Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999997 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:35648365T>GN/A show variant in all transcripts   IGV
HGNC symbol FXYD5
Ensembl transcript ID ENST00000392219
Genbank transcript ID NM_014164
UniProt peptide Q96DB9
alteration type single base exchange
alteration region CDS
DNA changes c.103T>G
cDNA.170T>G
g.2733T>G
AA changes S35A Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 35
frameshift no
known variant Reference ID: rs1688005
databasehomozygous (G/G)heterozygousallele carriers
1000G51410371551
ExAC75051775725262
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0040.001
-0.680
(flanking)0.2990.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2725wt: 0.24 / mu: 0.36wt: AGATACCACGTCCAGTTCTTCAGCAGACTCAACTATCATGG
mu: AGATACCACGTCCAGTTCTTCAGCAGACGCAACTATCATGG		 cttc|AGCA
Acc marginally increased2726wt: 0.7648 / mu: 0.8088 (marginal change - not scored)wt: GATACCACGTCCAGTTCTTCAGCAGACTCAACTATCATGGA
mu: GATACCACGTCCAGTTCTTCAGCAGACGCAACTATCATGGA		 ttca|GCAG
Donor increased2729wt: 0.23 / mu: 0.52wt: TCAGCAGACTCAACT
mu: TCAGCAGACGCAACT		 AGCA|gact
Donor gained27270.84mu: CTTCAGCAGACGCAA TCAG|caga
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      35LKDTTSSSSADSTIMDIQVPTRAP
mutated  all conserved    35LKDTTSSSSADATIMDIQVPTRA
Ptroglodytes  all identical  ENSPTRG00000010833  35LKDTTSSSSADSTIMDIQVPTRA
Mmulatta  not conserved  ENSMMUG00000023207  35PPSQASPTCAAGWVAGACERSVP
Fcatus  all conserved  ENSFCAG00000008891  35LKETASIPSADTTIVNIHALAQT
Mmusculus  not conserved  ENSMUSG00000009687  35PKKPTSIFTADQTSATTRDNVPD
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
22145TOPO_DOMExtracellular (Potential).lost
112112MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
140141CONFLICTHT -> SH (in Ref. 3; AAF29077).might get lost (downstream of altered splice site)
146164TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
165178TOPO_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 537 / 537
position (AA) of stopcodon in wt / mu AA sequence 179 / 179
position of stopcodon in wt / mu cDNA 604 / 604
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 68 / 68
chromosome 19
strand 1
last intron/exon boundary 555
theoretical NMD boundary in CDS 437
length of CDS 537
coding sequence (CDS) position 103
cDNA position
(for ins/del: last normal base / first normal base)		 170
gDNA position
(for ins/del: last normal base / first normal base)		 2733
chromosomal position
(for ins/del: last normal base / first normal base)		 35648365
original gDNA sequence snippet CGTCCAGTTCTTCAGCAGACTCAACTATCATGGACATTCAG
altered gDNA sequence snippet CGTCCAGTTCTTCAGCAGACGCAACTATCATGGACATTCAG
original cDNA sequence snippet CGTCCAGTTCTTCAGCAGACTCAACTATCATGGACATTCAG
altered cDNA sequence snippet CGTCCAGTTCTTCAGCAGACGCAACTATCATGGACATTCAG
wildtype AA sequence MSPSGRLCLL TIVGLILPTR GQTLKDTTSS SSADSTIMDI QVPTRAPDAV YTELQPTSPT
PTWPADETPQ PQTQTQQLEG TDGPLVTDPE THKSTKAAHP TDDTTTLSER PSPSTDVQTD
PQTLKPSGFH EDDPFFYDEH TLRKRGLLVA AVLFITGIII LTSGKCRQLS RLCRNRCR*
mutated AA sequence MSPSGRLCLL TIVGLILPTR GQTLKDTTSS SSADATIMDI QVPTRAPDAV YTELQPTSPT
PTWPADETPQ PQTQTQQLEG TDGPLVTDPE THKSTKAAHP TDDTTTLSER PSPSTDVQTD
PQTLKPSGFH EDDPFFYDEH TLRKRGLLVA AVLFITGIII LTSGKCRQLS RLCRNRCR*
speed 0.96 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