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 CM950111)
known disease mutation at this position (HGMD CM960124)
known disease mutation at this position (HGMD CP995079)
known disease mutation: rs3852 (pathogenic)

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

ENST00000448424

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.53162G>T

AA changes

N/A

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

N/A

frameshift

N/A

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

726

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

75 / 75

chromosome

strand

-1

last intron/exon boundary

3965

theoretical NMD boundary in CDS

3840

length of CDS

4164

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)

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

N/A

altered cDNA sequence snippet

N/A

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
GFEASVVSES CSTNPLGNHS AGNSMVQTTD GTPTSVQEVA PHTGRLPANH APDILAKSPQ
STRAVAPQKC FLQIKGMTCA SCVSNIERNL QKEAGVLSVL VALMAGKAEI KYDPEVIQPL
EIAQFIQDLG FEAAVMEDYA GSDGNIELTI TGMTCASCVH NIESKLTRTN GITYASVALA
TSKALVKFDP EIIGPRDIIK IIEEIGFHAS LAQRNPNAHH LDHKMEIKQW KKSFLCSLVF
GIPVMALMIY MLIPSNEPHQ SMVLDHNIIP GLSILNLIFF ILCTFVQSKT SEALAKLMSL
QATEATVVTL GEDNLIIREE QVPMELVQRG DIVKVVPGGK FPVDGKVLEG NTMADESLIT
GEAMPVTKKP GSTVIAGSIN AHGSVLIKAT HVGNDTTLAQ IVKLVEEAQM SKAPIQQLAD
RFSGYFVPFI IIMSTLTLVV WIVIGFIDFG VVQRYFPNPN KHISQTEVII RFAFQTSITV
LCIACPCSLG LATPTAVMVG TGVAAQNGIL IKGGKPLEMA HKIKTVMFDK TGTITHGVPR
VMRVLLLGDV ATLPLRKVLA VVGTAEASSE HPLGVAVTKY CKEELGTETL GYCTDFQAVP
GCGIGCKVSN VEGILAHSER PLSAPASHLN EAGSLPAEKD AVPQTFSVLI GNREWLRRNG
LTISSDVSDA MTDHEMKGQT AILVAIDGVL CGMIAIADAV KQEAALAVHT LQSMGVDVVL
ITGDNRKTAR AIATQVGINK VFAEVLPSHK VAKVQELQNK GKKVAMVGDG VNDSPALAQA
DMGVAIGTGT DVAIEAADVV LIRNDLLDVV ASIHLSKRTV RRIRINLVLA LIYNLVGIPI
AAGVFMPIGI VLQPWMGSAA MAASSVSVVL SSLQLKCYKK PDLERYEAQA HGHMKPLTAS
QVSVHIGMDD RWRDSPRATP WDQVSYVSQV SLSSLTSDKP SRHSAAADDD GDKWSLLLNG
RDEEQYI*

mutated AA sequence

N/A

speed

0.99 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