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 CM983729)
known disease mutation: rs6645 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:178357898G>AN/A show variant in all transcripts IGV

HGNC symbol

AGPS

Ensembl transcript ID

ENST00000409888

Genbank transcript ID

N/A

UniProt peptide

O00116

alteration type

single base exchange

alteration region

intron

DNA changes

g.100527G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434411
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs6645 (pathogenic for Rhizomelic chondrodysplasia punctata type 3) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983729)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983729)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983729)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.647	1
	5.394	1
(flanking)	0.865	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
Acc marginally increased	100528	wt: 0.5649 / mu: 0.5840 (marginal change - not scored)	wt: TGTGCTCCGGCATCTATTCGCCTCATGGACAACAAGCAGTT mu: TGTGCTCCGGCATCTATTCACCTCATGGACAACAAGCAGTT	tcgc\|CTCA
Acc marginally increased	100535	wt: 0.9535 / mu: 0.9572 (marginal change - not scored)	wt: CGGCATCTATTCGCCTCATGGACAACAAGCAGTTTCAGTTT mu: CGGCATCTATTCACCTCATGGACAACAAGCAGTTTCAGTTT	atgg\|ACAA
Donor increased	100528	wt: 0.55 / mu: 0.85	wt: ATTCGCCTCATGGAC mu: ATTCACCTCATGGAC	TCGC\|ctca

distance from splice site

28159

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
169	169	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
202	384	DOMAIN	FAD-binding PCMH-type.	might get lost (downstream of altered splice site)
347	347	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
578	578	ACT_SITE	By similarity.	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

23 / 23

chromosome

strand

last intron/exon boundary

471

theoretical NMD boundary in CDS

398

length of CDS

570

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)

100527

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

178357898

original gDNA sequence snippet

ATGTGCTCCGGCATCTATTCGCCTCATGGACAACAAGCAGT

altered gDNA sequence snippet

ATGTGCTCCGGCATCTATTCACCTCATGGACAACAAGCAGT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAEAAAAAGG TGLGAGASYG SAADRDRDPD PDRAGRRLRV LSGHLLGRPR EALSTNECKA
RRAASAATAA PTATPAAQES GTIPKKRQEV MKWNGWGYND SKFIFNKKGQ IELTGKRGIS
DPLTVFEQTE AAAREEILAN GGSLSHHHGV GKLRKQWLKE SISDVGFGML KSVKEYVDPN
NIFGNRNLL*

mutated AA sequence

N/A

speed

0.90 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