Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999945197 (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) chr19:54664209G>CN/A show variant in all transcripts   IGV
HGNC symbol TMC4
Ensembl transcript ID ENST00000376591
Genbank transcript ID NM_001145303
UniProt peptide Q7Z404
alteration type single base exchange
alteration region CDS
DNA changes c.2065C>G
cDNA.2197C>G
g.12736C>G
AA changes Q689E Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 689
frameshift no
known variant Reference ID: rs36657
databasehomozygous (C/C)heterozygousallele carriers
1000G72311191842
ExAC15602156317165
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3440.942
-0.390.084
(flanking)-0.3210.073
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased12735wt: 0.74 / mu: 0.99wt: CAGAGACAGACGGTG
mu: CAGAGAGAGACGGTG		 GAGA|caga
Donor lost127410.23wt: CAGACGGTGAGCCAG GACG|gtga
Donor gained127320.60mu: CGTCAGAGAGAGACG TCAG|agag
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      689GRLISELKRQRQTEAQNKVFLARR
mutated  all conserved    689GRLISELKRQRETEAQNKVFLAR
Ptroglodytes  all conserved  ENSPTRG00000011446  689GRLISELKRQRETEAQNKVFLAR
Mmulatta  all conserved  ENSMMUG00000009704  417GRLISELKRQRETEA
Fcatus  all conserved  ENSFCAG00000003603  411GRLISELKRQIETEA
Mmusculus  all conserved  ENSMUSG00000019734  671GRLISELKRQIETEVQNKVFLAQ
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000015812  570GKTVGLLRAQLKLEGRDKQFLVK
Drerio  not conserved  ENSDARG00000031757  670GKSVALLKSQCALEQRDKQFLIR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
678712TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2139 / 2139
position (AA) of stopcodon in wt / mu AA sequence 713 / 713
position of stopcodon in wt / mu cDNA 2271 / 2271
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 133 / 133
chromosome 19
strand -1
last intron/exon boundary 2203
theoretical NMD boundary in CDS 2020
length of CDS 2139
coding sequence (CDS) position 2065
cDNA position
(for ins/del: last normal base / first normal base)		 2197
gDNA position
(for ins/del: last normal base / first normal base)		 12736
chromosomal position
(for ins/del: last normal base / first normal base)		 54664209
original gDNA sequence snippet CTGAGCTCAAACGTCAGAGACAGACGGTGAGCCAGGCGGGT
altered gDNA sequence snippet CTGAGCTCAAACGTCAGAGAGAGACGGTGAGCCAGGCGGGT
original cDNA sequence snippet CTGAGCTCAAACGTCAGAGACAGACGGAGGCGCAGAATAAA
altered cDNA sequence snippet CTGAGCTCAAACGTCAGAGAGAGACGGAGGCGCAGAATAAA
wildtype AA sequence MEENPTLESE AWGSSRGWLA PREARGAPCS SPGPSLSSVL NELPSAATLR YRDPGVLPWG
ALEEEEEDGG RSRKAFTEVT QTELQDPHPS RELPWPMQAR RAHRQRNASR DQVVYGSGTK
TDRWARLLRR SKEKTKEGLR SLQPWAWTLK RIGGQFGAGT ESYFSLLRFL LLLNVLASVL
MACMTLLPTW LGGAPPGPPG PDISSPCGSY NPHSQGLVTF ATQLFNLLSG EGYLEWSPLF
YGFYPPRPRL AVTYLCWAFA VGLICLLLIL HRSVSGLKQT LLAESEALTS YSHRVFSAWD
FGLCGDVHVR LRQRIILYEL KVELEETVVR RQAAVRTLGQ QARVWLVRVL LNLLVVALLG
AAFYGVYWAT GCTVELQEMP LVQELPLLKL GVNYLPSIFI AGVNFVLPPV FKLIAPLEGY
TRSRQIVFIL LRTVFLRLAS LVVLLFSLWN QITCGGDSEA EDCKTCGYNY KQLPCWETVL
GQEMYKLLLF DLLTVLAVAL LIQFPRKLLC GLCPGALGRL AGTQEFQVPD EVLGLIYAQT
VVWVGSFFCP LLPLLNTVKF LLLFYLKKLT LFSTCSPAAR TFRASAANFF FPLVLLLGLA
ISSVPLLYSI FLIPPSKLCG PFRGQSSIWA QIPESISSLP ETTQNFLFFL GTQAFAVPLL
LISSILMAYT VALANSYGRL ISELKRQRQT EAQNKVFLAR RAVALTSTKP AL*
mutated AA sequence MEENPTLESE AWGSSRGWLA PREARGAPCS SPGPSLSSVL NELPSAATLR YRDPGVLPWG
ALEEEEEDGG RSRKAFTEVT QTELQDPHPS RELPWPMQAR RAHRQRNASR DQVVYGSGTK
TDRWARLLRR SKEKTKEGLR SLQPWAWTLK RIGGQFGAGT ESYFSLLRFL LLLNVLASVL
MACMTLLPTW LGGAPPGPPG PDISSPCGSY NPHSQGLVTF ATQLFNLLSG EGYLEWSPLF
YGFYPPRPRL AVTYLCWAFA VGLICLLLIL HRSVSGLKQT LLAESEALTS YSHRVFSAWD
FGLCGDVHVR LRQRIILYEL KVELEETVVR RQAAVRTLGQ QARVWLVRVL LNLLVVALLG
AAFYGVYWAT GCTVELQEMP LVQELPLLKL GVNYLPSIFI AGVNFVLPPV FKLIAPLEGY
TRSRQIVFIL LRTVFLRLAS LVVLLFSLWN QITCGGDSEA EDCKTCGYNY KQLPCWETVL
GQEMYKLLLF DLLTVLAVAL LIQFPRKLLC GLCPGALGRL AGTQEFQVPD EVLGLIYAQT
VVWVGSFFCP LLPLLNTVKF LLLFYLKKLT LFSTCSPAAR TFRASAANFF FPLVLLLGLA
ISSVPLLYSI FLIPPSKLCG PFRGQSSIWA QIPESISSLP ETTQNFLFFL GTQAFAVPLL
LISSILMAYT VALANSYGRL ISELKRQRET EAQNKVFLAR RAVALTSTKP AL*
speed 1.16 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