Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999341783083708 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002780)
  • known disease mutation: rs7684 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:117693139C>TN/A show variant in all transcripts   IGV
HGNC symbol FXYD2
Ensembl transcript ID ENST00000292079
Genbank transcript ID NM_001680
UniProt peptide P54710
alteration type single base exchange
alteration region CDS
DNA changes c.121G>A
cDNA.187G>A
g.6275G>A
AA changes G41R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 41
frameshift no
known variant Reference ID: rs28938168
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7684 (pathogenic for Renal hypomagnesemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0920.987
3.0921
(flanking)0.4651
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 increased6275wt: 0.8904 / mu: 0.9018 (marginal change - not scored)wt: CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
mu: CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT		 gtgg|GGCT
Donor gained62710.96mu: TTCATCGTGAGGCTC CATC|gtga
Donor gained62700.49mu: CTTCATCGTGAGGCT TCAT|cgtg
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      41GLIFAGLAFIVGLLILLSRRFRCG
mutated  not conserved    41GLIFAGLAFIVRLLILLSRRFRC
Ptroglodytes  no alignment  ENSPTRG00000004327  n/a
Mmulatta  all identical  ENSMMUG00000007796  41GLIFAGLAFIVGLLILLSKRFRC
Fcatus  all identical  ENSFCAG00000011760  80GLIFAALAFVVGLIIILS
Mmusculus  all identical  ENSMUSG00000059412  39GLIFAGLAFVVGLLIILSKRFRC
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000034242  37GLIFAAIAFVVGMLIIFSGRFRC
protein features
start (aa)end (aa)featuredetails 
2946TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 201 / 201
position (AA) of stopcodon in wt / mu AA sequence 67 / 67
position of stopcodon in wt / mu cDNA 267 / 267
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 67 / 67
chromosome 11
strand -1
last intron/exon boundary 274
theoretical NMD boundary in CDS 157
length of CDS 201
coding sequence (CDS) position 121
cDNA position
(for ins/del: last normal base / first normal base)		 187
gDNA position
(for ins/del: last normal base / first normal base)		 6275
chromosomal position
(for ins/del: last normal base / first normal base)		 117693139
original gDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
altered gDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT
original cDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGC
altered cDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGC
wildtype AA sequence MTGLSMDGGG SPKGDVDPFY YDYETVRNGG LIFAGLAFIV GLLILLSRRF RCGGNKKRRQ
INEDEP*
mutated AA sequence MTGLSMDGGG SPKGDVDPFY YDYETVRNGG LIFAGLAFIV RLLILLSRRF RCGGNKKRRQ
INEDEP*
speed 1.03 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