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 CM010147)
known disease mutation at this position (HGMD CM065951)
known disease mutation: rs5044 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:53715207G>TN/A show variant in all transcripts IGV

HGNC symbol

AAAS

Ensembl transcript ID

ENST00000550286

Genbank transcript ID

N/A

UniProt peptide

Q9NRG9

alteration type

single base exchange

alteration region

intron

DNA changes

g.3442C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121918549

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	28	28

known disease mutation: rs5044 (pathogenic for Glucocorticoid deficiency with achalasia|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)

regulatory features

Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding (1)
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding (1)
BCLAF1, Transcription Factor, BCLAF1 Transcription Factor Binding
CBP, Transcription Factor, CBP Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cjun, Transcription Factor, Cjun TF binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
ETS1, Transcription Factor, ETS1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K56ac, Histone, Histone 3 Lysine 56 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Pbx3, Transcription Factor, Pbx3 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.367	1
	2.991	1
(flanking)	-0.134	0.951

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -51) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	3433	wt: 0.8468 / mu: 0.8574 (marginal change - not scored)	wt: GGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCTA mu: GGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCTA	ccgc\|CTCG
Acc marginally increased	3432	wt: 0.8384 / mu: 0.8432 (marginal change - not scored)	wt: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCT mu: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCT	accg\|CCTC
Donor marginally increased	3444	wt: 0.8976 / mu: 0.9115 (marginal change - not scored)	wt: GGTCAAGTCACCCTA mu: GGTAAAGTCACCCTA	TCAA\|gtca
Donor gained	3438	0.46	mu: CCTCGGGGTAAAGTC	TCGG\|ggta

distance from splice site

731

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
33	33	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
122	122	CONFLICT	S -> P (in Ref. 5; BAA91394).	might get lost (downstream of altered splice site)
135	135	CONFLICT	R -> K (in Ref. 5; BAA91394).	might get lost (downstream of altered splice site)
149	188	REPEAT	WD 1.	might get lost (downstream of altered splice site)
191	230	REPEAT	WD 2.	might get lost (downstream of altered splice site)
243	282	REPEAT	WD 3.	might get lost (downstream of altered splice site)
285	324	REPEAT	WD 4.	might get lost (downstream of altered splice site)
479	479	CONFLICT	I -> V (in Ref. 5; BAA91394).	might get lost (downstream of altered splice site)
495	495	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
544	546	MOTIF	Microbody targeting signal (Potential).	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

355 / 355

chromosome

strand

-1

last intron/exon boundary

1399

theoretical NMD boundary in CDS

994

length of CDS

1269

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)

3442

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

53715207

original gDNA sequence snippet

CTCCTCCACCGCCTCGGGGTCAAGTCACCCTATATGAGCAC

altered gDNA sequence snippet

CTCCTCCACCGCCTCGGGGTAAAGTCACCCTATATGAGCAC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MKLQTQKKRL RSEDLIAEFA QVTNWSSCCL RVFAWHPHTN KFAVALLDDS VRVYNASSTI
VPSLKHRLQR NVASLAWKPL SASVLAVACQ SCILIWTLDP TSLSTRPSSG CAQVLSHPGH
TPVTSLAWAP SGGRLLSASP VDAAIRVWDV STETCVPLPW FRGGGVTNLL WSPDGSKILA
TTPSAVFRVW EAQMWTCERW PTLSGRCQTG CWSPDGSRLL FTVLGEPLIY SLSFPERCGE
GKGCVGGAKS ATIVADLSET TIQTPDGEER LGGEAHSMVW DPSGERLAVL MKGKPRVQDG
KPVILLFRTR NSPVFELLPC GIIQGEPGAQ PQLITFHPSF NKGALLSVGW STGRIAHIPL
YFVNAQFPRF SPVLGRAQEP PAGGGGSIHD LPLFTETSPT SAPWDPLPGP PPVLPHSPHS
HL*

mutated AA sequence

N/A

speed

0.76 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