mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999995190883267 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:52740182C>GN/A show variant in all transcripts IGV

HGNC symbol

SPCS1

Ensembl transcript ID

ENST00000423431

Genbank transcript ID

N/A

UniProt peptide

Q9Y6A9

alteration type

single base exchange

alteration region

intron

DNA changes

g.1212C>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6617

database	homozygous (G/G)	heterozygous	allele carriers
1000G	535	1160	1695
ExAC	1483	5131	6614

regulatory features

Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 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
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
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
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
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
HDAC1, Transcription Factor, HDAC1 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SIX5, Transcription Factor, SIX5 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
THAP1, Transcription Factor, THAP1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Tr4, Transcription Factor, Tr4 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.216	0
	-1.322	0
(flanking)	-1.072	0

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

splice sites

splice site change before start ATG (at aa -9) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	1206	0.52	mu: GCCAGACCTTAGCCC	CAGA\|cctt

distance from splice site

478

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	93	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
41	41	CONFLICT	P -> A (in Ref. 5; AAH00884 and 2; AAD40380).	might get lost (downstream of altered splice site)
94	114	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
95	95	CONFLICT	I -> Y (in Ref. 4; AAL31361).	might get lost (downstream of altered splice site)
115	115	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
116	136	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
128	128	CONFLICT	L -> LAQ (in Ref. 5; AAH00884).	might get lost (downstream of altered splice site)
137	169	TOPO_DOM	Cytoplasmic (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

235 / 235

chromosome

strand

last intron/exon boundary

352

theoretical NMD boundary in CDS

length of CDS

243

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)

1212

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

52740182

original gDNA sequence snippet

ACGCGCAGTGCCAGACCTTACCCCTCACGGTCCTTAAGTCT

altered gDNA sequence snippet

ACGCGCAGTGCCAGACCTTAGCCCTCACGGTCCTTAAGTCT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MFQGIILFSA IVGFIYGYVA EQFGWTVYIV MAGFAFSCLL TLPPWPIYRR HPLKWLPVQE
SSTDDKKPGE RKIKRHAKNN *

mutated AA sequence

N/A

speed

0.74 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