MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000333677
MT speed 0 s - this script 3.411723 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARHGEF37	polymorphism_automatic	5.79536418854332e-14	simple_aae		affected		M604V	single base exchange	rs1135093		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999942 (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)

chr5:149008521A>GN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF37

Ensembl transcript ID

ENST00000333677

Genbank transcript ID

NM_001001669

UniProt peptide

A1IGU5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1810A>G
cDNA.1973A>G
g.77012A>G

AA changes

M604V Score: 21 explain score(s)

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

604

frameshift

known variant

Reference ID: rs1135093

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1226	1022	2248
ExAC	29391	-26015	3376

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.971	0
	-0.989	0.003
(flanking)	1.31	0.147

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	77008	wt: 0.68 / mu: 0.80	wt: GCTCTAGTGCCCTCTATTCCCACCATGAACCAGGTGAGTAT mu: GCTCTAGTGCCCTCTATTCCCACCGTGAACCAGGTGAGTAT	tccc\|ACCA
Acc marginally increased	77006	wt: 0.8764 / mu: 0.8826 (marginal change - not scored)	wt: CAGCTCTAGTGCCCTCTATTCCCACCATGAACCAGGTGAGT mu: CAGCTCTAGTGCCCTCTATTCCCACCGTGAACCAGGTGAGT	attc\|CCAC
Acc increased	77004	wt: 0.69 / mu: 0.82	wt: CCCAGCTCTAGTGCCCTCTATTCCCACCATGAACCAGGTGA mu: CCCAGCTCTAGTGCCCTCTATTCCCACCGTGAACCAGGTGA	ctat\|TCCC
Acc marginally increased	77013	wt: 0.9695 / mu: 0.9741 (marginal change - not scored)	wt: AGTGCCCTCTATTCCCACCATGAACCAGGTGAGTATAGGAG mu: AGTGCCCTCTATTCCCACCGTGAACCAGGTGAGTATAGGAG	ccat\|GAAC
Acc marginally increased	77003	wt: 0.3741 / mu: 0.3781 (marginal change - not scored)	wt: GCCCAGCTCTAGTGCCCTCTATTCCCACCATGAACCAGGTG mu: GCCCAGCTCTAGTGCCCTCTATTCCCACCGTGAACCAGGTG	tcta\|TTCC
Donor increased	77011	wt: 0.34 / mu: 0.98	wt: CCCACCATGAACCAG mu: CCCACCGTGAACCAG	CACC\|atga
Acc gained	77011	0.34	mu: CTAGTGCCCTCTATTCCCACCGTGAACCAGGTGAGTATAGG	cacc\|GTGA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

604

mutated

all conserved

604

Ptroglodytes

all conserved

ENSPTRG00000017402

604

Mmulatta

all conserved

ENSMMUG00000017714

604

Fcatus

all conserved

ENSFCAG00000003628

604

Mmusculus

all identical

ENSMUSG00000045094

605

Ggallus

not conserved

ENSGALG00000001255

594

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000002463

638

Dmelanogaster

no homologue

Celegans

all conserved

Y37A1B.17

1463

Xtropicalis

not conserved

ENSXETG00000012714

570

protein features

start (aa)	end (aa)	feature	details
602	665	DOMAIN	SH3 2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2028 / 2028

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

676 / 676

position of stopcodon in wt / mu cDNA

2191 / 2191

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

164 / 164

chromosome

strand

last intron/exon boundary

1982

theoretical NMD boundary in CDS

1768

length of CDS

2028

coding sequence (CDS) position

1810

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

1973

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

77012

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

149008521

original gDNA sequence snippet

TAGTGCCCTCTATTCCCACCATGAACCAGGTGAGTATAGGA

altered gDNA sequence snippet

TAGTGCCCTCTATTCCCACCGTGAACCAGGTGAGTATAGGA

original cDNA sequence snippet

TAGTGCCCTCTATTCCCACCATGAACCAGGTCATAGCCGCG

altered cDNA sequence snippet

TAGTGCCCTCTATTCCCACCGTGAACCAGGTCATAGCCGCG

wildtype AA sequence

MAKHGADEPS SRSGSPDREG RASEDRSLLH QRLAVRELID TEVSYLHMLQ LCASDIRSRL
QQLPQGDLDV LFSNIDDIIK VNSRFLHDLQ ETASKEEEQV QLVGNIFLEF QEELEQVYKV
YCASYDQALL LVDTYRKEPE LQRHIQGIVE AVVPQAGSSG LSFLLVIPLQ RITRYPLLLQ
KILENTVPDA SAYPVLQRAV SALQDVNTNI NEYKMRKEVA SKYTKVEQLT LRERLARINT
HTLSKKTTRL SQLLKQEAGL IPRTEDKEFD DLEERFQWVS LCVTELKNNV AAYLDNLQAF
LYFRPHEYNL DIPEGPAVQY CNLARDLHLE AFLKFKQRLE GLVWQPLCSL AKALLGPQNL
IKKRLDKLLD FERVEEKLLE VGSVTYQEEA ARHTYQALNS LLVAELPQFN QLVMQWLGQI
MCTFVTLQRD LAKQVLQRAE GSMAQLPHHH VPEPAFRKLV EDALGRTSNQ LRSFQETFEK
VQPPPTTQPL LPGSERQVQA LLSRYGPGKL YQVTSNISGT GTLDLTLPRG QIVAILQNKD
TKGNSGRWLV DTGGHRGYVP AGKLQLYHVV PSAEELRRQA GLNKDPRCLT PEPSPALVPS
IPTMNQVIAA YPFVARSSHE VSLQAGQPVT ILEAQDKKGN PEWSLVEVNG QRGYVPSGFL
ARARSPVLWG WSLPS*

mutated AA sequence

MAKHGADEPS SRSGSPDREG RASEDRSLLH QRLAVRELID TEVSYLHMLQ LCASDIRSRL
QQLPQGDLDV LFSNIDDIIK VNSRFLHDLQ ETASKEEEQV QLVGNIFLEF QEELEQVYKV
YCASYDQALL LVDTYRKEPE LQRHIQGIVE AVVPQAGSSG LSFLLVIPLQ RITRYPLLLQ
KILENTVPDA SAYPVLQRAV SALQDVNTNI NEYKMRKEVA SKYTKVEQLT LRERLARINT
HTLSKKTTRL SQLLKQEAGL IPRTEDKEFD DLEERFQWVS LCVTELKNNV AAYLDNLQAF
LYFRPHEYNL DIPEGPAVQY CNLARDLHLE AFLKFKQRLE GLVWQPLCSL AKALLGPQNL
IKKRLDKLLD FERVEEKLLE VGSVTYQEEA ARHTYQALNS LLVAELPQFN QLVMQWLGQI
MCTFVTLQRD LAKQVLQRAE GSMAQLPHHH VPEPAFRKLV EDALGRTSNQ LRSFQETFEK
VQPPPTTQPL LPGSERQVQA LLSRYGPGKL YQVTSNISGT GTLDLTLPRG QIVAILQNKD
TKGNSGRWLV DTGGHRGYVP AGKLQLYHVV PSAEELRRQA GLNKDPRCLT PEPSPALVPS
IPTVNQVIAA YPFVARSSHE VSLQAGQPVT ILEAQDKKGN PEWSLVEVNG QRGYVPSGFL
ARARSPVLWG WSLPS*

speed

1.35 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems