mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.99999999855999 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960715)
known disease mutation: rs2086 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13008527G>AN/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.961G>A
cDNA.1219G>A
g.6688G>A

AA changes

E321K Score: 56 explain score(s)

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

321

frameshift

known variant

Reference ID: rs121434370

database	homozygous (A/A)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	2	2

known disease mutation: rs2086 (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 CM960715)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960715)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960715)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-5.286	0
	5.164	0.998
(flanking)	4.278	0.999

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 increased	6684	wt: 0.34 / mu: 0.94	wt: GCTGCCCCCGAGATG mu: GCTGCCCCCAAGATG	TGCC\|cccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

321

mutated

all conserved

321

Ptroglodytes

all identical

ENSPTRG00000010548

365

Mmulatta

all identical

ENSMMUG00000007043

365

Fcatus

all identical

ENSFCAG00000000477

365

Mmusculus

all identical

ENSMUSG00000003809

365

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008257

368

QKNT

Drerio

all identical

ENSDARG00000038361

335

Dmelanogaster

all conserved

FBgn0031824

348

Celegans

all identical

F54D5.7

339

Xtropicalis

all identical

ENSXETG00000007932

367

protein features

start (aa)	end (aa)	feature	details
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	ACT_SITE	Proton acceptor (Probable).	might get lost (downstream of altered splice site)
414	414	MUTAGEN	E->D: Reduced catalytic activity.	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

961

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

1219

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

6688

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

13008527

original gDNA sequence snippet

CCACTCCCAGGGCTGCCCCCGAGATGGTTTCTCTGCTGAAG

altered gDNA sequence snippet

CCACTCCCAGGGCTGCCCCCAAGATGGTTTCTCTGCTGAAG

original cDNA sequence snippet

ACCAGGACAAGGCTGCCCCCGAGATGGTTTCTCTGCTGAAG

altered cDNA sequence snippet

ACCAGGACAAGGCTGCCCCCAAGATGGTTTCTCTGCTGAAG

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
WARCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP KMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*

speed

0.64 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