Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000272895
MT speed 0 s - this script 3.88161 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCA12polymorphism_automatic0.00117637900460299simple_aaeaffectedN237Hsingle base exchangers11890512show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.998823620995397 (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) chr2:215910724T>GN/A show variant in all transcripts   IGV
HGNC symbol ABCA12
Ensembl transcript ID ENST00000272895
Genbank transcript ID NM_173076
UniProt peptide Q86UK0
alteration type single base exchange
alteration region CDS
DNA changes c.709A>C
cDNA.929A>C
g.92428A>C
AA changes N237H Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 237
frameshift no
known variant Reference ID: rs11890512
databasehomozygous (G/G)heterozygousallele carriers
1000G224379603
ExAC123345225755
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4010.98
0.0770.982
(flanking)1.9621
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 increased92419wt: 0.7754 / mu: 0.7965 (marginal change - not scored)wt: TTTTATATTTTAAGCTATCCAGTGACCCCAACAATCAGAAG
mu: TTTTATATTTTAAGCTATCCAGTGACCCCCACAATCAGAAG		 tcca|GTGA
Donor marginally increased92419wt: 0.9564 / mu: 0.9677 (marginal change - not scored)wt: TATCCAGTGACCCCA
mu: TATCCAGTGACCCCC		 TCCA|gtga
Donor increased92427wt: 0.30 / mu: 0.40wt: GACCCCAACAATCAG
mu: GACCCCCACAATCAG		 CCCC|aaca
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      237NKQFSQLSSDPNNQKIVFQEIVRM
mutated  all conserved    237NKQFSQLSSDPHNQK
Ptroglodytes  all identical  ENSPTRG00000012889  237NKQFSQLSSDPNNQK
Mmulatta  all conserved  ENSMMUG00000014813  214NKQFSQLSSDPDNQKIVFQEIVR
Fcatus  no alignment  ENSFCAG00000009215  n/a
Mmusculus  all conserved  ENSMUSG00000050296  237KYQVSQMSSDPDNQK
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074749  1441RRLFCWKRNAVQSYSPNED
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
275275CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
333333CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
367367CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
383383CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
412412CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
435435CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
528528CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
543543CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
577577CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
608608CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
623623CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
648648CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
651651CONFLICTY -> D (in Ref. 1; AAP21093).might get lost (downstream of altered splice site)
752752CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
811811CONFLICTY -> H (in Ref. 1; AAP21093).might get lost (downstream of altered splice site)
826826CONFLICTN -> D (in Ref. 2; AAK54355).might get lost (downstream of altered splice site)
826826CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
920920CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
963963CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
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 7788 / 7788
position (AA) of stopcodon in wt / mu AA sequence 2596 / 2596
position of stopcodon in wt / mu cDNA 8008 / 8008
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 221 / 221
chromosome 2
strand -1
last intron/exon boundary 7901
theoretical NMD boundary in CDS 7630
length of CDS 7788
coding sequence (CDS) position 709
cDNA position
(for ins/del: last normal base / first normal base)		 929
gDNA position
(for ins/del: last normal base / first normal base)		 92428
chromosomal position
(for ins/del: last normal base / first normal base)		 215910724
original gDNA sequence snippet TTAAGCTATCCAGTGACCCCAACAATCAGAAGATAGTGTTT
altered gDNA sequence snippet TTAAGCTATCCAGTGACCCCCACAATCAGAAGATAGTGTTT
original cDNA sequence snippet CCCAGCTATCCAGTGACCCCAACAATCAGAAGATAGTGTTT
altered cDNA sequence snippet CCCAGCTATCCAGTGACCCCCACAATCAGAAGATAGTGTTT
wildtype AA sequence MASLFHQLQI LVWKNWLGVK RQPLWTLVLI LWPVIIFIIL AITRTKFPPT AKPTCYLAPR
NLPSTGFFPF LQTLLCDTDS KCKDTPYGPQ DLLRRKGIDD ALFKDSEILR KSSNLDKDSS
LSFQSTQVPE RRHASLATVF PSPSSDLEIP GTYTFNGSQV LARILGLEKL LKQNSTSEDI
RRELCDSYSG YIVDDAFSWT FLGRNVFNKF CLSNMTLLES SLQELNKQFS QLSSDPNNQK
IVFQEIVRML SFFSQVQEQK AVWQLLSSFP NVFQNDTSLS NLFDVLRKAN SVLLVVQKVY
PRFATNEGFR TLQKSVKHLL YTLDSPAQGD SDNITHVWNE DDGQTLSPSS LAAQLLILEN
FEDALLNISA NSPYIPYLAC VRNVTDSLAR GSPENLRLLQ STIRFKKSFL RNGSYEDYFP
PVPEVLKSKL SQLRNLTELL CESETFSLIE KSCQLSDMSF GSLCEESEFD LQLLEAAELG
TEIAASLLYH DNVISKKVRD LLTGDPSKIN LNMDQFLEQA LQMNYLENIT QLIPIIEAML
HVNNSADASE KPGQLLEMFK NVEELKEDLR RTTGMSNRTI DKLLAIPIPD NRAEIISQVF
WLHSCDTNIT TPKLEDAMKE FCNLSLSERS RQSYLIGLTL LHYLNIYNFT YKVFFPRKDQ
KPVEKMMELF IRLKEILNQM ASGTHPLLDK MRSLKQMHLP RSVPLTQAMY RSNRMNTPQG
SFSTISQALC SQGITTEYLT AMLPSSQRPK GNHTKDFLTY KLTKEQIASK YGIPINSTPF
CFSLYKDIIN MPAGPVIWAF LKPMLLGRIL YAPYNPVTKA IMEKSNVTLR QLAELREKSQ
EWMDKSPLFM NSFHLLNQAI PMLQNTLRNP FVQVFVKFSV GLDAVELLKQ IDELDILRLK
LENNIDIIDQ LNTLSSLTVN ISSCVLYDRI QAAKTIDEME REAKRLYKSN ELFGSVIFKL
PSNRSWHRGY DSGNVFLPPV IKYTIRMSLK TAQTTRSLRT KIWAPGPHNS PSHNQIYGRA
FIYLQDSIER AIIELQTGRN SQEIAVQVQA IPYPCFMKDN FLTSVSYSLP IVLMVAWVVF
IAAFVKKLVY EKDLRLHEYM KMMGVNSCSH FFAWLIESVG FLLVTIVILI IILKFGNILP
KTNGFILFLY FSDYSFSVIA MSYLISVFFN NTNIAALIGS LIYIIAFFPF IVLVTVENEL
SYVLKVFMSL LSPTAFSYAS QYIARYEEQG IGLQWENMYT SPVQDDTTSF GWLCCLILAD
SFIYFLIAWY VRNVFPGTYG MAAPWYFPIL PSYWKERFGC AEVKPEKSNG LMFTNIMMQN
TNPSASPEYM FSSNIEPEPK DLTVGVALHG VTKIYGSKVA VDNLNLNFYE GHITSLLGPN
GAGKTTTISM LTGLFGASAG TIFVYGKDIK TDLHTVRKNM GVCMQHDVLF SYLTTKEHLL
LYGSIKVPHW TKKQLHEEVK RTLKDTGLYS HRHKRVGTLS GGMKRKLSIS IALIGGSRVV
ILDEPSTGVD PCSRRSIWDV ISKNKTARTI ILSTHHLDEA EVLSDRIAFL EQGGLRCCGS
PFYLKEAFGD GYHLTLTKKK SPNLNANAVC DTMAVTAMIQ SHLPEAYLKE DIGGELVYVL
PPFSTKVSGA YLSLLRALDN GMGDLNIGCY GISDTTVEEV FLNLTKESQK NSAMSLEHLT
QKKIGNSNAN GISTPDDLSV SSSNFTDRDD KILTRGERLD GFGLLLKKIM AILIKRFHHT
RRNWKGLIAQ VILPIVFVTT AMGLGTLRNS SNSYPEIQIS PSLYGTSEQT AFYANYHPST
EALVSAMWDF PGIDNMCLNT SDLQCLNKDS LEKWNTSGEP ITNFGVCSCS ENVQECPKFN
YSPPHRRTYS SQVIYNLTGQ RVENYLISTA NEFVQKRYGG WSFGLPLTKD LRFDITGVPA
NRTLAKVWYD PEGYHSLPAY LNSLNNFLLR VNMSKYDAAR HGIIMYSHPY PGVQDQEQAT
ISSLIDILVA LSILMGYSVT TASFVTYVVR EHQTKAKQLQ HISGIGVTCY WVTNFIYDMV
FYLVPVAFSI GIIAIFKLPA FYSENNLGAV SLLLLLFGYA TFSWMYLLAG LFHETGMAFI
TYVCVNLFFG INSIVSLSVV YFLSKEKPND PTLELISETL KRIFLIFPQF CFGYGLIELS
QQQSVLDFLK AYGVEYPNET FEMNKLGAMF VALVSQGTMF FSLRLLINES LIKKLRLFFR
KFNSSHVRET IDEDEDVRAE RLRVESGAAE FDLVQLYCLT KTYQLIHKKI IAVNNISIGI
PAGECFGLLG VNGAGKTTIF KMLTGDIIPS SGNILIRNKT GSLGHVDSHS SLVGYCPQED
ALDDLVTVEE HLYFYARVHG IPEKDIKETV HKLLRRLHLM PFKDRATSMC SYGTKRKLST
ALALIGKPSI LLLDEPSSGM DPKSKRHLWK IISEEVQNKC SVILTSHSME ECEALCTRLA
IMVNGKFQCI GSLQHIKSRF GRGFTVKVHL KNNKVTMETL TKFMQLHFPK TYLKDQHLSM
LEYHVPVTAG GVANIFDLLE TNKTALNITN FLVSQTTLEE VFINFAKDQK SYETADTSSQ
GSTISVDSQD DQMES*
mutated AA sequence MASLFHQLQI LVWKNWLGVK RQPLWTLVLI LWPVIIFIIL AITRTKFPPT AKPTCYLAPR
NLPSTGFFPF LQTLLCDTDS KCKDTPYGPQ DLLRRKGIDD ALFKDSEILR KSSNLDKDSS
LSFQSTQVPE RRHASLATVF PSPSSDLEIP GTYTFNGSQV LARILGLEKL LKQNSTSEDI
RRELCDSYSG YIVDDAFSWT FLGRNVFNKF CLSNMTLLES SLQELNKQFS QLSSDPHNQK
IVFQEIVRML SFFSQVQEQK AVWQLLSSFP NVFQNDTSLS NLFDVLRKAN SVLLVVQKVY
PRFATNEGFR TLQKSVKHLL YTLDSPAQGD SDNITHVWNE DDGQTLSPSS LAAQLLILEN
FEDALLNISA NSPYIPYLAC VRNVTDSLAR GSPENLRLLQ STIRFKKSFL RNGSYEDYFP
PVPEVLKSKL SQLRNLTELL CESETFSLIE KSCQLSDMSF GSLCEESEFD LQLLEAAELG
TEIAASLLYH DNVISKKVRD LLTGDPSKIN LNMDQFLEQA LQMNYLENIT QLIPIIEAML
HVNNSADASE KPGQLLEMFK NVEELKEDLR RTTGMSNRTI DKLLAIPIPD NRAEIISQVF
WLHSCDTNIT TPKLEDAMKE FCNLSLSERS RQSYLIGLTL LHYLNIYNFT YKVFFPRKDQ
KPVEKMMELF IRLKEILNQM ASGTHPLLDK MRSLKQMHLP RSVPLTQAMY RSNRMNTPQG
SFSTISQALC SQGITTEYLT AMLPSSQRPK GNHTKDFLTY KLTKEQIASK YGIPINSTPF
CFSLYKDIIN MPAGPVIWAF LKPMLLGRIL YAPYNPVTKA IMEKSNVTLR QLAELREKSQ
EWMDKSPLFM NSFHLLNQAI PMLQNTLRNP FVQVFVKFSV GLDAVELLKQ IDELDILRLK
LENNIDIIDQ LNTLSSLTVN ISSCVLYDRI QAAKTIDEME REAKRLYKSN ELFGSVIFKL
PSNRSWHRGY DSGNVFLPPV IKYTIRMSLK TAQTTRSLRT KIWAPGPHNS PSHNQIYGRA
FIYLQDSIER AIIELQTGRN SQEIAVQVQA IPYPCFMKDN FLTSVSYSLP IVLMVAWVVF
IAAFVKKLVY EKDLRLHEYM KMMGVNSCSH FFAWLIESVG FLLVTIVILI IILKFGNILP
KTNGFILFLY FSDYSFSVIA MSYLISVFFN NTNIAALIGS LIYIIAFFPF IVLVTVENEL
SYVLKVFMSL LSPTAFSYAS QYIARYEEQG IGLQWENMYT SPVQDDTTSF GWLCCLILAD
SFIYFLIAWY VRNVFPGTYG MAAPWYFPIL PSYWKERFGC AEVKPEKSNG LMFTNIMMQN
TNPSASPEYM FSSNIEPEPK DLTVGVALHG VTKIYGSKVA VDNLNLNFYE GHITSLLGPN
GAGKTTTISM LTGLFGASAG TIFVYGKDIK TDLHTVRKNM GVCMQHDVLF SYLTTKEHLL
LYGSIKVPHW TKKQLHEEVK RTLKDTGLYS HRHKRVGTLS GGMKRKLSIS IALIGGSRVV
ILDEPSTGVD PCSRRSIWDV ISKNKTARTI ILSTHHLDEA EVLSDRIAFL EQGGLRCCGS
PFYLKEAFGD GYHLTLTKKK SPNLNANAVC DTMAVTAMIQ SHLPEAYLKE DIGGELVYVL
PPFSTKVSGA YLSLLRALDN GMGDLNIGCY GISDTTVEEV FLNLTKESQK NSAMSLEHLT
QKKIGNSNAN GISTPDDLSV SSSNFTDRDD KILTRGERLD GFGLLLKKIM AILIKRFHHT
RRNWKGLIAQ VILPIVFVTT AMGLGTLRNS SNSYPEIQIS PSLYGTSEQT AFYANYHPST
EALVSAMWDF PGIDNMCLNT SDLQCLNKDS LEKWNTSGEP ITNFGVCSCS ENVQECPKFN
YSPPHRRTYS SQVIYNLTGQ RVENYLISTA NEFVQKRYGG WSFGLPLTKD LRFDITGVPA
NRTLAKVWYD PEGYHSLPAY LNSLNNFLLR VNMSKYDAAR HGIIMYSHPY PGVQDQEQAT
ISSLIDILVA LSILMGYSVT TASFVTYVVR EHQTKAKQLQ HISGIGVTCY WVTNFIYDMV
FYLVPVAFSI GIIAIFKLPA FYSENNLGAV SLLLLLFGYA TFSWMYLLAG LFHETGMAFI
TYVCVNLFFG INSIVSLSVV YFLSKEKPND PTLELISETL KRIFLIFPQF CFGYGLIELS
QQQSVLDFLK AYGVEYPNET FEMNKLGAMF VALVSQGTMF FSLRLLINES LIKKLRLFFR
KFNSSHVRET IDEDEDVRAE RLRVESGAAE FDLVQLYCLT KTYQLIHKKI IAVNNISIGI
PAGECFGLLG VNGAGKTTIF KMLTGDIIPS SGNILIRNKT GSLGHVDSHS SLVGYCPQED
ALDDLVTVEE HLYFYARVHG IPEKDIKETV HKLLRRLHLM PFKDRATSMC SYGTKRKLST
ALALIGKPSI LLLDEPSSGM DPKSKRHLWK IISEEVQNKC SVILTSHSME ECEALCTRLA
IMVNGKFQCI GSLQHIKSRF GRGFTVKVHL KNNKVTMETL TKFMQLHFPK TYLKDQHLSM
LEYHVPVTAG GVANIFDLLE TNKTALNITN FLVSQTTLEE VFINFAKDQK SYETADTSSQ
GSTISVDSQD DQMES*
speed 1.02 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
back to results table

Problems