mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999971309494 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM161467)
known disease mutation at this position (HGMD CM930060)
known disease mutation at this position (HGMD CM994116)
known disease mutation: rs3859 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:52511706T>CN/A show variant in all transcripts IGV

HGNC symbol

ATP7B

Ensembl transcript ID

ENST00000400370

Genbank transcript ID

N/A

UniProt peptide

P35670

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2519A>G
cDNA.2593A>G
g.73925A>G

AA changes

N840S Score: 46 explain score(s)

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

840

frameshift

known variant

Reference ID: rs121907990

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	18	18

known disease mutation: rs3859 (pathogenic for Wilson disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.499	0.82
	4.818	0.998
(flanking)	4.818	0.998

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	73924	0.89	mu: GGGTCAGTGACTCCC	GTCA\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

840

mutated

all conserved

840

Ptroglodytes

all identical

ENSPTRG00000005897

1218

Mmulatta

all identical

ENSMMUG00000016520

1229

Fcatus

all identical

ENSFCAG00000003710

1258

Mmusculus

all identical

ENSMUSG00000006567

1267

Ggallus

all identical

ENSGALG00000017021

1248

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0030343

1040

Celegans

all identical

Y76A2A.2

1044

Xtropicalis

all identical

ENSXETG00000020713

1214

protein features

start (aa)	end (aa)	feature	details
786	919	TOPO_DOM	Cytoplasmic (Potential).	lost
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

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3108 / 3108

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

1036 / 1036

position of stopcodon in wt / mu cDNA

3182 / 3182

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

75 / 75

chromosome

strand

-1

last intron/exon boundary

2909

theoretical NMD boundary in CDS

2784

length of CDS

3108

coding sequence (CDS) position

2519

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

2593

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

73925

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

52511706

original gDNA sequence snippet

CATGGTGGGGGATGGGGTCAATGACTCCCCGGCCTTGGCCC

altered gDNA sequence snippet

CATGGTGGGGGATGGGGTCAGTGACTCCCCGGCCTTGGCCC

original cDNA sequence snippet

CATGGTGGGGGATGGGGTCAATGACTCCCCGGCCTTGGCCC

altered cDNA sequence snippet

CATGGTGGGGGATGGGGTCAGTGACTCCCCGGCCTTGGCCC

wildtype AA sequence

MPEQERQITA REGASRKILS KLSLPTRAWE PAMKKSFAFD NVGYEGGLDG LGPSSQVATS
TVRILGMTCQ SCVKSIEDRI SNLKGIISMK VSLEQGSATV KYVPSVVCLQ QVCHQIGDMG
FEASIAEGKA ASWPSRSLPA QEAVVKLRVE GMTCQSCVSS IEGKVRKLQG VVRVKVSLSN
QEAVITYQPY LIQPEDLRDH VNDMGFEAAI KSKVAPLSLG PIDIERLQST NPKRPLSSAN
QNFNNSETLG HQGSHVVTLQ LRIDGMHCKS CVLNIEENIG QLLGVQSIQV SLENKTAQVK
YDPSCTSPVA LQRAIEALPP GNFKVSLPDG AEGSGTDHRS SSSHSPGSPP RNQVQGTCST
TLIAIAGMTC ASCVHSIEGM ISQLEGVQQI SVSLAEGTAT VLYNPSVISP EELRAAIEDM
GFEASVVSGE AMPVTKKPGS TVIAGSINAH GSVLIKATHV GNDTTLAQIV KLVEEAQMSK
APIQQLADRF SGYFVPFIII MSTLTLVVWI VIGFIDFGVV QRYFPNPNKH ISQTEVIIRF
AFQTSITVLC IACPCSLGLA TPTAVMVGTG VAAQNGILIK GGKPLEMAHK IKTVMFDKTG
TITHGVPRVM RVLLLGDVAT LPLRKVLAVV GTAEASSEHP LGVAVTKYCK EELGTETLGY
CTDFQAVPGC GIGCKVSNVE GILAHSERPL SAPASHLNEA GSLPAEKDAV PQTFSVLIGN
REWLRRNGLT ISSDVSDAMT DHEMKGQTAI LVAIDGVLCG MIAIADAVKQ EAALAVHTLQ
SMGVDVVLIT GDNRKTARAI ATQVGINKVF AEVLPSHKVA KVQELQNKGK KVAMVGDGVN
DSPALAQADM GVAIGTGTDV AIEAADVVLI RNDLLDVVAS IHLSKRTVRR IRINLVLALI
YNLVGIPIAA GVFMPIGIVL QPWMGSAAMA ASSVSVVLSS LQLKCYKKPD LERYEAQAHG
HMKPLTASQV SVHIGMDDRW RDSPRATPWD QVSYVSQVSL SSLTSDKPSR HSAAADDDGD
KWSLLLNGRD EEQYI*

mutated AA sequence

MPEQERQITA REGASRKILS KLSLPTRAWE PAMKKSFAFD NVGYEGGLDG LGPSSQVATS
TVRILGMTCQ SCVKSIEDRI SNLKGIISMK VSLEQGSATV KYVPSVVCLQ QVCHQIGDMG
FEASIAEGKA ASWPSRSLPA QEAVVKLRVE GMTCQSCVSS IEGKVRKLQG VVRVKVSLSN
QEAVITYQPY LIQPEDLRDH VNDMGFEAAI KSKVAPLSLG PIDIERLQST NPKRPLSSAN
QNFNNSETLG HQGSHVVTLQ LRIDGMHCKS CVLNIEENIG QLLGVQSIQV SLENKTAQVK
YDPSCTSPVA LQRAIEALPP GNFKVSLPDG AEGSGTDHRS SSSHSPGSPP RNQVQGTCST
TLIAIAGMTC ASCVHSIEGM ISQLEGVQQI SVSLAEGTAT VLYNPSVISP EELRAAIEDM
GFEASVVSGE AMPVTKKPGS TVIAGSINAH GSVLIKATHV GNDTTLAQIV KLVEEAQMSK
APIQQLADRF SGYFVPFIII MSTLTLVVWI VIGFIDFGVV QRYFPNPNKH ISQTEVIIRF
AFQTSITVLC IACPCSLGLA TPTAVMVGTG VAAQNGILIK GGKPLEMAHK IKTVMFDKTG
TITHGVPRVM RVLLLGDVAT LPLRKVLAVV GTAEASSEHP LGVAVTKYCK EELGTETLGY
CTDFQAVPGC GIGCKVSNVE GILAHSERPL SAPASHLNEA GSLPAEKDAV PQTFSVLIGN
REWLRRNGLT ISSDVSDAMT DHEMKGQTAI LVAIDGVLCG MIAIADAVKQ EAALAVHTLQ
SMGVDVVLIT GDNRKTARAI ATQVGINKVF AEVLPSHKVA KVQELQNKGK KVAMVGDGVS
DSPALAQADM GVAIGTGTDV AIEAADVVLI RNDLLDVVAS IHLSKRTVRR IRINLVLALI
YNLVGIPIAA GVFMPIGIVL QPWMGSAAMA ASSVSVVLSS LQLKCYKKPD LERYEAQAHG
HMKPLTASQV SVHIGMDDRW RDSPRATPWD QVSYVSQVSL SSLTSDKPSR HSAAADDDGD
KWSLLLNGRD EEQYI*

speed

1.04 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