mutation t@sting

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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 CM960300)
known disease mutation: rs18344 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4804140G>AN/A show variant in all transcripts IGV

HGNC symbol

C17orf107

Ensembl transcript ID

ENST00000381365

Genbank transcript ID

NM_001145536

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1112G>A
g.1428G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121909511
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18344 (pathogenic for Myasthenic syndrome, congenital, 4a, slow-channel) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960300)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960300)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960300)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.381	0.997
	5.304	1
(flanking)	1.272	1

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

splice sites

splice site change occurs after stopcodon (at aa 292) splice site change occurs after stopcodon (at aa 293)

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	1419	wt: 0.23 / mu: 0.27	wt: AGAAGTCTCTGGGATTTTCTGGGCAATGAGGAACAAGAAGA mu: AGAAGTCTCTGGGATTTTCTGGGCAATGAAGAACAAGAAGA	tctg\|GGCA
Donor marginally increased	1429	wt: 0.9348 / mu: 0.9677 (marginal change - not scored)	wt: ATGAGGAACAAGAAG mu: ATGAAGAACAAGAAG	GAGG\|aaca
Donor marginally increased	1420	wt: 0.9461 / mu: 0.9839 (marginal change - not scored)	wt: TTCTGGGCAATGAGG mu: TTCTGGGCAATGAAG	CTGG\|gcaa
Donor increased	1423	wt: 0.34 / mu: 0.99	wt: TGGGCAATGAGGAAC mu: TGGGCAATGAAGAAC	GGCA\|atga
Donor marginally increased	1432	wt: 0.9693 / mu: 0.9753 (marginal change - not scored)	wt: AGGAACAAGAAGACG mu: AAGAACAAGAAGACG	GAAC\|aaga
Donor marginally increased	1425	wt: 0.2113 / mu: 0.2408 (marginal change - not scored)	wt: GGCAATGAGGAACAA mu: GGCAATGAAGAACAA	CAAT\|gagg

distance from splice site

609

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

228 / 228

chromosome

strand

last intron/exon boundary

504

theoretical NMD boundary in CDS

226

length of CDS

573

coding sequence (CDS) position

N/A

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

1112

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

1428

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

4804140

original gDNA sequence snippet

TGGGATTTTCTGGGCAATGAGGAACAAGAAGACGGTCTGGG

altered gDNA sequence snippet

TGGGATTTTCTGGGCAATGAAGAACAAGAAGACGGTCTGGG

original cDNA sequence snippet

TGGGATTTTCTGGGCAATGAGGAACAAGAAGACGGTCTGGG

altered cDNA sequence snippet

TGGGATTTTCTGGGCAATGAAGAACAAGAAGACGGTCTGGG

wildtype AA sequence

MKGTPSSLDT LMWIYHFHSS TEVALQPPLL SSLELSVAAA HEYLEQRFRE LKSLEPPEPK
MQGMLPAPKP TLGLVLREAT ASLVSFGTTL LEISALWLQQ EARRLDGSAG PAPDGRDPGA
ALSRVAQAAG QGVRQAGAAV GASARLLVQG AWLCLCGRGL QGSASFLRQS QQQLGLGIPG
EPVSSGHGVS *

mutated AA sequence

N/A

speed

1.16 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