Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999995833801 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM085246)
  • known disease mutation: rs1991 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:93722608G>AN/A show variant in all transcripts   IGV
HGNC symbol ARL13B
Ensembl transcript ID ENST00000394222
Genbank transcript ID N/A
UniProt peptide Q3SXY8
alteration type single base exchange
alteration region CDS
DNA changes c.236G>A
cDNA.511G>A
g.23626G>A
AA changes R79Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 79
frameshift no
known variant Reference ID: rs121912606
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs1991 (pathogenic for Joubert syndrome 8) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085246)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085246)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085246)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.4841
6.3051
(flanking)-0.0730.972
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased23627wt: 0.20 / mu: 0.26wt: ATTCGGGGAATCTGG
mu: ATTCAGGGAATCTGG		 TCGG|ggaa
Donor increased23626wt: 0.65 / mu: 0.95wt: AATTCGGGGAATCTG
mu: AATTCAGGGAATCTG		 TTCG|ggga
Donor increased23617wt: 0.35 / mu: 0.44wt: TGGAATAAGAATTCG
mu: TGGAATAAGAATTCA		 GAAT|aaga
distance from splice site 106
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      79TIFDLGGGIRIRGIWKNYYAESYG
mutated  all conserved    79TIFDLGGGIRIQGIWKNYYAESY
Ptroglodytes  all identical  ENSPTRG00000015129  79TIFDLGGGIRIRGIWKNYYAESY
Mmulatta  all identical  ENSMMUG00000020335  80TIFDLGGGIRIRGIWKNYYAESY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022911  79TIFDLGGGKRIRGIWKNYYAESY
Ggallus  all identical  ENSGALG00000015412  80TIFDLGGGKRIRNIWRNYYAESY
Trubripes  all identical  ENSTRUG00000013035  79TIFDLGGGKRIRDIWKNYYTMSH
Drerio  all identical  ENSDARG00000012763  79TIFDLGGGKRIRGIWKNYYSESY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000032383  79TMFDLGGGKRIRGIWKNYYAESY
protein features
start (aa)end (aa)featuredetails 
7175NP_BINDGTP (By similarity).might get lost (downstream of altered splice site)
130133NP_BINDGTP (By similarity).might get lost (downstream of altered splice site)
192245COILEDPotential.might get lost (downstream of altered splice site)
369419COMPBIASPro-rich.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1287 / 1287
position (AA) of stopcodon in wt / mu AA sequence 429 / 429
position of stopcodon in wt / mu cDNA 1562 / 1562
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 276 / 276
chromosome 3
strand 1
last intron/exon boundary 1486
theoretical NMD boundary in CDS 1160
length of CDS 1287
coding sequence (CDS) position 236
cDNA position
(for ins/del: last normal base / first normal base)		 511
gDNA position
(for ins/del: last normal base / first normal base)		 23626
chromosomal position
(for ins/del: last normal base / first normal base)		 93722608
original gDNA sequence snippet GGGAGGTGGAATAAGAATTCGGGGAATCTGGAAGAATTACT
altered gDNA sequence snippet GGGAGGTGGAATAAGAATTCAGGGAATCTGGAAGAATTACT
original cDNA sequence snippet GGGAGGTGGAATAAGAATTCGGGGAATCTGGAAGAATTACT
altered cDNA sequence snippet GGGAGGTGGAATAAGAATTCAGGGAATCTGGAAGAATTACT
wildtype AA sequence MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA PTVGFSKINL
RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD EERMEETKEA MSEMLRHPRI
SGKPILVLAN KQDKEGALGE ADVIECLSLE KLVNEHKCLC QIEPCSAISG YGKKIDKSIK
KGLYWLLHVI ARDFDALNER IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL
DGTSGLAELD PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK LRMKRNHRVE
PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET HHNDFYRKPL PPLAVPQRPN
SDAHDVIS*
mutated AA sequence MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA PTVGFSKINL
RQGKFEVTIF DLGGGIRIQG IWKNYYAESY GVIFVVDSSD EERMEETKEA MSEMLRHPRI
SGKPILVLAN KQDKEGALGE ADVIECLSLE KLVNEHKCLC QIEPCSAISG YGKKIDKSIK
KGLYWLLHVI ARDFDALNER IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL
DGTSGLAELD PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK LRMKRNHRVE
PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET HHNDFYRKPL PPLAVPQRPN
SDAHDVIS*
speed 1.00 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