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 CM960120)
known disease mutation at this position (HGMD CM960121)
known disease mutation: rs156281 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:52532674C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP7B

Ensembl transcript ID

ENST00000417240

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.86G>A
g.52957G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs137853285
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs156281 (pathogenic for Wilson disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.028	0.993
	6.028	0.999
(flanking)	-0.493	0.82

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	52957	wt: 0.9808 / mu: 0.9847 (marginal change - not scored)	wt: TCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTCTACGTT mu: TCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTCTACGTT	ctcg\|GTGG
Acc marginally increased	52951	wt: 0.4235 / mu: 0.4439 (marginal change - not scored)	wt: TCACTGTCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTC mu: TCACTGTCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTC	cagc\|TCCT
Acc marginally increased	52954	wt: 0.5381 / mu: 0.5590 (marginal change - not scored)	wt: CTGTCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTCTAC mu: CTGTCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTCTAC	ctcc\|TCGG

distance from splice site

Kozak consensus sequence altered?

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

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)

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

52957

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

52532674

original gDNA sequence snippet

TCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTCTACGTT

altered gDNA sequence snippet

TCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTCTACGTT

original cDNA sequence snippet

ATGGAAATAAAGCACTCCTCGGTGGGTGGTACTTCTACGTT

altered cDNA sequence snippet

ATGGAAATAAAGCACTCCTCAGTGGGTGGTACTTCTACGTT

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

0.70 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