mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999996227 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001039)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:87069077G>TN/A show variant in all transcripts IGV

HGNC symbol

ABCB4

Ensembl transcript ID

ENST00000358400

Genbank transcript ID

NM_018850

UniProt peptide

P21439

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1637C>A
cDNA.1713C>A
g.40675C>A

AA changes

A546D Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

546

frameshift

known variant

Reference ID: rs121918441
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM001039)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001039)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001039)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.826	1
	6.147	1
(flanking)	4.476	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor gained	40671	0.51	mu: TTGCACGTGACCTGG	GCAC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

546

mutated

not conserved

546

Ptroglodytes

all identical

ENSPTRG00000024082

546

Mmulatta

all identical

ENSMMUG00000010788

528

Fcatus

all identical

ENSFCAG00000003276

501

Mmusculus

all identical

ENSMUSG00000042476

543

Ggallus

all identical

ENSGALG00000023271

521

Trubripes

all identical

ENSTRUG00000005770

578

Drerio

all identical

ENSDARG00000010936

549

Dmelanogaster

all identical

FBgn0010241

583

Celegans

all identical

C34G6.4

551

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
355	711	TOPO_DOM	Cytoplasmic (By similarity).	lost
394	630	DOMAIN	ABC transporter 1.	lost
625	647	REGION	Interaction with HAX1 (By similarity).	might get lost (downstream of altered splice site)
711	999	DOMAIN	ABC transmembrane type-1 2.	might get lost (downstream of altered splice site)
712	732	TRANSMEM	Helical; (By similarity).	might get lost (downstream of altered splice site)
733	755	TOPO_DOM	Extracellular (By similarity).	might get lost (downstream of altered splice site)
756	776	TRANSMEM	Helical; (By similarity).	might get lost (downstream of altered splice site)
777	831	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
832	852	TRANSMEM	Helical; (By similarity).	might get lost (downstream of altered splice site)
853	853	TOPO_DOM	Extracellular (By similarity).	might get lost (downstream of altered splice site)
854	873	TRANSMEM	Helical; (By similarity).	might get lost (downstream of altered splice site)
874	933	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
934	956	TRANSMEM	Helical; (By similarity).	might get lost (downstream of altered splice site)
957	972	TOPO_DOM	Extracellular (By similarity).	might get lost (downstream of altered splice site)
973	994	TRANSMEM	Helical; (By similarity).	might get lost (downstream of altered splice site)
995	1286	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
1034	1279	DOMAIN	ABC transporter 2.	might get lost (downstream of altered splice site)
1069	1076	NP_BIND	ATP 2 (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3699 / 3699

position (AA) of stopcodon in wt / mu AA sequence

1233 / 1233

position of stopcodon in wt / mu cDNA

3775 / 3775

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

77 / 77

chromosome

strand

-1

last intron/exon boundary

3569

theoretical NMD boundary in CDS

3442

length of CDS

3699

coding sequence (CDS) position

1637

cDNA position
(for ins/del: last normal base / first normal base)

1713

gDNA position
(for ins/del: last normal base / first normal base)

40675

chromosomal position
(for ins/del: last normal base / first normal base)

87069077

original gDNA sequence snippet

GAGGATCGCCATTGCACGTGCCCTGGTTCGCAACCCCAAGA

altered gDNA sequence snippet

GAGGATCGCCATTGCACGTGACCTGGTTCGCAACCCCAAGA

original cDNA sequence snippet

GAGGATCGCCATTGCACGTGCCCTGGTTCGCAACCCCAAGA

altered cDNA sequence snippet

GAGGATCGCCATTGCACGTGACCTGGTTCGCAACCCCAAGA

wildtype AA sequence

MDLEAAKNGT AWRPTSAEGD FELGISSKQK RKKTKTVKMI GVLTLFRYSD WQDKLFMSLG
TIMAIAHGSG LPLMMIVFGE MTDKFVDTAG NFSFPVNFSL SLLNPGKILE EEMTRYAYYY
SGLGAGVLVA AYIQVSFWTL AAGRQIRKIR QKFFHAILRQ EIGWFDINDT TELNTRLTDD
ISKISEGIGD KVGMFFQAVA TFFAGFIVGF IRGWKLTLVI MAISPILGLS AAVWAKILSA
FSDKELAAYA KAGAVAEEAL GAIRTVIAFG GQNKELERYQ KHLENAKEIG IKKAISANIS
MGIAFLLIYA SYALAFWYGS TLVISKEYTI GNAMTVFFSI LIGAFSVGQA APCIDAFANA
RGAAYVIFDI IDNNPKIDSF SERGHKPDSI KGNLEFNDVH FSYPSRANVK ILKGLNLKVQ
SGQTVALVGS SGCGKSTTVQ LIQRLYDPDE GTINIDGQDI RNFNVNYLRE IIGVVSQEPV
LFSTTIAENI CYGRGNVTMD EIKKAVKEAN AYEFIMKLPQ KFDTLVGERG AQLSGGQKQR
IAIARALVRN PKILLLDEAT SALDTESEAE VQAALDKARE GRTTIVIAHR LSTVRNADVI
AGFEDGVIVE QGSHSELMKK EGVYFKLVNM QTSGSQIQSE EFELNDEKAA TRMAPNGWKS
RLFRHSTQKN LKNSQMCQKS LDVETDGLEA NVPPVSFLKV LKLNKTEWPY FVVGTVCAIA
NGGLQPAFSV IFSEIIAIFG PGDDAVKQQK CNIFSLIFLF LGIISFFTFF LQGFTFGKAG
EILTRRLRSM AFKAMLRQDM SWFDDHKNST GALSTRLATD AAQVQGATGT RLALIAQNIA
NLGTGIIISF IYGWQLTLLL LAVVPIIAVS GIVEMKLLAG NAKRDKKELE AAGKIATEAI
ENIRTVVSLT QERKFESMYV EKLYGPYRVF SAIVFGAVAL GHASSFAPDY AKAKLSAAHL
FMLFERQPLI DSYSEEGLKP DKFEGNITFN EVVFNYPTRA NVPVLQGLSL EVKKGQTLAL
VGSSGCGKST VVQLLERFYD PLAGTVLLDG QEAKKLNVQW LRAQLGIVSQ EPILFDCSIA
ENIAYGDNSR VVSQDEIVSA AKAANIHPFI ETLPHKYETR VGDKGTQLSG GQKQRIAIAR
ALIRQPQILL LDEATSALDT ESEKVVQEAL DKAREGRTCI VIAHRLSTIQ NADLIVVFQN
GRVKEHGTHQ QLLAQKGIYF SMVSVQAGTQ NL*

mutated AA sequence

MDLEAAKNGT AWRPTSAEGD FELGISSKQK RKKTKTVKMI GVLTLFRYSD WQDKLFMSLG
TIMAIAHGSG LPLMMIVFGE MTDKFVDTAG NFSFPVNFSL SLLNPGKILE EEMTRYAYYY
SGLGAGVLVA AYIQVSFWTL AAGRQIRKIR QKFFHAILRQ EIGWFDINDT TELNTRLTDD
ISKISEGIGD KVGMFFQAVA TFFAGFIVGF IRGWKLTLVI MAISPILGLS AAVWAKILSA
FSDKELAAYA KAGAVAEEAL GAIRTVIAFG GQNKELERYQ KHLENAKEIG IKKAISANIS
MGIAFLLIYA SYALAFWYGS TLVISKEYTI GNAMTVFFSI LIGAFSVGQA APCIDAFANA
RGAAYVIFDI IDNNPKIDSF SERGHKPDSI KGNLEFNDVH FSYPSRANVK ILKGLNLKVQ
SGQTVALVGS SGCGKSTTVQ LIQRLYDPDE GTINIDGQDI RNFNVNYLRE IIGVVSQEPV
LFSTTIAENI CYGRGNVTMD EIKKAVKEAN AYEFIMKLPQ KFDTLVGERG AQLSGGQKQR
IAIARDLVRN PKILLLDEAT SALDTESEAE VQAALDKARE GRTTIVIAHR LSTVRNADVI
AGFEDGVIVE QGSHSELMKK EGVYFKLVNM QTSGSQIQSE EFELNDEKAA TRMAPNGWKS
RLFRHSTQKN LKNSQMCQKS LDVETDGLEA NVPPVSFLKV LKLNKTEWPY FVVGTVCAIA
NGGLQPAFSV IFSEIIAIFG PGDDAVKQQK CNIFSLIFLF LGIISFFTFF LQGFTFGKAG
EILTRRLRSM AFKAMLRQDM SWFDDHKNST GALSTRLATD AAQVQGATGT RLALIAQNIA
NLGTGIIISF IYGWQLTLLL LAVVPIIAVS GIVEMKLLAG NAKRDKKELE AAGKIATEAI
ENIRTVVSLT QERKFESMYV EKLYGPYRVF SAIVFGAVAL GHASSFAPDY AKAKLSAAHL
FMLFERQPLI DSYSEEGLKP DKFEGNITFN EVVFNYPTRA NVPVLQGLSL EVKKGQTLAL
VGSSGCGKST VVQLLERFYD PLAGTVLLDG QEAKKLNVQW LRAQLGIVSQ EPILFDCSIA
ENIAYGDNSR VVSQDEIVSA AKAANIHPFI ETLPHKYETR VGDKGTQLSG GQKQRIAIAR
ALIRQPQILL LDEATSALDT ESEKVVQEAL DKAREGRTCI VIAHRLSTIQ NADLIVVFQN
GRVKEHGTHQ QLLAQKGIYF SMVSVQAGTQ NL*

speed

0.96 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