mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999964076258424 (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)

chr2:11702661A>CN/A show variant in all transcripts IGV

HGNC symbol

GREB1

Ensembl transcript ID

ENST00000389825

Genbank transcript ID

N/A

UniProt peptide

Q4ZG55

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.211A>C
g.28420A>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs10929757

database	homozygous (C/C)	heterozygous	allele carriers
1000G	570	942	1512
ExAC	18162	-3557	14605

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.462	0.009
	0.601	0.007
(flanking)	-0.546	0.004

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

splice sites

splice site change before start ATG (at aa -30) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	28429	wt: 0.74 / mu: 0.93	wt: TGGCCCCCCAAACCCTTTCCAGCTGCACCCTCTGCCTGAAG mu: TGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAG	tcca\|GCTG
Acc gained	28428	0.45	mu: ATGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAA	ttcc\|AGCT
Acc gained	28430	0.37	mu: GGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAGG	ccag\|CTGC

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
829	829	CONFLICT	I -> S (in Ref. 1; AAG39036).	might get lost (downstream of altered splice site)
1109	1232	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
1868	1888	TRANSMEM	Helical; (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

312 / 312

chromosome

strand

last intron/exon boundary

754

theoretical NMD boundary in CDS

392

length of CDS

762

coding sequence (CDS) position

N/A

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

211

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

28420

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

11702661

original gDNA sequence snippet

GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC

altered gDNA sequence snippet

GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC

original cDNA sequence snippet

GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC

altered cDNA sequence snippet

GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC

wildtype AA sequence

MDVPAGFLLV GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE
FSNHINLKLT TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP
ALESTAAFPS EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN
LLALPRPSAL GSSACPGRPG DPALLWAKAR GGMGAAGLGP LSLLESDVAS MRVRPGPQVP
PESVGLGPGP GAL*

mutated AA sequence

N/A

speed

0.29 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