Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 5.11552504718526e-06 (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) chr15:85448875C>AN/A show variant in all transcripts   IGV
HGNC symbol SLC28A1
Ensembl transcript ID ENST00000538177
Genbank transcript ID N/A
UniProt peptide O00337
alteration type single base exchange
alteration region CDS
DNA changes c.709C>A
cDNA.816C>A
g.20991C>A
AA changes Q237K Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 237
frameshift no
known variant Reference ID: rs8187758
databasehomozygous (A/A)heterozygousallele carriers
1000G2549971251
ExAC51612244527606
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6540.572
3.5180.995
(flanking)2.9231
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased20994wt: 0.51 / mu: 0.59wt: AGCAGATCCGGGTAG
mu: AGAAGATCCGGGTAG		 CAGA|tccg
Donor gained209871.00mu: CTGGGCGAGAAGATC GGGC|gaga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      237PGFIAFEWLGEQIRIFLSYTKAGS
mutated  all conserved    237PGFIAFEWLGEKIRI
Ptroglodytes  all identical  ENSPTRG00000007407  237PGFIAFEWLGEQIRI
Mmulatta  all identical  ENSMMUG00000016772  237PGFIAFQWLGEQIRI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000025726  237PGFVAFQWLGDQIRV
Ggallus  all identical  ENSGALG00000002522  231PGIQAFQWLGDQIQVFL
Trubripes  all identical  ENSTRUG00000003627  187PGLVAFEWLGHQVKVFLD
Drerio  all identical  ENSDARG00000060879  234PGLVAFEWLGKQVQIFLDY
Dmelanogaster  all conserved  FBgn0025709  238VGRKIFECLGNKVATFLGYATDG
Celegans  not conserved  F27E11.2  205TGQWFFQKFAELIVGFLEFAQVG
Xtropicalis  all identical  ENSXETG00000009806  216PGYQAFKFVGEQIQIILSWLPFG
protein features
start (aa)end (aa)featuredetails 
261281TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
361381TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
428448TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
532552TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
572592TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
609612COMPBIASPoly-Ser.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1452 / 1452
position (AA) of stopcodon in wt / mu AA sequence 484 / 484
position of stopcodon in wt / mu cDNA 1559 / 1559
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 108 / 108
chromosome 15
strand 1
last intron/exon boundary 1484
theoretical NMD boundary in CDS 1326
length of CDS 1452
coding sequence (CDS) position 709
cDNA position
(for ins/del: last normal base / first normal base)		 816
gDNA position
(for ins/del: last normal base / first normal base)		 20991
chromosomal position
(for ins/del: last normal base / first normal base)		 85448875
original gDNA sequence snippet CGTTCGAGTGGCTGGGCGAGCAGATCCGGGTAGGTATGTGG
altered gDNA sequence snippet CGTTCGAGTGGCTGGGCGAGAAGATCCGGGTAGGTATGTGG
original cDNA sequence snippet CGTTCGAGTGGCTGGGCGAGCAGATCCGGATCTTCCTGAGC
altered cDNA sequence snippet CGTTCGAGTGGCTGGGCGAGAAGATCCGGATCTTCCTGAGC
wildtype AA sequence MENDPSRRRE SISLTPVAKG LENMGADFLE SLEEGQLPRS DLSPAEIRSS WSEAAPKPFS
RWRNLQPALR ARSFCREHMQ LFRWIGTGLL CTGLSAFLLV ACLLDFQRAL ALFVLTCVVL
TFLGHRLLKR LLGPKLRRFL KPQGHPRLLL WFKRGLALAA FLGLVLWLSL DTSQRPEQLV
SFAGICVFVA LLFACSKHHC AVSWRAVSWG LGLQFVLGLL VIRTEPGFIA FEWLGEQIRI
FLSYTKAGSS FVFGEALVKD VFAFQVLPII VFFSCVISVL YHVGLMQWVI LKIAWLMQVT
MGTTATETLS VAGNIFVSQT EAPLLIRPYL ADMTLSEVHV VMTGGYATIA GSLLGAYISF
GVRAEVLTTF ALCGFANFSS IGIMLGGLTS MVPQRKSDFS QIVLRALFTG ACVSLVNACM
AGILYMPRGA EVDCMSLLNT TLSSSSFEIY QCCREAFQSV NPEFSPEALD NCCRFYNHTI
CAQ*
mutated AA sequence MENDPSRRRE SISLTPVAKG LENMGADFLE SLEEGQLPRS DLSPAEIRSS WSEAAPKPFS
RWRNLQPALR ARSFCREHMQ LFRWIGTGLL CTGLSAFLLV ACLLDFQRAL ALFVLTCVVL
TFLGHRLLKR LLGPKLRRFL KPQGHPRLLL WFKRGLALAA FLGLVLWLSL DTSQRPEQLV
SFAGICVFVA LLFACSKHHC AVSWRAVSWG LGLQFVLGLL VIRTEPGFIA FEWLGEKIRI
FLSYTKAGSS FVFGEALVKD VFAFQVLPII VFFSCVISVL YHVGLMQWVI LKIAWLMQVT
MGTTATETLS VAGNIFVSQT EAPLLIRPYL ADMTLSEVHV VMTGGYATIA GSLLGAYISF
GVRAEVLTTF ALCGFANFSS IGIMLGGLTS MVPQRKSDFS QIVLRALFTG ACVSLVNACM
AGILYMPRGA EVDCMSLLNT TLSSSSFEIY QCCREAFQSV NPEFSPEALD NCCRFYNHTI
CAQ*
speed 0.79 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