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 CM960722)
known disease mutation: rs2082 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13010300C>TN/A show variant in all transcripts IGV

HGNC symbol

GCDH

Ensembl transcript ID

ENST00000457854

Genbank transcript ID

NM_013976

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.8461C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434367

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	23	23

known disease mutation: rs2082 (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 CM960722)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960722)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960722)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.605	1
	5.605	1
(flanking)	-2.749	0.021

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	8472	wt: 0.2675 / mu: 0.3327 (marginal change - not scored)	wt: ACATTCACGCCCTGATCCTTGGGAGAGCTATCACGGGAATC mu: ACATTCACGTCCTGATCCTTGGGAGAGCTATCACGGGAATC	cttg\|GGAG
Donor marginally increased	8454	wt: 0.9706 / mu: 0.9861 (marginal change - not scored)	wt: ATGACATTCACGCCC mu: ATGACATTCACGTCC	GACA\|ttca

distance from splice site

214

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

78 / 78

chromosome

strand

last intron/exon boundary

1321

theoretical NMD boundary in CDS

1193

length of CDS

1287

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)

8461

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

13010300

original gDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered gDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEVVQMCS
LKRRWNSL*

mutated AA sequence

N/A

speed

0.57 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