Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99898815888397 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032165)
  • known disease mutation: rs2855 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:215851290T>CN/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.3185A>G
cDNA.3344A>G
g.151862A>G
AA changes N1062S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1062
frameshift no
known variant Reference ID: rs28940269
databasehomozygous (C/C)heterozygousallele carriers
1000G011
ExAC099

known disease mutation: rs2855 (pathogenic for Autosomal recessive congenital ichthyosis 4B|Autosomal recessive congenital ichthyosis 4A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032165)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032165)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032165)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1920.965
3.5631
(flanking)5.1261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased151855wt: 0.61 / mu: 0.71wt: GGCATATTACTTCATTGCTGGGGCCCAATGGAGCTGGGAAA
mu: GGCATATTACTTCATTGCTGGGGCCCAGTGGAGCTGGGAAA		 ctgg|GGCC
Acc marginally increased151854wt: 0.8602 / mu: 0.9048 (marginal change - not scored)wt: GGGCATATTACTTCATTGCTGGGGCCCAATGGAGCTGGGAA
mu: GGGCATATTACTTCATTGCTGGGGCCCAGTGGAGCTGGGAA		 gctg|GGGC
Donor marginally increased151861wt: 0.9654 / mu: 0.9961 (marginal change - not scored)wt: GGCCCAATGGAGCTG
mu: GGCCCAGTGGAGCTG		 CCCA|atgg
Donor gained1518560.55mu: GCTGGGGCCCAGTGG TGGG|gccc
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1062YEGHITSLLGPNGAGKTTTISMLT
mutated  all conserved    1062YEGHITSLLGPSGAGKTTTISML
Ptroglodytes  all identical  ENSPTRG00000012889  1380YEGHITSLLGPNGAGKTTTISML
Mmulatta  all identical  ENSMMUG00000014813  1359YEGHITSLLGPNGAGKTTTISML
Fcatus  no alignment  ENSFCAG00000009215  n/a
Mmusculus  all identical  ENSMUSG00000050296  1380YEGHITSLLGPNGAGKTTTISML
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074749  596LGHNGAGKTTTMSLL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
10651085TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
11121132TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
11451165TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
11701170CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11741194TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 3185
cDNA position
(for ins/del: last normal base / first normal base)		 3344
gDNA position
(for ins/del: last normal base / first normal base)		 151862
chromosomal position
(for ins/del: last normal base / first normal base)		 215851290
original gDNA sequence snippet TACTTCATTGCTGGGGCCCAATGGAGCTGGGAAAACTACTA
altered gDNA sequence snippet TACTTCATTGCTGGGGCCCAGTGGAGCTGGGAAAACTACTA
original cDNA sequence snippet TACTTCATTGCTGGGGCCCAATGGAGCTGGGAAAACTACTA
altered cDNA sequence snippet TACTTCATTGCTGGGGCCCAGTGGAGCTGGGAAAACTACTA
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 PSGAGKTTTI 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*
speed 1.22 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