mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.542217438099579 (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)

chr2:135893372A>GN/A show variant in all transcripts IGV

HGNC symbol

RAB3GAP1

Ensembl transcript ID

ENST00000539493

Genbank transcript ID

N/A

UniProt peptide

Q15042

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1661A>G
cDNA.2073A>G
g.83538A>G

AA changes

N554S Score: 46 explain score(s)

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

554

frameshift

known variant

Reference ID: rs10445686

database	homozygous (G/G)	heterozygous	allele carriers
1000G	175	724	899
ExAC	3313	17683	20996

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.883	1
	1.794	1
(flanking)	0.658	1

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
Donor marginally increased	83532	wt: 0.9454 / mu: 0.9939 (marginal change - not scored)	wt: ACTTAAAGGAAATGG mu: ACTTAAAGGAAGTGG	TTAA\|agga
Donor gained	83537	0.67	mu: AAGGAAGTGGACAAG	GGAA\|gtgg

distance from splice site

131

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

554

mutated

all conserved

554

Ptroglodytes

all identical

ENSPTRG00000012491

598

Mmulatta

all identical

ENSMMUG00000014630

599

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036104

598

Ggallus

all identical

ENSGALG00000012214

599

TKEGN

Trubripes

not conserved

ENSTRUG00000005671

593

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0051935

586

Celegans

not conserved

F20D1.6

565

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
579	579	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
581	581	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
590	590	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
619	619	MUTAGEN	R->A: No effect.	might get lost (downstream of altered splice site)
700	700	MUTAGEN	R->A: No effect.	might get lost (downstream of altered splice site)
728	728	MUTAGEN	R->A: Loss of function.	might get lost (downstream of altered splice site)
753	753	MUTAGEN	R->A: No effect.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2808 / 2808

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

936 / 936

position of stopcodon in wt / mu cDNA

3220 / 3220

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

413 / 413

chromosome

strand

last intron/exon boundary

3572

theoretical NMD boundary in CDS

3109

length of CDS

2808

coding sequence (CDS) position

1661

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

2073

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

83538

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

135893372

original gDNA sequence snippet

TACTGAAGAACTTAAAGGAAATGGACAAGAGAGTGGCAAGA

altered gDNA sequence snippet

TACTGAAGAACTTAAAGGAAGTGGACAAGAGAGTGGCAAGA

original cDNA sequence snippet

TACTGAAGAACTTAAAGGAAATGGACAAGAGAGTGGCAAGA

altered cDNA sequence snippet

TACTGAAGAACTTAAAGGAAGTGGACAAGAGAGTGGCAAGA

wildtype AA sequence

MFSLISGIFT SGTWEEKSDE ISFADFKFSV THHYLVQEST DKEGKDELLE DVVPQSMQDL
LGMNNDFPPR AHCLVRWYGL REFVVIAPAA HSDAVLSESK CNLLLSSVSI ALGNTGCQVP
LFVQIHHKWR RMYVGECQGP GVRTDFEMVH LRKVPNQYTH LSGLLDIFKS KIGCPLTPLP
PVSIAIRFTY VLQDWQQYFW PQQPPDIDAL VGGEVGGLEF GKLPFGACED PISELHLATT
WPHLTEGIIV DNDVYSDLDP IQAPHWSVRV RKAENPQCLL GDFVTEFFKI CRRKESTDEI
LGRSAFEEEG KETADITHAL SKLTEPASVP IHKLSVSNMV HTAKKKIRKH RGVEESPLNN
DVLNTILLFL FPDAVSEKPL DGTTSTDNNN PPSESEDYNL YNQFKSAPSD SLTYKLALCL
CMINFYHGGL KGVAHLWQEF VLEMRFRWEN NFLIPGLASG PPDLRCCLLH QKLQMLNCCI
ERKKARDEGK KTSASDVTNI YPGDAGKAGD QLVPDNLKET DKEKGEVGKS WDSWSDSEEE
FFECLSDTEE LKGNGQESGK KGGPKEMANL RPEGRLYQHG KLTLLHNGEP LYIPVTQEPA
PMTEDLLEEQ SEVLAKLGTS AEGAHLRARM QSACLLSDME SFKAANPGCS LEDFVRWYSP
RDYIEEEVID EKGNVVLKGE LSARMKIPSN MWVEAWETAK PIPARRQRRL FDDTREAEKV
LHYLAIQKPA DLARHLLPCV IHAAVLKVKE EESLENISSV KKIIKQIISH SSKVLHFPNP
EDKKLEEIIH QITNVEALIA RARSLKAKFG TEKCEQEEEK EDLERFVSCL LEQPEVLVTG
AGRGHAGRII HKLFVNAQRA AAMTPPEEEL KRMGSPEERR QNSVSDFPPP AGREFILRTT
VPRPAPYSKA LPQRMYSVLT KEDFRLAVKI IDGDV*

mutated AA sequence

MFSLISGIFT SGTWEEKSDE ISFADFKFSV THHYLVQEST DKEGKDELLE DVVPQSMQDL
LGMNNDFPPR AHCLVRWYGL REFVVIAPAA HSDAVLSESK CNLLLSSVSI ALGNTGCQVP
LFVQIHHKWR RMYVGECQGP GVRTDFEMVH LRKVPNQYTH LSGLLDIFKS KIGCPLTPLP
PVSIAIRFTY VLQDWQQYFW PQQPPDIDAL VGGEVGGLEF GKLPFGACED PISELHLATT
WPHLTEGIIV DNDVYSDLDP IQAPHWSVRV RKAENPQCLL GDFVTEFFKI CRRKESTDEI
LGRSAFEEEG KETADITHAL SKLTEPASVP IHKLSVSNMV HTAKKKIRKH RGVEESPLNN
DVLNTILLFL FPDAVSEKPL DGTTSTDNNN PPSESEDYNL YNQFKSAPSD SLTYKLALCL
CMINFYHGGL KGVAHLWQEF VLEMRFRWEN NFLIPGLASG PPDLRCCLLH QKLQMLNCCI
ERKKARDEGK KTSASDVTNI YPGDAGKAGD QLVPDNLKET DKEKGEVGKS WDSWSDSEEE
FFECLSDTEE LKGSGQESGK KGGPKEMANL RPEGRLYQHG KLTLLHNGEP LYIPVTQEPA
PMTEDLLEEQ SEVLAKLGTS AEGAHLRARM QSACLLSDME SFKAANPGCS LEDFVRWYSP
RDYIEEEVID EKGNVVLKGE LSARMKIPSN MWVEAWETAK PIPARRQRRL FDDTREAEKV
LHYLAIQKPA DLARHLLPCV IHAAVLKVKE EESLENISSV KKIIKQIISH SSKVLHFPNP
EDKKLEEIIH QITNVEALIA RARSLKAKFG TEKCEQEEEK EDLERFVSCL LEQPEVLVTG
AGRGHAGRII HKLFVNAQRA AAMTPPEEEL KRMGSPEERR QNSVSDFPPP AGREFILRTT
VPRPAPYSKA LPQRMYSVLT KEDFRLAVKI IDGDV*

speed

0.97 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