mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999997600786 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM950111)
known disease mutation at this position (HGMD CM960124)
known disease mutation at this position (HGMD CP995079)
known disease mutation: rs3852 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:52532469C>AN/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

CDS

DNA changes

c.149G>T
cDNA.291G>T
g.53162G>T

AA changes

R50L Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs28942074

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	20	20

known disease mutation: rs3852 (pathogenic for Wilson disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960124)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960124)
known disease mutation at this position, please check HGMD for details (HGMD ID CP995079)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960124)
known disease mutation at this position, please check HGMD for details (HGMD ID CP995079)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960124)
known disease mutation at this position, please check HGMD for details (HGMD ID CP995079)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960124)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960124)
known disease mutation at this position, please check HGMD for details (HGMD ID CP995079)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950111)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960124)
known disease mutation at this position, please check HGMD for details (HGMD ID CP995079)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.499	1
	6.038	1
(flanking)	1.423	0.794

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
Acc marginally increased	53162	wt: 0.7731 / mu: 0.7998 (marginal change - not scored)	wt: TGTGTTCATTGCCCTGGGCCGGTGGCTGGAACACTTGGCAA mu: TGTGTTCATTGCCCTGGGCCTGTGGCTGGAACACTTGGCAA	gccg\|GTGG
Acc marginally increased	53152	wt: 0.9797 / mu: 0.9830 (marginal change - not scored)	wt: CCATGCTCTTTGTGTTCATTGCCCTGGGCCGGTGGCTGGAA mu: CCATGCTCTTTGTGTTCATTGCCCTGGGCCTGTGGCTGGAA	attg\|CCCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005897

726

Mmulatta

all identical

ENSMMUG00000016520

761

Fcatus

all identical

ENSFCAG00000003710

766

Mmusculus

all identical

ENSMUSG00000006567

780

Ggallus

all identical

ENSGALG00000017021

755

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0030343

498

GKT

Celegans

all identical

Y76A2A.2

543

Xtropicalis

all identical

ENSXETG00000020713

733

protein features

start (aa)	end (aa)	feature	details
1	653	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2031 / 2031

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

677 / 677

position of stopcodon in wt / mu cDNA

2173 / 2173

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

149

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

291

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

53162

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

52532469

original gDNA sequence snippet

TGTGTTCATTGCCCTGGGCCGGTGGCTGGAACACTTGGCAA

altered gDNA sequence snippet

TGTGTTCATTGCCCTGGGCCTGTGGCTGGAACACTTGGCAA

original cDNA sequence snippet

TGTGTTCATTGCCCTGGGCCGGTGGCTGGAACACTTGGCAA

altered cDNA sequence snippet

TGTGTTCATTGCCCTGGGCCTGTGGCTGGAACACTTGGCAA

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

MDVLIVLATS IAYVYSLVIL VVAVAEKAER SPVTFFDTPP MLFVFIALGL 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*

speed

1.18 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