mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999645756 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960133)
known disease mutation: rs35725 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:52513227G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP7B

Ensembl transcript ID

ENST00000344297

Genbank transcript ID

NM_001005918

UniProt peptide

P35670

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3038C>T
cDNA.3195C>T
g.72404C>T

AA changes

T1013M Score: 81 explain score(s)

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

1013

frameshift

known variant

Reference ID: rs193922107
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs35725 (pathogenic for Wilson disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960133)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960133)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960133)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.731	0.003
	5.96	1
(flanking)	4.924	1

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	72406	wt: 0.6587 / mu: 0.7368 (marginal change - not scored)	wt: TGGACGTGGTTCTGATCACGGGGGACAACCGGAAGACAGCC mu: TGGACGTGGTTCTGATCATGGGGGACAACCGGAAGACAGCC	acgg\|GGGA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1013

mutated

not conserved

1013

Ptroglodytes

all identical

ENSPTRG00000005897

1168

Mmulatta

all identical

ENSMMUG00000016520

1179

Fcatus

all identical

ENSFCAG00000003710

1208

Mmusculus

all identical

ENSMUSG00000006567

1217

Ggallus

all identical

ENSGALG00000017021

1198

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0030343

990

Celegans

all identical

Y76A2A.2

994

Xtropicalis

all identical

ENSXETG00000020713

1164

protein features

start (aa)	end (aa)	feature	details
995	1322	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3777 / 3777

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

1259 / 1259

position of stopcodon in wt / mu cDNA

3934 / 3934

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

158 / 158

chromosome

strand

-1

last intron/exon boundary

3661

theoretical NMD boundary in CDS

3453

length of CDS

3777

coding sequence (CDS) position

3038

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

3195

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

72404

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

52513227

original gDNA sequence snippet

TGTGGACGTGGTTCTGATCACGGGGGACAACCGGAAGACAG

altered gDNA sequence snippet

TGTGGACGTGGTTCTGATCATGGGGGACAACCGGAAGACAG

original cDNA sequence snippet

TGTGGACGTGGTTCTGATCACGGGGGACAACCGGAAGACAG

altered cDNA sequence snippet

TGTGGACGTGGTTCTGATCATGGGGGACAACCGGAAGACAG

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 IIESKTSEAL AKLMSLQATE ATVVTLGEDN LIIREEQVPM
ELVQRGDIVK VVPGGKFPVD GKVLEGNTMA DESLITGEAM PVTKKPGSTV IAGSINAHGS
VLIKATHVGN DTTLAQIVKL VEEAQMSKNP NKHISQTEVI IRFAFQTSIT VLCIACPCSL
GLATPTAVMV GTGVAAQNGI LIKGGKPLEM AHKIKTVMFD KTGTITHGVP RVMRVLLLGD
VATLPLRKVL AVVGTAEASS EHPLGVAVTK YCKEELGTET LGYCTDFQAV PGCGIGCKVS
NVEGILAHSE RPLSAPASHL NEAGSLPAEK DAVPQTFSVL IGNREWLRRN GLTISSDVSD
AMTDHEMKGQ TAILVAIDGV LCGMIAIADA VKQEAALAVH TLQSMGVDVV LITGDNRKTA
RAIATQVGIN KVFAEVLPSH KVAKVQELQN KGKKVAMVGD GVNDSPALAQ ADMGVAIGTG
TDVAIEAADV VLIRNDLLDV VASIHLSKRT VRRIRINLVL ALIYNLVGIP IAAGVFMPIG
IVLQPWMGSA AMAASSVSVV LSSLQLKCYK KPDLERYEAQ AHGHMKPLTA SQVSVHIGMD
DRWRDSPRAT PWDQVSYVSQ VSLSSLTSDK PSRHSAAADD DGDKWSLLLN GRDEEQYI*

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
GFEASVVSES CSTNPLGNHS AGNSMVQTTD GTPTSVQEVA PHTGRLPANH APDILAKSPQ
STRAVAPQKC FLQIKGMTCA SCVSNIERNL QKEAGVLSVL VALMAGKAEI KYDPEVIQPL
EIAQFIQDLG FEAAVMEDYA GSDGNIELTI TGMTCASCVH NIESKLTRTN GITYASVALA
TSKALVKFDP EIIGPRDIIK IIESKTSEAL AKLMSLQATE ATVVTLGEDN LIIREEQVPM
ELVQRGDIVK VVPGGKFPVD GKVLEGNTMA DESLITGEAM PVTKKPGSTV IAGSINAHGS
VLIKATHVGN DTTLAQIVKL VEEAQMSKNP NKHISQTEVI IRFAFQTSIT VLCIACPCSL
GLATPTAVMV GTGVAAQNGI LIKGGKPLEM AHKIKTVMFD KTGTITHGVP RVMRVLLLGD
VATLPLRKVL AVVGTAEASS EHPLGVAVTK YCKEELGTET LGYCTDFQAV PGCGIGCKVS
NVEGILAHSE RPLSAPASHL NEAGSLPAEK DAVPQTFSVL IGNREWLRRN GLTISSDVSD
AMTDHEMKGQ TAILVAIDGV LCGMIAIADA VKQEAALAVH TLQSMGVDVV LIMGDNRKTA
RAIATQVGIN KVFAEVLPSH KVAKVQELQN KGKKVAMVGD GVNDSPALAQ ADMGVAIGTG
TDVAIEAADV VLIRNDLLDV VASIHLSKRT VRRIRINLVL ALIYNLVGIP IAAGVFMPIG
IVLQPWMGSA AMAASSVSVV LSSLQLKCYK KPDLERYEAQ AHGHMKPLTA SQVSVHIGMD
DRWRDSPRAT PWDQVSYVSQ VSLSSLTSDK PSRHSAAADD DGDKWSLLLN GRDEEQYI*

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