mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999999903226758 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:29523872A>GN/A show variant in all transcripts IGV

HGNC symbol

GABBR1

Ensembl transcript ID

ENST00000355973

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.3040T>C
g.77882T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2076486

database	homozygous (G/G)	heterozygous	allele carriers
1000G	181	638	819
ExAC	1298	7693	8991

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.379	0
	-0.788	0
(flanking)	-0.071	0.017

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

splice sites

splice site change occurs after stopcodon (at aa 932)

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	77877	wt: 0.8023 / mu: 0.8796 (marginal change - not scored)	wt: GGAGCTGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAA mu: GGAGCTGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAA	ttgt\|GGAG
Donor marginally increased	77880	wt: 0.9922 / mu: 0.9926 (marginal change - not scored)	wt: TGTGGAGTCAGGTGA mu: TGTGGAGCCAGGTGA	TGGA\|gtca
Donor increased	77884	wt: 0.51 / mu: 0.61	wt: GAGTCAGGTGATGAG mu: GAGCCAGGTGATGAG	GTCA\|ggtg

distance from splice site

256

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

248 / 248

chromosome

strand

-1

last intron/exon boundary

2785

theoretical NMD boundary in CDS

2487

length of CDS

2535

coding sequence (CDS) position

N/A

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

3040

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

77882

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

29523872

original gDNA sequence snippet

TGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAAAGAGG

altered gDNA sequence snippet

TGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAAAGAGG

original cDNA sequence snippet

TGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAAAGAGG

altered cDNA sequence snippet

TGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAAAGAGG

wildtype AA sequence

MGPGAPFARV GWPLPLLVVM AAGVAPVWAS HSPHLPRPHS RVPPHPSSER RAVYIGALFP
MSGGWPGGQA CQPAVEMALE DVNSRRDILP DYELKLIHHD SKCDPGQATK YLYELLYNDP
IKIILMPGCS SVSTLVAEAA RMWNLIVLSY GSSSPALSNR QRFPTFFRTH PSATLHNPTR
VKLFEKWGWK KIATIQQTTE VFTSTLDDLE ERVKEAGIEI TFRQSFFSDP AVPVKNLKRQ
DARIIVGLFY ETEARKVFCE VYKERLFGKK YVWFLIGWYA DNWFKIYDPS INCTVDEMTE
AVEGHITTEI VMLNPANTRS ISNMTSQEFV EKLTKRLKRH PEETGGFQEA PLAYDAIWAL
ALALNKTSGG GGRSGVRLED FNYNNQTITD QIYRAMNSSS FEGVSGHVVF DASGSRMAWT
LIEQLQGGSY KKIGYYDSTK DDLSWSKTDK WIGGSPPADQ TLVIKTFRFL SQKLFISVSV
LSSLGIVLAV VCLSFNIYNS HVRYIQNSQP NLNNLTAVGC SLALAAVFPL GLDGYHIGRN
QFPFVCQARL WLLGLGFSLG YGSMFTKIWW VHTVFTKKEE KKEWRKTLEP WKLYATVGLL
VGMDVLTLAI WQIVDPLHRT IETFAKEEPK EDIDVSILPQ LEHCSSRKMN TWLGIFYGYK
GLLLLLGIFL AYETKSVSTE KINDHRAVGM AIYNVAVLCL ITAPVTMILS SQQDAAFAFA
SLAIVFSSYI TLVVLFVPKM RRLITRGEWQ SEAQDTMKTG SSTNNNEEEK SRLLEKENRE
LEKIIAEKEE RVSELRHQLQ SRQQLRSRRH PPTPPEPSGG LPRGPPEPPD RLSCDGSRVH
LLYK*

mutated AA sequence

N/A

speed

0.84 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