Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999995 (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) chr17:42398052A>GN/A show variant in all transcripts   IGV
HGNC symbol SLC25A39
Ensembl transcript ID ENST00000586016
Genbank transcript ID N/A
UniProt peptide Q9BZJ4
alteration type single base exchange
alteration region CDS
DNA changes c.343T>C
cDNA.487T>C
g.4187T>C
AA changes F115L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 115
frameshift no
known variant Reference ID: rs2011951
databasehomozygous (G/G)heterozygousallele carriers
1000G12469192165
ExAC18508-424914259
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3040
-0.140
(flanking)-0.0220
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased4185wt: 0.32 / mu: 0.36wt: CAATGGGTTCAGGCC
mu: CAATGGGCTCAGGCC		 ATGG|gttc
Donor marginally increased4192wt: 0.9768 / mu: 0.9780 (marginal change - not scored)wt: TTCAGGCCGAAGGAC
mu: CTCAGGCCGAAGGAC		 CAGG|ccga
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      115NYELVKSWLNGFRPKDQTSVGMSF
mutated  not conserved    115NYELVKSWLNGLRPKDQ
Ptroglodytes  not conserved  ENSPTRG00000009272  247NYELVKSWLNGLRPKDQ
Mmulatta  not conserved  ENSMMUG00000017944  247NYELVKSWLNGLRPKDQ
Fcatus  not conserved  ENSFCAG00000003053  247NYELVKSWLSGLRPKDQ
Mmusculus  not conserved  ENSMUSG00000018677  247NYELVKSWLSGLRPKDQ
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000000159  246NYELLKSRLCQWCQLTE
Drerio  not conserved  ENSDARG00000007449  245NYELVKAQLCEHYRTPQ
Dmelanogaster  not conserved  FBgn0031039  267LKSSFGVVEP----TFSFS
Celegans  not conserved  C16C10.1  260TNLQRRQGPDHNPFVVS
Xtropicalis  not conserved  ENSXETG00000011613  251NYELVKKKMSNTKAAVE
protein features
start (aa)end (aa)featuredetails 
9151REPEATSolcar 1.lost
122142TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
159243REPEATSolcar 2.might get lost (downstream of altered splice site)
161181TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
215235TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
253347REPEATSolcar 3.might get lost (downstream of altered splice site)
259279TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
266266CONFLICTG -> R (in Ref. 7; AAF69618).might get lost (downstream of altered splice site)
318338TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 684 / 684
position (AA) of stopcodon in wt / mu AA sequence 228 / 228
position of stopcodon in wt / mu cDNA 828 / 828
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 145 / 145
chromosome 17
strand -1
last intron/exon boundary 713
theoretical NMD boundary in CDS 518
length of CDS 684
coding sequence (CDS) position 343
cDNA position
(for ins/del: last normal base / first normal base)		 487
gDNA position
(for ins/del: last normal base / first normal base)		 4187
chromosomal position
(for ins/del: last normal base / first normal base)		 42398052
original gDNA sequence snippet TGAAGAGCTGGCTCAATGGGTTCAGGCCGAAGGACCAGACT
altered gDNA sequence snippet TGAAGAGCTGGCTCAATGGGCTCAGGCCGAAGGACCAGACT
original cDNA sequence snippet TGAAGAGCTGGCTCAATGGGTTCAGGCCGAAGGACCAGACT
altered cDNA sequence snippet TGAAGAGCTGGCTCAATGGGCTCAGGCCGAAGGACCAGACT
wildtype AA sequence MTVPATAIYF TAYDQLKAFL CGRALTSDLY APMVAGALAR LGTVTVISPL ELMRTKLQAQ
HVSYRELGAC VRTAVAQGGW RSLWLGWGPT ALRDVPFSAL YWFNYELVKS WLNGFRPKDQ
TSVGMSFVAG GISGTVAAVL TLPFDVVKTQ RQVALGAMEA VRVNPLHVDS TWLLLRRIRA
ESGTKGLFAG FLPRIIKAAP SCAIMISTYE FGKSFFQRLN QDRLLGG*
mutated AA sequence MTVPATAIYF TAYDQLKAFL CGRALTSDLY APMVAGALAR LGTVTVISPL ELMRTKLQAQ
HVSYRELGAC VRTAVAQGGW RSLWLGWGPT ALRDVPFSAL YWFNYELVKS WLNGLRPKDQ
TSVGMSFVAG GISGTVAAVL TLPFDVVKTQ RQVALGAMEA VRVNPLHVDS TWLLLRRIRA
ESGTKGLFAG FLPRIIKAAP SCAIMISTYE FGKSFFQRLN QDRLLGG*
speed 1.07 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