mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.977488179812674 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM033743)
known disease mutation: rs2603 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:80975496A>GN/A show variant in all transcripts IGV

HGNC symbol

ANTXR2

Ensembl transcript ID

ENST00000346652

Genbank transcript ID

N/A

UniProt peptide

P58335

alteration type

single base exchange

alteration region

CDS

DNA changes

c.566T>C
cDNA.706T>C
g.71113T>C

AA changes

I189T Score: 89 explain score(s)

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

189

frameshift

known variant

Reference ID: rs137852905
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2603 (pathogenic for Hyaline fibromatosis syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033743)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033743)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033743)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.151	0.998
	4.268	1
(flanking)	2.726	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 increased	71105	wt: 0.50 / mu: 0.66	wt: TTCCTCTTCTTTCTAAAGCTTGAAAGAATTGCTGATTCCAA mu: TTCCTCTTCTTTCTAAAGCTTGAAAGAACTGCTGATTCCAA	gctt\|GAAA
Donor marginally increased	71104	wt: 0.8586 / mu: 0.9337 (marginal change - not scored)	wt: AAAGCTTGAAAGAAT mu: AAAGCTTGAAAGAAC	AGCT\|tgaa
Donor marginally increased	71107	wt: 0.9572 / mu: 0.9661 (marginal change - not scored)	wt: GCTTGAAAGAATTGC mu: GCTTGAAAGAACTGC	TTGA\|aaga
Donor increased	71114	wt: 0.49 / mu: 0.72	wt: AGAATTGCTGATTCC mu: AGAACTGCTGATTCC	AATT\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

189

mutated

not conserved

189

Ptroglodytes

all identical

ENSPTRG00000016207

246

SGRGFMLGSRNGSVLCTYTVNETYTTSVKPV

SMLCPAP

Mmulatta

not conserved

ENSMMUG00000003333

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000029338

252

KPVSIQPSSILCPAP

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000060520

180

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000021531

187

protein features

start (aa)	end (aa)	feature	details
34	318	TOPO_DOM	Extracellular (Potential).	lost
44	213	DOMAIN	VWFA.	lost
183	189	HELIX		lost
190	192	STRAND		might get lost (downstream of altered splice site)
193	195	HELIX		might get lost (downstream of altered splice site)
196	201	STRAND		might get lost (downstream of altered splice site)
204	215	HELIX		might get lost (downstream of altered splice site)
218	218	DISULFID		might get lost (downstream of altered splice site)
250	250	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
260	260	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
319	341	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
342	489	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
352	360	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
362	366	COMPBIAS	Poly-Glu.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1161 / 1161

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

387 / 387

position of stopcodon in wt / mu cDNA

1301 / 1301

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

141 / 141

chromosome

strand

-1

last intron/exon boundary

1179

theoretical NMD boundary in CDS

988

length of CDS

1161

coding sequence (CDS) position

566

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

706

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

71113

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

80975496

original gDNA sequence snippet

CTTTCTAAAGCTTGAAAGAATTGCTGATTCCAAGGAGCAAG

altered gDNA sequence snippet

CTTTCTAAAGCTTGAAAGAACTGCTGATTCCAAGGAGCAAG

original cDNA sequence snippet

ACAAGCACAGCTTGAAAGAATTGCTGATTCCAAGGAGCAAG

altered cDNA sequence snippet

ACAAGCACAGCTTGAAAGAACTGCTGATTCCAAGGAGCAAG

wildtype AA sequence

MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSSNGIAAII VILVLLLLLG IGLMWWFWPL
CCKVVIKDPP PPPAPAPKEE EEEPLPTKKW PTVDASYYGG RGVGGIKRME VRWGDKGSTE
EGARLEKAKN AVVKIPEETE EPIRPRPPRP KPTHQPPQTK WYTPIKGRLD ALWALLRRQY
DRVSLMRPQE GDEVCIWECI EKELTA*

mutated AA sequence

MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERTA DSKEQVFPVK GGFQALKGII NSSNGIAAII VILVLLLLLG IGLMWWFWPL
CCKVVIKDPP PPPAPAPKEE EEEPLPTKKW PTVDASYYGG RGVGGIKRME VRWGDKGSTE
EGARLEKAKN AVVKIPEETE EPIRPRPPRP KPTHQPPQTK WYTPIKGRLD ALWALLRRQY
DRVSLMRPQE GDEVCIWECI EKELTA*

speed

0.58 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