mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.998840947676158 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960711)
known disease mutation: rs2089 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13007063G>CN/A show variant in all transcripts IGV

HGNC symbol

GCDH

Ensembl transcript ID

ENST00000422947

Genbank transcript ID

N/A

UniProt peptide

Q92947

alteration type

single base exchange

alteration region

CDS

DNA changes

c.548G>C
cDNA.806G>C
g.5224G>C

AA changes

R183P Score: 103 explain score(s)

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

183

frameshift

known variant

Reference ID: rs121434373

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	21	21

known disease mutation: rs2089 (pathogenic for Glutaric aciduria, type 1|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960711)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960711)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960711)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.183	0.985
	0.561	0.979
(flanking)	0.102	0.975

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	5228	wt: 0.54 / mu: 0.87	wt: TTTGTAGTGTGGGCTCGGTGTGAAGATGGCTGCATTCGGGG mu: TTTGTAGTGTGGGCTCCGTGTGAAGATGGCTGCATTCGGGG	gtgt\|GAAG
Donor marginally increased	5226	wt: 0.9927 / mu: 0.9961 (marginal change - not scored)	wt: CTCGGTGTGAAGATG mu: CTCCGTGTGAAGATG	CGGT\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

183

mutated

not conserved

183

Ptroglodytes

all identical

ENSPTRG00000010548

227

Mmulatta

all identical

ENSMMUG00000007043

227

Fcatus

all identical

ENSFCAG00000000477

227

Mmusculus

all identical

ENSMUSG00000003809

227

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000008257

230

Drerio

all conserved

ENSDARG00000038361

197

Dmelanogaster

all conserved

FBgn0031824

208

Celegans

all identical

F54D5.7

199

SAR

Xtropicalis

not conserved

ENSXETG00000007932

229

protein features

start (aa)	end (aa)	feature	details
177	186	NP_BIND	FAD.	lost
184	186	STRAND		might get lost (downstream of altered splice site)
186	186	BINDING	Substrate; via carbonyl oxygen.	might get lost (downstream of altered splice site)
188	190	HELIX		might get lost (downstream of altered splice site)
194	198	STRAND		might get lost (downstream of altered splice site)
199	202	TURN		might get lost (downstream of altered splice site)
203	214	STRAND		might get lost (downstream of altered splice site)
212	214	NP_BIND	FAD.	might get lost (downstream of altered splice site)
216	218	HELIX		might get lost (downstream of altered splice site)
220	228	STRAND		might get lost (downstream of altered splice site)
233	239	STRAND		might get lost (downstream of altered splice site)
254	256	STRAND		might get lost (downstream of altered splice site)
261	272	STRAND		might get lost (downstream of altered splice site)
273	275	HELIX		might get lost (downstream of altered splice site)
284	318	HELIX		might get lost (downstream of altered splice site)
287	294	REGION	Substrate binding.	might get lost (downstream of altered splice site)
319	319	BINDING	FAD (By similarity).	might get lost (downstream of altered splice site)
326	328	HELIX		might get lost (downstream of altered splice site)
330	330	BINDING	FAD (By similarity).	might get lost (downstream of altered splice site)
330	358	HELIX		might get lost (downstream of altered splice site)
364	388	HELIX		might get lost (downstream of altered splice site)
387	391	NP_BIND	FAD (By similarity).	might get lost (downstream of altered splice site)
389	394	HELIX		might get lost (downstream of altered splice site)
396	398	HELIX		might get lost (downstream of altered splice site)
400	410	HELIX		might get lost (downstream of altered splice site)
413	415	STRAND		might get lost (downstream of altered splice site)
414	414	MUTAGEN	E->D: Reduced catalytic activity.	might get lost (downstream of altered splice site)
414	414	ACT_SITE	Proton acceptor (Probable).	might get lost (downstream of altered splice site)
415	415	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
416	418	NP_BIND	FAD.	might get lost (downstream of altered splice site)
417	429	HELIX		might get lost (downstream of altered splice site)
434	434	BINDING	FAD; via carbonyl oxygen.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1185 / 1185

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

395 / 395

position of stopcodon in wt / mu cDNA

1443 / 1443

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

259 / 259

chromosome

strand

last intron/exon boundary

1370

theoretical NMD boundary in CDS

1061

length of CDS

1185

coding sequence (CDS) position

548

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

806

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

5224

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

13007063

original gDNA sequence snippet

TCTGTTTGTAGTGTGGGCTCGGTGTGAAGATGGCTGCATTC

altered gDNA sequence snippet

TCTGTTTGTAGTGTGGGCTCCGTGTGAAGATGGCTGCATTC

original cDNA sequence snippet

TCTGTTTGTAGTGTGGGCTCGGTGTGAAGATGGCTGCATTC

altered cDNA sequence snippet

TCTGTTTGTAGTGTGGGCTCCGTGTGAAGATGGCTGCATTC

wildtype AA sequence

MRSSSGTPSA PTARRDSCLA SCWPIATKSL ALLPRLECSG TILAHCKFCL PGSSDSPAST
PLVAGITGYG CAGVSSVAYG LLARELERVD SGYRSAMSVQ SSLVMHPIYA YGSEEQRQKY
LPQLAKGELL GCFGLTEPNS GSDPSSMETR AHYNSSNKSY TLNGTKTWIT NSPMADLFVV
WARCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*

mutated AA sequence

MRSSSGTPSA PTARRDSCLA SCWPIATKSL ALLPRLECSG TILAHCKFCL PGSSDSPAST
PLVAGITGYG CAGVSSVAYG LLARELERVD SGYRSAMSVQ SSLVMHPIYA YGSEEQRQKY
LPQLAKGELL GCFGLTEPNS GSDPSSMETR AHYNSSNKSY TLNGTKTWIT NSPMADLFVV
WAPCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*

speed

1.23 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