mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM980170)
known disease mutation: rs3866 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:52534334C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP7B

Ensembl transcript ID

ENST00000417240

Genbank transcript ID

N/A

UniProt peptide

P35670

alteration type

single base exchange

alteration region

intron

DNA changes

g.51297G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121908001
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs3866 (pathogenic for Wilson disease) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980170)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980170)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980170)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.032	1
	6.032	1
(flanking)	0.006	0.995

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

splice sites

splice site change before start ATG (at aa -20) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	51292	0.96	mu: CATCATTCCAAGACT	TCAT\|tcca

distance from splice site

1639

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	653	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
59	125	DOMAIN	HMA 1.	might get lost (downstream of altered splice site)
144	210	DOMAIN	HMA 2.	might get lost (downstream of altered splice site)
258	265	STRAND		might get lost (downstream of altered splice site)
258	327	DOMAIN	HMA 3.	might get lost (downstream of altered splice site)
266	268	HELIX		might get lost (downstream of altered splice site)
271	278	HELIX		might get lost (downstream of altered splice site)
285	291	STRAND		might get lost (downstream of altered splice site)
292	295	TURN		might get lost (downstream of altered splice site)
296	301	STRAND		might get lost (downstream of altered splice site)
303	305	TURN		might get lost (downstream of altered splice site)
308	315	HELIX		might get lost (downstream of altered splice site)
318	321	STRAND		might get lost (downstream of altered splice site)
323	326	STRAND		might get lost (downstream of altered splice site)
340	345	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)
359	366	STRAND		might get lost (downstream of altered splice site)
360	426	DOMAIN	HMA 4.	might get lost (downstream of altered splice site)
372	380	HELIX		might get lost (downstream of altered splice site)
381	383	HELIX		might get lost (downstream of altered splice site)
384	393	STRAND		might get lost (downstream of altered splice site)
394	397	TURN		might get lost (downstream of altered splice site)
398	403	STRAND		might get lost (downstream of altered splice site)
405	407	TURN		might get lost (downstream of altered splice site)
410	420	HELIX		might get lost (downstream of altered splice site)
424	426	STRAND		might get lost (downstream of altered splice site)
488	488	CONFLICT	Q -> G (in Ref. 8; AAA16173).	might get lost (downstream of altered splice site)
488	495	STRAND		might get lost (downstream of altered splice site)
489	555	DOMAIN	HMA 5.	might get lost (downstream of altered splice site)
499	501	STRAND		might get lost (downstream of altered splice site)
502	511	HELIX		might get lost (downstream of altered splice site)
519	522	STRAND		might get lost (downstream of altered splice site)
523	526	TURN		might get lost (downstream of altered splice site)
527	532	STRAND		might get lost (downstream of altered splice site)
534	536	TURN		might get lost (downstream of altered splice site)
539	549	HELIX		might get lost (downstream of altered splice site)
552	555	STRAND		might get lost (downstream of altered splice site)
562	572	STRAND		might get lost (downstream of altered splice site)
565	631	DOMAIN	HMA 6.	might get lost (downstream of altered splice site)
576	588	HELIX		might get lost (downstream of altered splice site)
589	591	STRAND		might get lost (downstream of altered splice site)
594	598	STRAND		might get lost (downstream of altered splice site)
599	602	TURN		might get lost (downstream of altered splice site)
603	607	STRAND		might get lost (downstream of altered splice site)
610	612	TURN		might get lost (downstream of altered splice site)
615	625	HELIX		might get lost (downstream of altered splice site)
628	630	STRAND		might get lost (downstream of altered splice site)
635	635	CONFLICT	N -> T (in Ref. 8; AAA16173).	might get lost (downstream of altered splice site)
654	675	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
676	697	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
698	717	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
718	724	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
725	745	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
746	764	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
765	785	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
767	767	CONFLICT	P -> L (in Ref. 8; AAA16173).	might get lost (downstream of altered splice site)
786	919	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
837	837	CONFLICT	G -> A (in Ref. 8; AAA16173).	might get lost (downstream of altered splice site)
920	942	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
943	972	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
973	994	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
995	1322	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1027	1027	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
1039	1044	STRAND		might get lost (downstream of altered splice site)
1048	1050	TURN		might get lost (downstream of altered splice site)
1053	1064	HELIX		might get lost (downstream of altered splice site)
1072	1083	HELIX		might get lost (downstream of altered splice site)
1091	1097	STRAND		might get lost (downstream of altered splice site)
1098	1100	TURN		might get lost (downstream of altered splice site)
1101	1107	STRAND		might get lost (downstream of altered splice site)
1109	1113	HELIX		might get lost (downstream of altered splice site)
1127	1130	STRAND		might get lost (downstream of altered splice site)
1143	1149	STRAND		might get lost (downstream of altered splice site)
1151	1158	HELIX		might get lost (downstream of altered splice site)
1163	1173	HELIX		might get lost (downstream of altered splice site)
1174	1176	TURN		might get lost (downstream of altered splice site)
1177	1184	STRAND		might get lost (downstream of altered splice site)
1187	1194	STRAND		might get lost (downstream of altered splice site)
1267	1267	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
1271	1271	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
1323	1340	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1341	1351	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1352	1371	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1372	1465	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

143 / 143

chromosome

strand

-1

last intron/exon boundary

1900

theoretical NMD boundary in CDS

1707

length of CDS

2031

coding sequence (CDS) position

N/A

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

N/A

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

51297

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

52534334

original gDNA sequence snippet

TGGACCACAACATCATTCCAGGACTGTCCATTCTAAATCTC

altered gDNA sequence snippet

TGGACCACAACATCATTCCAAGACTGTCCATTCTAAATCTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MDVLIVLATS IAYVYSLVIL VVAVAEKAER SPVTFFDTPP MLFVFIALGR WLEHLAKSKT
SEALAKLMSL QATEATVVTL GEDNLIIREE QVPMELVQRG DIVKVVPGGK FPVDGKVLEG
NTMADESLIT GEAMPVTKKP GSTVIAGSIN AHGSVLIKAT HVGNDTTLAQ IVKLVEEAQM
SKAPIQQLAD RFSGYFVPFI IIMSTLTLVV WIVIGFIDFG VVQRYFPNPN KHISQTEVII
RFAFQTSITV LCIACPCSLG LATPTAVMVG TGVAAQNGIL IKGGKPLEMA HKELGTETLG
YCTDFQAVPG CGIGCKVSNV EGILAHSERP LSAPASHLNE AGSLPAEKDA VPQTFSVLIG
NREWLRRNGL TISSDVSDAM TDHEMKGQTA ILVAIDGVLC GMIAIADAVK QEAALAVHTL
QSMGVDVVLI TGDNRKTARA IATQVGINKV FAEVLPSHKV AKVQELQNKG KKVAMVGDGV
NDSPALAQAD MGVAIGTGTD VAIEAADVVL IRNDLLDVVA SIHLSKRTVR RIRINLVLAL
IYNLVGIPIA AGVFMPIGIV LQPWMGSAAM AASSVSVVLS SLQLKCYKKP DLERYEAQAH
GHMKPLTASQ VSVHIGMDDR WRDSPRATPW DQVSYVSQVS LSSLTSDKPS RHSAAADDDG
DKWSLLLNGR DEEQYI*

mutated AA sequence

N/A

speed

0.75 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