mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.958432691332149 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM012894)
known disease mutation: rs5808 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:136321260G>AN/A show variant in all transcripts IGV

HGNC symbol

ADAMTS13

Ensembl transcript ID

ENST00000371910

Genbank transcript ID

N/A

UniProt peptide

Q76LX8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.26G>A
cDNA.222G>A
g.41783G>A

AA changes

C9Y Score: 194 explain score(s)

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

frameshift

known variant

Reference ID: rs121908474
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5808 (pathogenic for Upshaw-Schulman syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012894)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012894)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012894)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.462	0.948
	3.31	0.936
(flanking)	-0.058	0.098

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
Donor increased	41787	wt: 0.24 / mu: 0.35	wt: TGTGCAGTGGCCATT mu: TATGCAGTGGCCATT	TGCA\|gtgg
Donor increased	41784	wt: 0.34 / mu: 0.68	wt: GACTGTGCAGTGGCC mu: GACTATGCAGTGGCC	CTGT\|gcag
Donor increased	41775	wt: 0.54 / mu: 0.67	wt: GGGCAGGCAGACTGT mu: GGGCAGGCAGACTAT	GCAG\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000022942

1171

Mmulatta

all identical

ENSMMUG00000000937

1207

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000014852

1217

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000076270

1165

Dmelanogaster

no alignment

FBgn0086408

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	29	SIGNAL	Potential.	lost
30	74	PROPEP	/FTId=PRO_0000247510.	might get lost (downstream of altered splice site)
71	71	MUTAGEN	R->K: Abolishes pro-domain removal but no loss of proteolytic activity; when associated with D-73.	might get lost (downstream of altered splice site)
73	73	MUTAGEN	R->D: Abolishes pro-domain removal but no loss of proteolytic activity; when associated with K-71.	might get lost (downstream of altered splice site)
80	286	DOMAIN	Peptidase M12B.	might get lost (downstream of altered splice site)
83	83	METAL	Calcium (Potential).	might get lost (downstream of altered splice site)
101	101	CONFLICT	E -> R (in Ref. 1; AA sequence).	might get lost (downstream of altered splice site)
142	142	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
146	146	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
173	173	METAL	Calcium (Potential).	might get lost (downstream of altered splice site)
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

672 / 672

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

224 / 224

position of stopcodon in wt / mu cDNA

868 / 868

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

197 / 197

chromosome

strand

last intron/exon boundary

662

theoretical NMD boundary in CDS

415

length of CDS

672

coding sequence (CDS) position

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

222

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

41783

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

136321260

original gDNA sequence snippet

AGGCCCAGGGCAGGCAGACTGTGCAGTGGCCATTGGGCGGC

altered gDNA sequence snippet

AGGCCCAGGGCAGGCAGACTATGCAGTGGCCATTGGGCGGC

original cDNA sequence snippet

AGGCCCAGGGCAGGCAGACTGTGCAGTGGCCATTGGGCGGC

altered cDNA sequence snippet

AGGCCCAGGGCAGGCAGACTATGCAGTGGCCATTGGGCGGC

wildtype AA sequence

MRGPGQADCA VAIGRPLGEV VTLRVLESSL NCSAGDMLLL WGRLTWRKMC RKLLDMTFSS
KTNTLVVRQR CGRPGGGVLL RYGSQLAPET FYRECDMQLF GPWGEIVSPS LSPATSNAGG
CRLFINVAPH ARIAIHALAT NMGAGTEGAN ASYILIRDTH SLRTTAFHGQ QVLYWESESS
QAEMEFSEGF LKAQASLRGQ YWTLQSWVPE MQDPQSWKGK EGT*

mutated AA sequence

MRGPGQADYA VAIGRPLGEV VTLRVLESSL NCSAGDMLLL WGRLTWRKMC RKLLDMTFSS
KTNTLVVRQR CGRPGGGVLL RYGSQLAPET FYRECDMQLF GPWGEIVSPS LSPATSNAGG
CRLFINVAPH ARIAIHALAT NMGAGTEGAN ASYILIRDTH SLRTTAFHGQ QVLYWESESS
QAEMEFSEGF LKAQASLRGQ YWTLQSWVPE MQDPQSWKGK EGT*

speed

0.90 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