mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999156457 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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

ENST00000381486

Genbank transcript ID

NM_014668

UniProt peptide

Q4ZG55

alteration type

single base exchange

alteration region

CDS

DNA changes

c.230A>C
cDNA.530A>C
g.28420A>C

AA changes

N77T Score: 65 explain score(s)

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

frameshift

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

effect	gDNA position	score	wt 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?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000022786

Mmulatta

all identical

ENSMMUG00000020249

Fcatus

all identical

ENSFCAG00000008510

Mmusculus

all identical

ENSMUSG00000036523

Ggallus

not conserved

ENSGALG00000016455

Trubripes

not conserved

ENSTRUG00000000142

Drerio

not conserved

ENSDARG00000070794

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000023793

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

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5850 / 5850

position (AA) of stopcodon in wt / mu AA sequence

1950 / 1950

position of stopcodon in wt / mu cDNA

6150 / 6150

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

301 / 301

chromosome

strand

last intron/exon boundary

5987

theoretical NMD boundary in CDS

5636

length of CDS

5850

coding sequence (CDS) position

230

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

530

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

MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPNPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAA DQVPLMEDLE QIFLRSWRES HLTEIRQYQQ
APPQPFPPAP SAAAPVTSAQ LPWLASLAAS SCNDSVHVIE CAYSLAEGLS EMFRLLVEGK
LAKTNYVVII CACRSAAIDS CIAVTGKYQA RILSESLLTP AEYQKEVNYE LVTGKVDSLG
AFFSTLCPEG DIDILLDKFH QENQGHISSS LAASSVTKAA SLDVSGTPVC TSYNLEPHSI
RPFQLAVAQK LLSHVCSIAD SSTQNLDLGS FEKVDFLICI PPSEVTYQQT LLHVWHSGVL
LELGLKKEHM TKQRVEQYVL KLDTEAQTKF KAFLQNSFQN PHTLFVLIHD HAHWDLVSST
VHNLYSQSDP SVGLVDRLLN CREVKEAPNI VTLHVTSFPY ALQTQHTLIS PYNEIHWPAS
CSNGVDLYHE NKKYFGLSEF IESTLSGHSL PLLRYDSSFE AMVTALGKRF PRLHSAVIRT
FVLVQHYAAA LMAVSGLPQM KNYTSVETLE ITQNLLNSPK QCPCGHGLMV LLRVPCSPLA
VVAYERLAHV RARLALEEHF EIILGSPSSG VTVGKHFVKQ LRMWQKIEDV EWRPQTYLEL
EGLPCILIFS GMDPHGESLP RSLRYCDLRL INSSCLVRTA LEQELGLAAY FVSNEVPLEK
GARNEALESD AEKLSSTDNE DEELGTEGST SEKRSPMKRE RSRSHDSASS SLSSKASGSA
LGGESSAQPT ALPQGEHARS PQPRGPAEEG RAPGEKQRPR ASQGPPSAIS RHSPGPTPQP
DCSLRTGQRS VQVSVTSSCS QLSSSSGSSS SSVAPAAGTW VLQASQCSLT KACRQPPIVF
LPKLVYDMVV STDSSGLPKA ASLLPSPSVM WASSFRPLLS KTMTSTEQSL YYRQWTVPRP
SHMDYGNRAE GRVDGFHPRR LLLSGPPQIG KTGAYLQFLS VLSRMLVRLT EVDVYDEEEI
NINLREESDW HYLQLSDPWP DLELFKKLPF DYIIHDPKYE DASLICSHYQ GIKSEDRGMS
RKPEDLYVRR QTARMRLSKY AAYNTYHHCE QCHQYMGFHP RYQLYESTLH AFAFSYSMLG
EEIQLHFIIP KSKEHHFVFS QPGGQLESMR LPLVTDKSHE YIKSPTFTPT TGRHEHGLFN
LYHAMDGASH LHVLVVKEYE MAIYKKYWPN HIMLVLPSIF NSAGVGAAHF LIKELSYHNL
ELERNRQEEL GIKPQDIWPF IVISDDSCVM WNVVDVNSAG ERSREFSWSE RNVSLKHIMQ
HIEAAPDIMH YALLGLRKWS SKTRASEVQE PFSRCHVHNF IILNVDLTQN VQYNQNRFLC
DDVDFNLRVH SAGLLLCRFN RFSVMKKQIV VGGHRSFHIT SKVSDNSAAV VPAQYICAPD
SKHTFLAAPA QLLLEKFLQH HSHLFFPLSL KNHDHPVLSV DCYLNLGSQI SVCYVSSRPH
SLNISCSDLL FSGLLLYLCD SFVGASFLKK FHFLKGATLC VICQDRSSLR QTVVRLELED
EWQFRLRDEF QTANAREDRP LFFLTGRHI*

mutated AA sequence

MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPTPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAA DQVPLMEDLE QIFLRSWRES HLTEIRQYQQ
APPQPFPPAP SAAAPVTSAQ LPWLASLAAS SCNDSVHVIE CAYSLAEGLS EMFRLLVEGK
LAKTNYVVII CACRSAAIDS CIAVTGKYQA RILSESLLTP AEYQKEVNYE LVTGKVDSLG
AFFSTLCPEG DIDILLDKFH QENQGHISSS LAASSVTKAA SLDVSGTPVC TSYNLEPHSI
RPFQLAVAQK LLSHVCSIAD SSTQNLDLGS FEKVDFLICI PPSEVTYQQT LLHVWHSGVL
LELGLKKEHM TKQRVEQYVL KLDTEAQTKF KAFLQNSFQN PHTLFVLIHD HAHWDLVSST
VHNLYSQSDP SVGLVDRLLN CREVKEAPNI VTLHVTSFPY ALQTQHTLIS PYNEIHWPAS
CSNGVDLYHE NKKYFGLSEF IESTLSGHSL PLLRYDSSFE AMVTALGKRF PRLHSAVIRT
FVLVQHYAAA LMAVSGLPQM KNYTSVETLE ITQNLLNSPK QCPCGHGLMV LLRVPCSPLA
VVAYERLAHV RARLALEEHF EIILGSPSSG VTVGKHFVKQ LRMWQKIEDV EWRPQTYLEL
EGLPCILIFS GMDPHGESLP RSLRYCDLRL INSSCLVRTA LEQELGLAAY FVSNEVPLEK
GARNEALESD AEKLSSTDNE DEELGTEGST SEKRSPMKRE RSRSHDSASS SLSSKASGSA
LGGESSAQPT ALPQGEHARS PQPRGPAEEG RAPGEKQRPR ASQGPPSAIS RHSPGPTPQP
DCSLRTGQRS VQVSVTSSCS QLSSSSGSSS SSVAPAAGTW VLQASQCSLT KACRQPPIVF
LPKLVYDMVV STDSSGLPKA ASLLPSPSVM WASSFRPLLS KTMTSTEQSL YYRQWTVPRP
SHMDYGNRAE GRVDGFHPRR LLLSGPPQIG KTGAYLQFLS VLSRMLVRLT EVDVYDEEEI
NINLREESDW HYLQLSDPWP DLELFKKLPF DYIIHDPKYE DASLICSHYQ GIKSEDRGMS
RKPEDLYVRR QTARMRLSKY AAYNTYHHCE QCHQYMGFHP RYQLYESTLH AFAFSYSMLG
EEIQLHFIIP KSKEHHFVFS QPGGQLESMR LPLVTDKSHE YIKSPTFTPT TGRHEHGLFN
LYHAMDGASH LHVLVVKEYE MAIYKKYWPN HIMLVLPSIF NSAGVGAAHF LIKELSYHNL
ELERNRQEEL GIKPQDIWPF IVISDDSCVM WNVVDVNSAG ERSREFSWSE RNVSLKHIMQ
HIEAAPDIMH YALLGLRKWS SKTRASEVQE PFSRCHVHNF IILNVDLTQN VQYNQNRFLC
DDVDFNLRVH SAGLLLCRFN RFSVMKKQIV VGGHRSFHIT SKVSDNSAAV VPAQYICAPD
SKHTFLAAPA QLLLEKFLQH HSHLFFPLSL KNHDHPVLSV DCYLNLGSQI SVCYVSSRPH
SLNISCSDLL FSGLLLYLCD SFVGASFLKK FHFLKGATLC VICQDRSSLR QTVVRLELED
EWQFRLRDEF QTANAREDRP LFFLTGRHI*

speed

0.75 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