mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999895611 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM060784)
known disease mutation at this position (HGMD CM064946)
known disease mutation at this position (HGMD CM960012)
known disease mutation: rs8244 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:52309898T>GN/A show variant in all transcripts IGV

HGNC symbol

ACVRL1

Ensembl transcript ID

ENST00000419526

Genbank transcript ID

N/A

UniProt peptide

P37023

alteration type

single base exchange

alteration region

CDS

DNA changes

c.605T>G
cDNA.667T>G
g.9207T>G

AA changes

M202R Score: 91 explain score(s)

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

202

frameshift

known variant

Reference ID: rs28936399
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8244 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960012)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)
known disease mutation at this position, please check HGMD for details (HGMD ID CM064946)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)
known disease mutation at this position, please check HGMD for details (HGMD ID CM064946)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)
known disease mutation at this position, please check HGMD for details (HGMD ID CM064946)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)
known disease mutation at this position, please check HGMD for details (HGMD ID CM064946)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)
known disease mutation at this position, please check HGMD for details (HGMD ID CM064946)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060784)
known disease mutation at this position, please check HGMD for details (HGMD ID CM064946)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960012)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.854	1
	4.854	1
(flanking)	5.878	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
Donor marginally increased	9211	wt: 0.7021 / mu: 0.7570 (marginal change - not scored)	wt: ATGGCACCCGAGGTG mu: AGGGCACCCGAGGTG	GGCA\|cccg
Donor gained	9201	0.68	mu: CAAGCGGTACAGGGC	AGCG\|gtac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

202

mutated

not conserved

202

Ptroglodytes

all identical

ENSPTRG00000004963

376

Mmulatta

all identical

ENSMMUG00000004982

383

Fcatus

all identical

ENSFCAG00000000265

378

Mmusculus

all identical

ENSMUSG00000000530

375

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000012725

343

Drerio

all identical

ENSDARG00000018179

371

Dmelanogaster

all identical

FBgn0003317

438

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031897

346

protein features

start (aa)	end (aa)	feature	details
142	503	TOPO_DOM	Cytoplasmic (Potential).	lost
172	201	DOMAIN	GS.	might get lost (downstream of altered splice site)
198	201	HELIX		might get lost (downstream of altered splice site)
202	492	DOMAIN	Protein kinase.	lost
203	211	STRAND		might get lost (downstream of altered splice site)
208	216	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)
214	221	STRAND		might get lost (downstream of altered splice site)
224	231	STRAND		might get lost (downstream of altered splice site)
229	229	BINDING	ATP (By similarity).	might get lost (downstream of altered splice site)
233	235	HELIX		might get lost (downstream of altered splice site)
236	248	HELIX		might get lost (downstream of altered splice site)
259	265	STRAND		might get lost (downstream of altered splice site)
272	278	STRAND		might get lost (downstream of altered splice site)
285	291	HELIX		might get lost (downstream of altered splice site)
296	314	HELIX		might get lost (downstream of altered splice site)
325	327	STRAND		might get lost (downstream of altered splice site)
330	330	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
335	338	STRAND		might get lost (downstream of altered splice site)
344	346	STRAND		might get lost (downstream of altered splice site)
353	355	STRAND		might get lost (downstream of altered splice site)
357	359	STRAND		might get lost (downstream of altered splice site)
373	375	HELIX		might get lost (downstream of altered splice site)
378	381	HELIX		might get lost (downstream of altered splice site)
390	410	HELIX		might get lost (downstream of altered splice site)
424	428	TURN		might get lost (downstream of altered splice site)
435	442	HELIX		might get lost (downstream of altered splice site)
455	459	STRAND		might get lost (downstream of altered splice site)
460	462	TURN		might get lost (downstream of altered splice site)
463	469	HELIX		might get lost (downstream of altered splice site)
476	478	HELIX		might get lost (downstream of altered splice site)
482	491	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

990 / 990

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

330 / 330

position of stopcodon in wt / mu cDNA

1052 / 1052

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

63 / 63

chromosome

strand

last intron/exon boundary

918

theoretical NMD boundary in CDS

805

length of CDS

990

coding sequence (CDS) position

605

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

667

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

9207

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

52309898

original gDNA sequence snippet

AGTGGGCACCAAGCGGTACATGGCACCCGAGGTGCTGGACG

altered gDNA sequence snippet

AGTGGGCACCAAGCGGTACAGGGCACCCGAGGTGCTGGACG

original cDNA sequence snippet

AGTGGGCACCAAGCGGTACATGGCACCCGAGGTGCTGGACG

altered cDNA sequence snippet

AGTGGGCACCAAGCGGTACAGGGCACCCGAGGTGCTGGACG

wildtype AA sequence

MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGKGRYG EVWRGLWHGE SVAVKIFSSR
DEQSWFRETE IYNTVLLRHD NILGFIASDM TSRNSSTQLW LITHYHEHGS LYDFLQRQTL
EPHLALRLAV SAACGLAHLH VEIFGTQGKP AIAHRDFKSR NVLVKSNLQC CIADLGLAVM
HSQGSDYLDI GNNPRVGTKR YMAPEVLDEQ IRTDCFESYK WTDIWAFGLV LWEIARRTIV
NGIVEDYRPP FYDVVPNDPS FEDMKKVVCV DQQTPTIPNR LAADPVLSGL AQMMRECWYP
NPSARLTALR IKKTLQKISN SPEKPKVIQ*

mutated AA sequence

MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGKGRYG EVWRGLWHGE SVAVKIFSSR
DEQSWFRETE IYNTVLLRHD NILGFIASDM TSRNSSTQLW LITHYHEHGS LYDFLQRQTL
EPHLALRLAV SAACGLAHLH VEIFGTQGKP AIAHRDFKSR NVLVKSNLQC CIADLGLAVM
HSQGSDYLDI GNNPRVGTKR YRAPEVLDEQ IRTDCFESYK WTDIWAFGLV LWEIARRTIV
NGIVEDYRPP FYDVVPNDPS FEDMKKVVCV DQQTPTIPNR LAADPVLSGL AQMMRECWYP
NPSARLTALR IKKTLQKISN SPEKPKVIQ*

speed

1.12 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