Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0448956985385625 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM890013)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:51064416T>CN/A show variant in all transcripts   IGV
HGNC symbol ARSA
Ensembl transcript ID ENST00000356098
Genbank transcript ID NM_001085426
UniProt peptide P15289
alteration type single base exchange
alteration region CDS
DNA changes c.1055A>G
cDNA.1293A>G
g.2192A>G
AA changes N352S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 352
frameshift no
known variant Reference ID: rs2071421
databasehomozygous (C/C)heterozygousallele carriers
1000G167792959
ExAC83970017840

known disease mutation at this position, please check HGMD for details (HGMD ID CM890013)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.8460.107
1.9670.961
(flanking)1.8580.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased2203wt: 0.4200 / mu: 0.4229 (marginal change - not scored)wt: CACTGCCCAATGTCACCTTGGATGGCTTTGACCTCAGCCCC
mu: CACTGCCCAGTGTCACCTTGGATGGCTTTGACCTCAGCCCC		 ttgg|ATGG
Acc marginally increased2190wt: 0.2262 / mu: 0.2490 (marginal change - not scored)wt: CTGGCTGGGGCCCCACTGCCCAATGTCACCTTGGATGGCTT
mu: CTGGCTGGGGCCCCACTGCCCAGTGTCACCTTGGATGGCTT		 gccc|AATG
Donor gained21860.85mu: CCCACTGCCCAGTGT CACT|gccc
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      352TLAALAGAPLPNVTLDGFDLSPLL
mutated  all conserved    352TLAALAGAPLPSVTLDGFDL
Ptroglodytes  all identical  ENSPTRG00000014550  351TLAALAGAPLPNVTLDGFDLSPL
Mmulatta  all identical  ENSMMUG00000016274  350TLAALAGAPLPNVTLDGFDLSP
Fcatus  all identical  ENSFCAG00000010597  352TLAALTGAPLPNVTLDGVDL
Mmusculus  all identical  ENSMUSG00000022620  349TLAALTGAPLPNVTLDGVDISPL
Ggallus  all identical  ENSGALG00000009746  342TLTALAGAALPNVSLDGYDLSPL
Trubripes  not conserved  ENSTRUG00000012206  352TIASLAGAKLPQVMLDGVDMSNI
Drerio  not conserved  ENSDARG00000042270  353TFAKLAGAPLPEVQLDGVEMTDI
Dmelanogaster  no homologue    
Celegans  no alignment  D1014.1  n/a
Xtropicalis  all identical  ENSXETG00000033466  352TIAALTGAPLPNVTLDGYDLSKL
protein features
start (aa)end (aa)featuredetails 
350350CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
359363HELIXmight get lost (downstream of altered splice site)
372375STRANDmight get lost (downstream of altered splice site)
382384TURNmight get lost (downstream of altered splice site)
387391STRANDmight get lost (downstream of altered splice site)
394400STRANDmight get lost (downstream of altered splice site)
404406HELIXmight get lost (downstream of altered splice site)
408410STRANDmight get lost (downstream of altered splice site)
412414HELIXmight get lost (downstream of altered splice site)
414414DISULFIDmight get lost (downstream of altered splice site)
421430STRANDmight get lost (downstream of altered splice site)
431433TURNmight get lost (downstream of altered splice site)
450469HELIXmight get lost (downstream of altered splice site)
477479HELIXmight get lost (downstream of altered splice site)
483485HELIXmight get lost (downstream of altered splice site)
488488DISULFIDmight get lost (downstream of altered splice site)
489489DISULFIDmight get lost (downstream of altered splice site)
493493DISULFIDmight get lost (downstream of altered splice site)
496499TURNmight get lost (downstream of altered splice site)
499499DISULFIDmight get lost (downstream of altered splice site)
500500DISULFIDmight get lost (downstream of altered splice site)
502502DISULFIDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1530 / 1530
position (AA) of stopcodon in wt / mu AA sequence 510 / 510
position of stopcodon in wt / mu cDNA 1768 / 1768
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 239 / 239
chromosome 22
strand -1
last intron/exon boundary 1449
theoretical NMD boundary in CDS 1160
length of CDS 1530
coding sequence (CDS) position 1055
cDNA position
(for ins/del: last normal base / first normal base)		 1293
gDNA position
(for ins/del: last normal base / first normal base)		 2192
chromosomal position
(for ins/del: last normal base / first normal base)		 51064416
original gDNA sequence snippet GGCTGGGGCCCCACTGCCCAATGTCACCTTGGATGGCTTTG
altered gDNA sequence snippet GGCTGGGGCCCCACTGCCCAGTGTCACCTTGGATGGCTTTG
original cDNA sequence snippet GGCTGGGGCCCCACTGCCCAATGTCACCTTGGATGGCTTTG
altered cDNA sequence snippet GGCTGGGGCCCCACTGCCCAGTGTCACCTTGGATGGCTTTG
wildtype AA sequence MSMGAPRSLL LALAAGLAVA RPPNIVLIFA DDLGYGDLGC YGHPSSTTPN LDQLAAGGLR
FTDFYVPVSL CTPSRAALLT GRLPVRMGMY PGVLVPSSRG GLPLEEVTVA EVLAARGYLT
GMAGKWHLGV GPEGAFLPPH QGFHRFLGIP YSHDQGPCQN LTCFPPATPC DGGCDQGLVP
IPLLANLSVE AQPPWLPGLE ARYMAFAHDL MADAQRQDRP FFLYYASHHT HYPQFSGQSF
AERSGRGPFG DSLMELDAAV GTLMTAIGDL GLLEETLVIF TADNGPETMR MSRGGCSGLL
RCGKGTTYEG GVREPALAFW PGHIAPGVTH ELASSLDLLP TLAALAGAPL PNVTLDGFDL
SPLLLGTGKS PRQSLFFYPS YPDEVRGVFA VRTGKYKAHF FTQGSAHSDT TADPACHASS
SLTAHEPPLL YDLSKDPGEN YNLLGGVAGA TPEVLQALKQ LQLLKAQLDA AVTFGPSQVA
RGEDPALQIC CHPGCTPRPA CCHCPDPHA*
mutated AA sequence MSMGAPRSLL LALAAGLAVA RPPNIVLIFA DDLGYGDLGC YGHPSSTTPN LDQLAAGGLR
FTDFYVPVSL CTPSRAALLT GRLPVRMGMY PGVLVPSSRG GLPLEEVTVA EVLAARGYLT
GMAGKWHLGV GPEGAFLPPH QGFHRFLGIP YSHDQGPCQN LTCFPPATPC DGGCDQGLVP
IPLLANLSVE AQPPWLPGLE ARYMAFAHDL MADAQRQDRP FFLYYASHHT HYPQFSGQSF
AERSGRGPFG DSLMELDAAV GTLMTAIGDL GLLEETLVIF TADNGPETMR MSRGGCSGLL
RCGKGTTYEG GVREPALAFW PGHIAPGVTH ELASSLDLLP TLAALAGAPL PSVTLDGFDL
SPLLLGTGKS PRQSLFFYPS YPDEVRGVFA VRTGKYKAHF FTQGSAHSDT TADPACHASS
SLTAHEPPLL YDLSKDPGEN YNLLGGVAGA TPEVLQALKQ LQLLKAQLDA AVTFGPSQVA
RGEDPALQIC CHPGCTPRPA CCHCPDPHA*
speed 0.50 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