mutation t@sting

documentation

Prediction

disease causing

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

Summary

known disease mutation at this position (HGMD CM030015)
known disease mutation: rs18364 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:233394841C>AN/A show variant in all transcripts IGV

HGNC symbol

CHRND

Ensembl transcript ID

ENST00000457943

Genbank transcript ID

N/A

UniProt peptide

Q07001

alteration type

single base exchange

alteration region

intron

DNA changes

g.4139C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121909503
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18364 (pathogenic for Congenital myasthenic syndrome 3B) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.02	1
	4.36	0.999
(flanking)	-2.409	0.009

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 marginally increased	4139	wt: 0.3633 / mu: 0.3942 (marginal change - not scored)	wt: CAACCTGGTCTTCTACCTACCGGCTGACAGTGAGCCTCCAG mu: CAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCAG	tacc\|GGCT
Acc gained	4138	0.33	mu: TCAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCA	ctac\|AGGC

distance from splice site

1221

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
22	245	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
97	97	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
151	151	DISULFID	By similarity.	might get lost (downstream of altered splice site)
164	164	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
165	165	DISULFID	By similarity.	might get lost (downstream of altered splice site)
246	270	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
278	299	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
312	333	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
334	471	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
390	390	MOD_RES	Phosphotyrosine; by Tyr-kinases (By similarity).	might get lost (downstream of altered splice site)
472	490	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

300 / 300

chromosome

strand

last intron/exon boundary

1089

theoretical NMD boundary in CDS

739

length of CDS

972

coding sequence (CDS) position

N/A

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

N/A

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

4139

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

233394841

original gDNA sequence snippet

CAACCTGGTCTTCTACCTACCGGCTGACAGTGAGCCTCCAG

altered gDNA sequence snippet

CAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MLKNLETSVS CASPRTWCGS QRLCWRTTMT APSRSPTPAT CLSTTTASCT GCHLPSSAPP
APSLSPISPS TGRTAPSSSG GEKTSVAISV LLAQSVFLLL ISKRLPATSM AIPLIGKFLL
FGMVLVTMVV VICVIVLNIH FRTPSTHVLS EGVKKLFLET LPELLHMSRP AEDGPSPGAL
VRRSSSLGYI SKAEEYFLLK SRSDLMFEKQ SERHGLARRL TTARRPPASS EQAQQELFNE
LKPAVDGANF IVNHMRDQNN YNEEKDSWNR VARTVDRLCL FVVTPVMVVG TAWIFLQGVY
NQPPPQPFPG DPYSYNVQDK RFI*

mutated AA sequence

N/A

speed

1.07 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