mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM012890)
known disease mutation: rs5804 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:136303015A>GN/A show variant in all transcripts IGV

HGNC symbol

ADAMTS13

Ensembl transcript ID

ENST00000536611

Genbank transcript ID

N/A

UniProt peptide

Q76LX8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.598A>G
cDNA.1218A>G
g.23538A>G

AA changes

R200G Score: 125 explain score(s)

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

200

frameshift

known variant

Reference ID: rs121908473

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs5804 (pathogenic for Upshaw-Schulman syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012890)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012890)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012890)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.195	1
	0.428	1
(flanking)	0.626	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	23539	sequence motif lost	-	wt: CAGG\|gtag mu: CGGG.gtag
Acc marginally increased	23528	wt: 0.3771 / mu: 0.4347 (marginal change - not scored)	wt: ACCCTGAGCCTGTGTGTGTCGGGCAGCTGCAGGGTAGGCGT mu: ACCCTGAGCCTGTGTGTGTCGGGCAGCTGCGGGGTAGGCGT	gtcg\|GGCA
Donor decreased	23539	wt: 0.69 / mu: 0.28	wt: CTGCAGGGTAGGCGT mu: CTGCGGGGTAGGCGT	GCAG\|ggta
Donor increased	23532	wt: 0.25 / mu: 0.72	wt: CGGGCAGCTGCAGGG mu: CGGGCAGCTGCGGGG	GGCA\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

200

mutated

not conserved

200

Ptroglodytes

all identical

ENSPTRG00000022942

486

Mmulatta

all identical

ENSMMUG00000000937

524

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000014852

533

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000076270

527

Dmelanogaster

not conserved

FBgn0086408

825

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
80	286	DOMAIN	Peptidase M12B.	lost
202	202	DISULFID	By similarity.	might get lost (downstream of altered splice site)
224	224	METAL	Zinc; catalytic (By similarity).	might get lost (downstream of altered splice site)
225	225	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
228	228	METAL	Zinc; catalytic (By similarity).	might get lost (downstream of altered splice site)
234	234	METAL	Zinc; catalytic (By similarity).	might get lost (downstream of altered splice site)
242	242	DISULFID	By similarity.	might get lost (downstream of altered splice site)
265	265	DISULFID	By similarity.	might get lost (downstream of altered splice site)
281	281	DISULFID	By similarity.	might get lost (downstream of altered splice site)
281	281	METAL	Calcium (Potential).	might get lost (downstream of altered splice site)
284	284	METAL	Calcium (Potential).	might get lost (downstream of altered splice site)
287	383	DOMAIN	Disintegrin.	might get lost (downstream of altered splice site)
300	374	REGION	Cysteine-rich.	might get lost (downstream of altered splice site)
301	303	HELIX		might get lost (downstream of altered splice site)
307	314	HELIX		might get lost (downstream of altered splice site)
331	334	HELIX		might get lost (downstream of altered splice site)
337	340	STRAND		might get lost (downstream of altered splice site)
359	361	STRAND		might get lost (downstream of altered splice site)
364	367	STRAND		might get lost (downstream of altered splice site)
370	373	STRAND		might get lost (downstream of altered splice site)
374	377	HELIX		might get lost (downstream of altered splice site)
384	439	DOMAIN	TSP type-1 1.	might get lost (downstream of altered splice site)
396	396	DISULFID	By similarity.	might get lost (downstream of altered splice site)
399	401	STRAND		might get lost (downstream of altered splice site)
400	400	DISULFID	By similarity.	might get lost (downstream of altered splice site)
403	406	STRAND		might get lost (downstream of altered splice site)
411	411	DISULFID	By similarity.	might get lost (downstream of altered splice site)
417	419	STRAND		might get lost (downstream of altered splice site)
423	423	DISULFID	By similarity.	might get lost (downstream of altered splice site)
430	433	STRAND		might get lost (downstream of altered splice site)
433	433	DISULFID	By similarity.	might get lost (downstream of altered splice site)
438	438	DISULFID	By similarity.	might get lost (downstream of altered splice site)
442	451	HELIX		might get lost (downstream of altered splice site)
452	455	TURN		might get lost (downstream of altered splice site)
470	472	STRAND		might get lost (downstream of altered splice site)
474	476	TURN		might get lost (downstream of altered splice site)
479	483	HELIX		might get lost (downstream of altered splice site)
486	489	STRAND		might get lost (downstream of altered splice site)
495	497	STRAND		might get lost (downstream of altered splice site)
498	500	MOTIF	Cell attachment site (Potential).	might get lost (downstream of altered splice site)
519	523	STRAND		might get lost (downstream of altered splice site)
526	530	STRAND		might get lost (downstream of altered splice site)
534	536	STRAND		might get lost (downstream of altered splice site)
552	552	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
554	562	STRAND		might get lost (downstream of altered splice site)
556	685	REGION	Spacer.	might get lost (downstream of altered splice site)
569	576	STRAND		might get lost (downstream of altered splice site)
579	579	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
581	588	STRAND		might get lost (downstream of altered splice site)
592	599	STRAND		might get lost (downstream of altered splice site)
602	605	STRAND		might get lost (downstream of altered splice site)
608	610	STRAND		might get lost (downstream of altered splice site)
614	614	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
614	618	STRAND		might get lost (downstream of altered splice site)
623	632	STRAND		might get lost (downstream of altered splice site)
634	636	STRAND		might get lost (downstream of altered splice site)
638	647	STRAND		might get lost (downstream of altered splice site)
653	661	STRAND		might get lost (downstream of altered splice site)
663	665	HELIX		might get lost (downstream of altered splice site)
667	667	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
667	669	HELIX		might get lost (downstream of altered splice site)
673	680	STRAND		might get lost (downstream of altered splice site)
682	730	DOMAIN	TSP type-1 2.	might get lost (downstream of altered splice site)
707	707	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
742	805	DOMAIN	TSP type-1 3.	might get lost (downstream of altered splice site)
808	859	DOMAIN	TSP type-1 4.	might get lost (downstream of altered splice site)
828	828	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
896	950	DOMAIN	TSP type-1 5.	might get lost (downstream of altered splice site)
951	1011	DOMAIN	TSP type-1 6.	might get lost (downstream of altered splice site)
1012	1068	DOMAIN	TSP type-1 7.	might get lost (downstream of altered splice site)
1072	1131	DOMAIN	TSP type-1 8.	might get lost (downstream of altered splice site)
1192	1298	DOMAIN	CUB 1.	might get lost (downstream of altered splice site)
1235	1235	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1299	1427	DOMAIN	CUB 2.	might get lost (downstream of altered splice site)
1354	1354	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1095 / 1095

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

365 / 365

position of stopcodon in wt / mu cDNA

1715 / 1715

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

621 / 621

chromosome

strand

last intron/exon boundary

2046

theoretical NMD boundary in CDS

1375

length of CDS

1095

coding sequence (CDS) position

598

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

1218

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

23538

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

136303015

original gDNA sequence snippet

TGTGTGTGTCGGGCAGCTGCAGGGTAGGCGTGTGTGGACAT

altered gDNA sequence snippet

TGTGTGTGTCGGGCAGCTGCGGGGTAGGCGTGTGTGGACAT

original cDNA sequence snippet

TGTGTGTGTCGGGCAGCTGCAGGACATTTGGCTGTGATGGT

altered cDNA sequence snippet

TGTGTGTGTCGGGCAGCTGCGGGACATTTGGCTGTGATGGT

wildtype AA sequence

MDMCQALSCH TDPLDQSSCS RLLVPLLDGT ECGVEKWCSK GRCRSLVELT PIAAVHGRWS
SWGPRSPCSR SCGGGVVTRR RQCNNPRPAF GGRACVGADL QAEMCNTQAC EKTQLEFMSQ
QCARTDGQPL RSSPGGASFY HWGAAVPHSQ GDALCRHMCR AIGESFIMKR GDSFLDGTRC
MPSGPREDGT LSLCVSGSCR TFGCDGRMDS QQVWDRCQVC GGDNSTCSPR KGSFTAGRAR
EYVTFLTVTP NLTSVYIANH RPLFTHLAVR IGGRYVVAGK MSISPNTTYP SLLEDGRVEY
RVALTEDRLP RLEEIRIWGP LQEDADIQVG GVRAQLMHIS WWSRPGLGER DLCARGRWPG
GSSD*

mutated AA sequence

MDMCQALSCH TDPLDQSSCS RLLVPLLDGT ECGVEKWCSK GRCRSLVELT PIAAVHGRWS
SWGPRSPCSR SCGGGVVTRR RQCNNPRPAF GGRACVGADL QAEMCNTQAC EKTQLEFMSQ
QCARTDGQPL RSSPGGASFY HWGAAVPHSQ GDALCRHMCR AIGESFIMKR GDSFLDGTRC
MPSGPREDGT LSLCVSGSCG TFGCDGRMDS QQVWDRCQVC GGDNSTCSPR KGSFTAGRAR
EYVTFLTVTP NLTSVYIANH RPLFTHLAVR IGGRYVVAGK MSISPNTTYP SLLEDGRVEY
RVALTEDRLP RLEEIRIWGP LQEDADIQVG GVRAQLMHIS WWSRPGLGER DLCARGRWPG
GSSD*

speed

0.33 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