mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999979897147 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM950116)
known disease mutation: rs3860 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:52520574C>TN/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.1616G>A
cDNA.1690G>A
g.65057G>A

AA changes

R539Q Score: 43 explain score(s)

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

539

frameshift

known variant

Reference ID: rs121907996

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	4	4

known disease mutation: rs3860 (pathogenic for Wilson disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950116)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.173	0.961
	5.96	1
(flanking)	3.205	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

539

mutated

all conserved

539

Ptroglodytes

all identical

ENSPTRG00000005897

917

Mmulatta

all identical

ENSMMUG00000016520

928

Fcatus

all identical

ENSFCAG00000003710

957

Mmusculus

all identical

ENSMUSG00000006567

971

Ggallus

all identical

ENSGALG00000017021

946

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0030343

689

Celegans

all conserved

Y76A2A.2

734

Xtropicalis

all identical

ENSXETG00000020713

924

protein features

start (aa)	end (aa)	feature	details
1	653	TOPO_DOM	Cytoplasmic (Potential).	lost
489	555	DOMAIN	HMA 5.	lost
539	549	HELIX		lost

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

1616

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

1690

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

65057

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

52520574

original gDNA sequence snippet

CCAGACAGAGGTGATCATCCGGTTTGCTTTCCAGACGTCCA

altered gDNA sequence snippet

CCAGACAGAGGTGATCATCCAGTTTGCTTTCCAGACGTCCA

original cDNA sequence snippet

CCAGACAGAGGTGATCATCCGGTTTGCTTTCCAGACGTCCA

altered cDNA sequence snippet

CCAGACAGAGGTGATCATCCAGTTTGCTTTCCAGACGTCCA

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 ISQTEVIIQF
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*

speed

0.96 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