mutation t@sting

Prediction

disease causing

Model: without_aae, prob: 0.99999999999999 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM960729)
known disease mutation: rs9283 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:55310817T>CN/A show variant in all transcripts IGV

HGNC symbol

GCH1

Ensembl transcript ID

ENST00000543643

Genbank transcript ID

NM_001024070

UniProt peptide

P30793

alteration type

single base exchange

alteration region

intron

DNA changes

g.58754A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs41298442

database	homozygous (C/C)	heterozygous	allele carriers
1000G	0	2	2
ExAC	0	44	44

known disease mutation: rs9283 (pathogenic for Dystonia 5|Autosomal recessive DOPA responsive dystonia|GTP cyclohydrolase I deficiency|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960729)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960729)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960729)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.358	0.999
	1.304	1
(flanking)	3.383	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	58745	wt: 0.9216 / mu: 0.9238 (marginal change - not scored)	wt: GAAAATGAACAGCAA mu: GAAAATGAACAGCAG	AAAT\|gaac
Donor gained	58753	0.38	mu: ACAGCAGAACTGTGA	AGCA\|gaac

distance from splice site

230

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
202	210	STRAND		might get lost (downstream of altered splice site)
211	214	HELIX		might get lost (downstream of altered splice site)
212	212	METAL	Zinc.	might get lost (downstream of altered splice site)
215	217	TURN		might get lost (downstream of altered splice site)
224	230	STRAND		might get lost (downstream of altered splice site)
233	236	HELIX		might get lost (downstream of altered splice site)
238	248	HELIX		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

145 / 145

chromosome

strand

-1

last intron/exon boundary

859

theoretical NMD boundary in CDS

664

length of CDS

702

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)

58754

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

55310817

original gDNA sequence snippet

TGTACAGAAAATGAACAGCAAAACTGTGACCAGCACAATGT

altered gDNA sequence snippet

TGTACAGAAAATGAACAGCAGAACTGTGACCAGCACAATGT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATK SNKYNKGLSP LLSSCHLFVA ILK*

mutated AA sequence

N/A

speed

0.73 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