mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999985 (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)

chr17:43507008G>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGAP27

Ensembl transcript ID

ENST00000290470

Genbank transcript ID

N/A

UniProt peptide

Q6ZUM4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.638C>G
cDNA.1087C>G
g.4780C>G

AA changes

P213R Score: 103 explain score(s)

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

213

frameshift

known variant

Reference ID: rs2959953

database	homozygous (C/C)	heterozygous	allele carriers
1000G	975	1153	2128
ExAC	13872	5023	18895

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.012	0
	-0.566	0
(flanking)	0.314	0.001

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 gained	4774	0.91	mu: CGTCCCGCCGCGGGA	TCCC\|gccg
Donor gained	4779	0.49	mu: CGCCGCGGGAGGAGA	CCGC\|ggga

distance from splice site

290

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

213

mutated

not conserved

213

Ptroglodytes

not conserved

ENSPTRG00000009304

213

VDD

Mmulatta

not conserved

ENSMMUG00000021932

319

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000034255

212

VDD

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000005700

n/a

Drerio

no alignment

ENSDARG00000061798

n/a

Dmelanogaster

no homologue

Celegans

all identical

C38D4.5

ELNSRP

Xtropicalis

no alignment

ENSXETG00000003467

n/a

protein features

start (aa)	end (aa)	feature	details
213	213	CONFLICT	P -> R (in Ref. 4; AAH67345).	lost
216	216	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
228	228	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
246	280	DOMAIN	WW 1.	might get lost (downstream of altered splice site)
299	333	DOMAIN	WW 2.	might get lost (downstream of altered splice site)
411	444	DOMAIN	WW 3.	might get lost (downstream of altered splice site)
496	612	DOMAIN	PH.	might get lost (downstream of altered splice site)
499	510	STRAND		might get lost (downstream of altered splice site)
521	528	STRAND		might get lost (downstream of altered splice site)
531	536	STRAND		might get lost (downstream of altered splice site)
549	552	HELIX		might get lost (downstream of altered splice site)
554	560	STRAND		might get lost (downstream of altered splice site)
565	568	STRAND		might get lost (downstream of altered splice site)
571	573	HELIX		might get lost (downstream of altered splice site)
575	583	STRAND		might get lost (downstream of altered splice site)
589	593	STRAND		might get lost (downstream of altered splice site)
597	611	HELIX		might get lost (downstream of altered splice site)
638	638	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
697	886	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

792 / 792

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

264 / 264

position of stopcodon in wt / mu cDNA

1241 / 1241

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

450 / 450

chromosome

strand

-1

last intron/exon boundary

432

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

792

coding sequence (CDS) position

638

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

1087

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

4780

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

43507008

original gDNA sequence snippet

GGACTTGCACGTCCCGCCGCCGGAGGAGAGCGCAGAGCAGG

altered gDNA sequence snippet

GGACTTGCACGTCCCGCCGCGGGAGGAGAGCGCAGAGCAGG

original cDNA sequence snippet

GGACTTGCACGTCCCGCCGCCGGAGGAGAGCGCAGAGCAGG

altered cDNA sequence snippet

GGACTTGCACGTCCCGCCGCGGGAGGAGAGCGCAGAGCAGG

wildtype AA sequence

MAADVVGDVY VLVEHPFEYT GKDGRRVAIR PNERYRLLRR STEHWWHVRR EPGGRPFYLP
AQYVRELPAL GNPAAAAPPG PHPSPAAPEP LAYDYRFVSA AATAGPDGAP EESGGRASSL
CGPAQRGAAT QRSSLAPGLP ACLYLRPAAP VRPAQSLNDL ACAAVSPPAG LLGSSGSFKA
CSVAGSWVCP RPLARSDSEN VYEVIQDLHV PPPEESAEQV PPRALGRGGG WRARDRARTE
PGRKETRSAQ RRARRPPLSE DFG*

mutated AA sequence

MAADVVGDVY VLVEHPFEYT GKDGRRVAIR PNERYRLLRR STEHWWHVRR EPGGRPFYLP
AQYVRELPAL GNPAAAAPPG PHPSPAAPEP LAYDYRFVSA AATAGPDGAP EESGGRASSL
CGPAQRGAAT QRSSLAPGLP ACLYLRPAAP VRPAQSLNDL ACAAVSPPAG LLGSSGSFKA
CSVAGSWVCP RPLARSDSEN VYEVIQDLHV PPREESAEQV PPRALGRGGG WRARDRARTE
PGRKETRSAQ RRARRPPLSE DFG*

speed

0.81 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