPADSDFQ GILSPKAMGL LENGLAAEMK SPSPQPPYVR LWEEAAYDQS LPDFSHIQMK
VMSYSEDHRS LLAPEMGQPK LGTSDGGEGG PGDVQAWMEA AVVIHKGSDE SEGERRLTQS
WPGPLACPQG PAPLASFQDD LDMDSSEGSS PNASPHDREE ACSPQQEPQG CRCPLDRFQD
FALIDAPTLE DEPQEGQQWE IALPNNWQRY PRTKVEEKEA SDTGGEEPEK EEEDLYYGLP
DGAGDLLPDK ELGFEPDTQG *
speed 1.37 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
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