Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997821226788 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032167)
  • known disease mutation: rs2857 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:215846949C>TN/A show variant in all transcripts   IGV
HGNC symbol ABCA12
Ensembl transcript ID ENST00000389661
Genbank transcript ID NM_015657
UniProt peptide Q86UK0
alteration type single base exchange
alteration region CDS
DNA changes c.3587G>A
cDNA.3746G>A
g.156203G>A
AA changes R1196H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1196
frameshift no
known variant Reference ID: rs28940270
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2857 (pathogenic for Autosomal recessive congenital ichthyosis 4A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032167)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032167)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032167)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2180.938
6.2081
(flanking)2.1371
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased156206wt: 0.35 / mu: 0.54wt: AGTTGACCCATGTTCTCGCCGAAGTATATGGGATGTTATAT
mu: AGTTGACCCATGTTCTCACCGAAGTATATGGGATGTTATAT		 gccg|AAGT
Donor marginally increased156203wt: 0.9869 / mu: 0.9902 (marginal change - not scored)wt: TTCTCGCCGAAGTAT
mu: TTCTCACCGAAGTAT		 CTCG|ccga
Donor increased156208wt: 0.28 / mu: 0.39wt: GCCGAAGTATATGGG
mu: ACCGAAGTATATGGG		 CGAA|gtat
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1196DEPSTGVDPCSRRSIWDVISKNKT
mutated  not conserved    1196DEPSTGVDPCSHRSIW
Ptroglodytes  all identical  ENSPTRG00000012889  1514DEPSTGVDPCSRRSIWDVISKNK
Mmulatta  all identical  ENSMMUG00000014813  1493DEPSTGVDPCSRRSIWDVISKNK
Fcatus  all identical  ENSFCAG00000009215  1514DEPSTGVDPCSRRSIWDVI
Mmusculus  all identical  ENSMUSG00000050296  1514DEPSTGVDPCSRRSIWDVISKNK
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074749  730DEPTTGVDPCSRRSIWDIIIQHK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
12001220TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
12501270TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
13461577DOMAINABC transporter 1.might get lost (downstream of altered splice site)
13781385NP_BINDATP 1 (Potential).might get lost (downstream of altered splice site)
15241524CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16631663CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
17041704CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
17471767TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
17691769CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
18191819CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
18351835CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
18761876CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
19211921CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
19521952CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
19791999TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
20352055TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
20722092TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
20792079CONFLICTY -> H (in Ref. 1; AAP21093).might get lost (downstream of altered splice site)
21032123TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
21782178CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
21872207TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
22082208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
22232223CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
22542489DOMAINABC transporter 2.might get lost (downstream of altered splice site)
22702290TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
22902297NP_BINDATP 2 (Potential).might get lost (downstream of altered splice site)
23182318CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
25422542CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
25472547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6834 / 6834
position (AA) of stopcodon in wt / mu AA sequence 2278 / 2278
position of stopcodon in wt / mu cDNA 6993 / 6993
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 160 / 160
chromosome 2
strand -1
last intron/exon boundary 6886
theoretical NMD boundary in CDS 6676
length of CDS 6834
coding sequence (CDS) position 3587
cDNA position
(for ins/del: last normal base / first normal base)		 3746
gDNA position
(for ins/del: last normal base / first normal base)		 156203
chromosomal position
(for ins/del: last normal base / first normal base)		 215846949
original gDNA sequence snippet TGGAGTTGACCCATGTTCTCGCCGAAGTATATGGGATGTTA
altered gDNA sequence snippet TGGAGTTGACCCATGTTCTCACCGAAGTATATGGGATGTTA
original cDNA sequence snippet TGGAGTTGACCCATGTTCTCGCCGAAGTATATGGGATGTTA
altered cDNA sequence snippet TGGAGTTGACCCATGTTCTCACCGAAGTATATGGGATGTTA
wildtype AA sequence MFTYIKIITS GDSDNITHVW NEDDGQTLSP SSLAAQLLIL ENFEDALLNI SANSPYIPYL
ACVRNVTDSL ARGSPENLRL LQSTIRFKKS FLRNGSYEDY FPPVPEVLKS KLSQLRNLTE
LLCESETFSL IEKSCQLSDM SFGSLCEESE FDLQLLEAAE LGTEIAASLL YHDNVISKKV
RDLLTGDPSK INLNMDQFLE QALQMNYLEN ITQLIPIIEA MLHVNNSADA SEKPGQLLEM
FKNVEELKED LRRTTGMSNR TIDKLLAIPI PDNRAEIISQ VFWLHSCDTN ITTPKLEDAM
KEFCNLSLSE RSRQSYLIGL TLLHYLNIYN FTYKVFFPRK DQKPVEKMME LFIRLKEILN
QMASGTHPLL DKMRSLKQMH LPRSVPLTQA MYRSNRMNTP QGSFSTISQA LCSQGITTEY
LTAMLPSSQR PKGNHTKDFL TYKLTKEQIA SKYGIPINST PFCFSLYKDI INMPAGPVIW
AFLKPMLLGR ILYAPYNPVT KAIMEKSNVT LRQLAELREK SQEWMDKSPL FMNSFHLLNQ
AIPMLQNTLR NPFVQVFVKF SVGLDAVELL KQIDELDILR LKLENNIDII DQLNTLSSLT
VNISSCVLYD RIQAAKTIDE MEREAKRLYK SNELFGSVIF KLPSNRSWHR GYDSGNVFLP
PVIKYTIRMS LKTAQTTRSL RTKIWAPGPH NSPSHNQIYG RAFIYLQDSI ERAIIELQTG
RNSQEIAVQV QAIPYPCFMK DNFLTSVSYS LPIVLMVAWV VFIAAFVKKL VYEKDLRLHE
YMKMMGVNSC SHFFAWLIES VGFLLVTIVI LIIILKFGNI LPKTNGFILF LYFSDYSFSV
IAMSYLISVF FNNTNIAALI GSLIYIIAFF PFIVLVTVEN ELSYVLKVFM SLLSPTAFSY
ASQYIARYEE QGIGLQWENM YTSPVQDDTT SFGWLCCLIL ADSFIYFLIA WYVRNVFPGT
YGMAAPWYFP ILPSYWKERF GCAEVKPEKS NGLMFTNIMM QNTNPSASPE YMFSSNIEPE
PKDLTVGVAL HGVTKIYGSK VAVDNLNLNF YEGHITSLLG PNGAGKTTTI SMLTGLFGAS
AGTIFVYGKD IKTDLHTVRK NMGVCMQHDV LFSYLTTKEH LLLYGSIKVP HWTKKQLHEE
VKRTLKDTGL YSHRHKRVGT LSGGMKRKLS ISIALIGGSR VVILDEPSTG VDPCSRRSIW
DVISKNKTAR TIILSTHHLD EAEVLSDRIA FLEQGGLRCC GSPFYLKEAF GDGYHLTLTK
KKSPNLNANA VCDTMAVTAM IQSHLPEAYL KEDIGGELVY VLPPFSTKVS GAYLSLLRAL
DNGMGDLNIG CYGISDTTVE EVFLNLTKES QKNSAMSLEH LTQKKIGNSN ANGISTPDDL
SVSSSNFTDR DDKILTRGER LDGFGLLLKK IMAILIKRFH HTRRNWKGLI AQVILPIVFV
TTAMGLGTLR NSSNSYPEIQ ISPSLYGTSE QTAFYANYHP STEALVSAMW DFPGIDNMCL
NTSDLQCLNK DSLEKWNTSG EPITNFGVCS CSENVQECPK FNYSPPHRRT YSSQVIYNLT
GQRVENYLIS TANEFVQKRY GGWSFGLPLT KDLRFDITGV PANRTLAKVW YDPEGYHSLP
AYLNSLNNFL LRVNMSKYDA ARHGIIMYSH PYPGVQDQEQ ATISSLIDIL VALSILMGYS
VTTASFVTYV VREHQTKAKQ LQHISGIGVT CYWVTNFIYD MVFYLVPVAF SIGIIAIFKL
PAFYSENNLG AVSLLLLLFG YATFSWMYLL AGLFHETGMA FITYVCVNLF FGINSIVSLS
VVYFLSKEKP NDPTLELISE TLKRIFLIFP QFCFGYGLIE LSQQQSVLDF LKAYGVEYPN
ETFEMNKLGA MFVALVSQGT MFFSLRLLIN ESLIKKLRLF FRKFNSSHVR ETIDEDEDVR
AERLRVESGA AEFDLVQLYC LTKTYQLIHK KIIAVNNISI GIPAGECFGL LGVNGAGKTT
IFKMLTGDII PSSGNILIRN KTGSLGHVDS HSSLVGYCPQ EDALDDLVTV EEHLYFYARV
HGIPEKDIKE TVHKLLRRLH LMPFKDRATS MCSYGTKRKL STALALIGKP SILLLDEPSS
GMDPKSKRHL WKIISEEVQN KCSVILTSHS MEECEALCTR LAIMVNGKFQ CIGSLQHIKS
RFGRGFTVKV HLKNNKVTME TLTKFMQLHF PKTYLKDQHL SMLEYHVPVT AGGVANIFDL
LETNKTALNI TNFLVSQTTL EEVFINFAKD QKSYETADTS SQGSTISVDS QDDQMES*
mutated AA sequence MFTYIKIITS GDSDNITHVW NEDDGQTLSP SSLAAQLLIL ENFEDALLNI SANSPYIPYL
ACVRNVTDSL ARGSPENLRL LQSTIRFKKS FLRNGSYEDY FPPVPEVLKS KLSQLRNLTE
LLCESETFSL IEKSCQLSDM SFGSLCEESE FDLQLLEAAE LGTEIAASLL YHDNVISKKV
RDLLTGDPSK INLNMDQFLE QALQMNYLEN ITQLIPIIEA MLHVNNSADA SEKPGQLLEM
FKNVEELKED LRRTTGMSNR TIDKLLAIPI PDNRAEIISQ VFWLHSCDTN ITTPKLEDAM
KEFCNLSLSE RSRQSYLIGL TLLHYLNIYN FTYKVFFPRK DQKPVEKMME LFIRLKEILN
QMASGTHPLL DKMRSLKQMH LPRSVPLTQA MYRSNRMNTP QGSFSTISQA LCSQGITTEY
LTAMLPSSQR PKGNHTKDFL TYKLTKEQIA SKYGIPINST PFCFSLYKDI INMPAGPVIW
AFLKPMLLGR ILYAPYNPVT KAIMEKSNVT LRQLAELREK SQEWMDKSPL FMNSFHLLNQ
AIPMLQNTLR NPFVQVFVKF SVGLDAVELL KQIDELDILR LKLENNIDII DQLNTLSSLT
VNISSCVLYD RIQAAKTIDE MEREAKRLYK SNELFGSVIF KLPSNRSWHR GYDSGNVFLP
PVIKYTIRMS LKTAQTTRSL RTKIWAPGPH NSPSHNQIYG RAFIYLQDSI ERAIIELQTG
RNSQEIAVQV QAIPYPCFMK DNFLTSVSYS LPIVLMVAWV VFIAAFVKKL VYEKDLRLHE
YMKMMGVNSC SHFFAWLIES VGFLLVTIVI LIIILKFGNI LPKTNGFILF LYFSDYSFSV
IAMSYLISVF FNNTNIAALI GSLIYIIAFF PFIVLVTVEN ELSYVLKVFM SLLSPTAFSY
ASQYIARYEE QGIGLQWENM YTSPVQDDTT SFGWLCCLIL ADSFIYFLIA WYVRNVFPGT
YGMAAPWYFP ILPSYWKERF GCAEVKPEKS NGLMFTNIMM QNTNPSASPE YMFSSNIEPE
PKDLTVGVAL HGVTKIYGSK VAVDNLNLNF YEGHITSLLG PNGAGKTTTI SMLTGLFGAS
AGTIFVYGKD IKTDLHTVRK NMGVCMQHDV LFSYLTTKEH LLLYGSIKVP HWTKKQLHEE
VKRTLKDTGL YSHRHKRVGT LSGGMKRKLS ISIALIGGSR VVILDEPSTG VDPCSHRSIW
DVISKNKTAR TIILSTHHLD EAEVLSDRIA FLEQGGLRCC GSPFYLKEAF GDGYHLTLTK
KKSPNLNANA VCDTMAVTAM IQSHLPEAYL KEDIGGELVY VLPPFSTKVS GAYLSLLRAL
DNGMGDLNIG CYGISDTTVE EVFLNLTKES QKNSAMSLEH LTQKKIGNSN ANGISTPDDL
SVSSSNFTDR DDKILTRGER LDGFGLLLKK IMAILIKRFH HTRRNWKGLI AQVILPIVFV
TTAMGLGTLR NSSNSYPEIQ ISPSLYGTSE QTAFYANYHP STEALVSAMW DFPGIDNMCL
NTSDLQCLNK DSLEKWNTSG EPITNFGVCS CSENVQECPK FNYSPPHRRT YSSQVIYNLT
GQRVENYLIS TANEFVQKRY GGWSFGLPLT KDLRFDITGV PANRTLAKVW YDPEGYHSLP
AYLNSLNNFL LRVNMSKYDA ARHGIIMYSH PYPGVQDQEQ ATISSLIDIL VALSILMGYS
VTTASFVTYV VREHQTKAKQ LQHISGIGVT CYWVTNFIYD MVFYLVPVAF SIGIIAIFKL
PAFYSENNLG AVSLLLLLFG YATFSWMYLL AGLFHETGMA FITYVCVNLF FGINSIVSLS
VVYFLSKEKP NDPTLELISE TLKRIFLIFP QFCFGYGLIE LSQQQSVLDF LKAYGVEYPN
ETFEMNKLGA MFVALVSQGT MFFSLRLLIN ESLIKKLRLF FRKFNSSHVR ETIDEDEDVR
AERLRVESGA AEFDLVQLYC LTKTYQLIHK KIIAVNNISI GIPAGECFGL LGVNGAGKTT
IFKMLTGDII PSSGNILIRN KTGSLGHVDS HSSLVGYCPQ EDALDDLVTV EEHLYFYARV
HGIPEKDIKE TVHKLLRRLH LMPFKDRATS MCSYGTKRKL STALALIGKP SILLLDEPSS
GMDPKSKRHL WKIISEEVQN KCSVILTSHS MEECEALCTR LAIMVNGKFQ CIGSLQHIKS
RFGRGFTVKV HLKNNKVTME TLTKFMQLHF PKTYLKDQHL SMLEYHVPVT AGGVANIFDL
LETNKTALNI TNFLVSQTTL EEVFINFAKD QKSYETADTS SQGSTISVDS QDDQMES*
speed 1.12 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