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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000270747
Querying Taster for transcript #2: ENST00000421561
MT speed 0 s - this script 4.299769 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARHGEF19	polymorphism_automatic	0.00162270671286202	simple_aae		affected		G163R	single base exchange	rs221058		show file
ARHGEF19	polymorphism_automatic	0.00162270671286202	simple_aae		affected		G163R	single base exchange	rs221058		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.998377293287138 (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)

chr1:16534646C>GN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF19

Ensembl transcript ID

ENST00000270747

Genbank transcript ID

NM_153213

UniProt peptide

Q8IW93

alteration type

single base exchange

alteration region

CDS

DNA changes

c.487G>C
cDNA.624G>C
g.4495G>C

AA changes

G163R Score: 125 explain score(s)

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

163

frameshift

known variant

Reference ID: rs221058

database	homozygous (G/G)	heterozygous	allele carriers
1000G	208	806	1014
ExAC	5079	22317	27396

regulatory features

Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.716	0.569
	0.465	0.549
(flanking)	0.267	0.537

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	4490	wt: 0.44 / mu: 0.54	wt: GGCCCACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGCAAG mu: GGCCCACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAG	taga\|GCCT
Acc marginally increased	4487	wt: 0.7923 / mu: 0.8231 (marginal change - not scored)	wt: CGAGGCCCACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGC mu: CGAGGCCCACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGC	tcct\|AGAG
Donor increased	4490	wt: 0.56 / mu: 0.89	wt: CCTAGAGCCTGGCCA mu: CCTAGAGCCTCGCCA	TAGA\|gcct
Donor increased	4500	wt: 0.42 / mu: 0.74	wt: GGCCAGGTAGTGCAA mu: CGCCAGGTAGTGCAA	CCAG\|gtag
Acc gained	4499	0.54	mu: TGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAGAGCAGGCCC	gcca\|GGTA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

163

mutated

not conserved

163

Ptroglodytes

all identical

ENSPTRG00000000223

163

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028919

161

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078853

278

PKPFLNP

EGVND

Dmelanogaster

no alignment

FBgn0261547

n/a

Celegans

no alignment

K07D4.7

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
376	560	DOMAIN	DH.	might get lost (downstream of altered splice site)
592	704	DOMAIN	PH.	might get lost (downstream of altered splice site)
715	776	DOMAIN	SH3.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2409 / 2409

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

803 / 803

position of stopcodon in wt / mu cDNA

2546 / 2546

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

138 / 138

chromosome

strand

-1

last intron/exon boundary

2389

theoretical NMD boundary in CDS

2201

length of CDS

2409

coding sequence (CDS) position

487

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

624

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

4495

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

16534646

original gDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGCAAGAGCAG

altered gDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAGAGCAG

original cDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGCAAGAGCAG

altered cDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAGAGCAG

wildtype AA sequence

MDCGPPATLQ PHLTGPPGTA HHPVAVCQQE SLSFAELPAL KPPSPVCLDL FPVAPEELRA
PGSRWSLGTP APLQGLLWPL SPGGSDTEIT SGGMRPSRAG SWPHCPGAQP PALEGPWSPR
HTQPQRRASH GSEKKSAWRK MRVYQREEVP GCPEAHAVFL EPGQVVQEQA LSTEEPRVEL
SGSTRVSLEG PERRRFSASE LMTRLHSSLR LGRNSAARAL ISGSGTGAAR EGKASGMEAR
SVEMSGDRVS RPAPGDSREG DWSEPRLDTQ EEPPLGSRST NERRQSRFLL NSVLYQEYSD
VASARELRRQ QREEEGPGDE AEGAEEGPGP PRANLSPSSS FRAQRSARGS TFSLWQDIPD
VRGSGVLATL SLRDCKLQEA KFELITSEAS YIHSLSVAVG HFLGSAELSE CLGAQDKQWL
FSKLPEVKST SERFLQDLEQ RLEADVLRFS VCDVVLDHCP AFRRVYLPYV TNQAYQERTY
QRLLLENPRF PGILARLEES PVCQRLPLTS FLILPFQRIT RLKMLVENIL KRTAQGSEDE
DMATKAFNAL KELVQECNAS VQSMKRTEEL IHLSKKIHFE GKIFPLISQA RWLVRHGELV
ELAPLPAAPP AKLKLSSKAV YLHLFNDCLL LSRRKELGKF AVFVHAKMAE LQVRDLSLKL
QGIPGHVFLL QLLHGQHMKH QFLLRARTES EKQRWISALC PSSPQEDKEV ISEGEDCPQV
QCVRTYKALH PDELTLEKTD ILSVRTWTSD GWLEGVRLAD GEKGWVPQAY VEEISSLSAR
LRNLRENKRV TSATSKLGEA PV*

mutated AA sequence

MDCGPPATLQ PHLTGPPGTA HHPVAVCQQE SLSFAELPAL KPPSPVCLDL FPVAPEELRA
PGSRWSLGTP APLQGLLWPL SPGGSDTEIT SGGMRPSRAG SWPHCPGAQP PALEGPWSPR
HTQPQRRASH GSEKKSAWRK MRVYQREEVP GCPEAHAVFL EPRQVVQEQA LSTEEPRVEL
SGSTRVSLEG PERRRFSASE LMTRLHSSLR LGRNSAARAL ISGSGTGAAR EGKASGMEAR
SVEMSGDRVS RPAPGDSREG DWSEPRLDTQ EEPPLGSRST NERRQSRFLL NSVLYQEYSD
VASARELRRQ QREEEGPGDE AEGAEEGPGP PRANLSPSSS FRAQRSARGS TFSLWQDIPD
VRGSGVLATL SLRDCKLQEA KFELITSEAS YIHSLSVAVG HFLGSAELSE CLGAQDKQWL
FSKLPEVKST SERFLQDLEQ RLEADVLRFS VCDVVLDHCP AFRRVYLPYV TNQAYQERTY
QRLLLENPRF PGILARLEES PVCQRLPLTS FLILPFQRIT RLKMLVENIL KRTAQGSEDE
DMATKAFNAL KELVQECNAS VQSMKRTEEL IHLSKKIHFE GKIFPLISQA RWLVRHGELV
ELAPLPAAPP AKLKLSSKAV YLHLFNDCLL LSRRKELGKF AVFVHAKMAE LQVRDLSLKL
QGIPGHVFLL QLLHGQHMKH QFLLRARTES EKQRWISALC PSSPQEDKEV ISEGEDCPQV
QCVRTYKALH PDELTLEKTD ILSVRTWTSD GWLEGVRLAD GEKGWVPQAY VEEISSLSAR
LRNLRENKRV TSATSKLGEA PV*

speed

1.21 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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.998377293287138 (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)

chr1:16534646C>GN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF19

Ensembl transcript ID

ENST00000421561

Genbank transcript ID

N/A

UniProt peptide

Q8IW93

alteration type

single base exchange

alteration region

CDS

DNA changes

c.487G>C
cDNA.660G>C
g.4495G>C

AA changes

G163R Score: 125 explain score(s)

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

163

frameshift

known variant

Reference ID: rs221058

database	homozygous (G/G)	heterozygous	allele carriers
1000G	208	806	1014
ExAC	5079	22317	27396

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.716	0.569
	0.465	0.549
(flanking)	0.267	0.537

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	4490	wt: 0.44 / mu: 0.54	wt: GGCCCACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGCAAG mu: GGCCCACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAG	taga\|GCCT
Acc marginally increased	4487	wt: 0.7923 / mu: 0.8231 (marginal change - not scored)	wt: CGAGGCCCACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGC mu: CGAGGCCCACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGC	tcct\|AGAG
Donor increased	4490	wt: 0.56 / mu: 0.89	wt: CCTAGAGCCTGGCCA mu: CCTAGAGCCTCGCCA	TAGA\|gcct
Donor increased	4500	wt: 0.42 / mu: 0.74	wt: GGCCAGGTAGTGCAA mu: CGCCAGGTAGTGCAA	CCAG\|gtag
Acc gained	4499	0.54	mu: TGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAGAGCAGGCCC	gcca\|GGTA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

163

mutated

not conserved

163

Ptroglodytes

all identical

ENSPTRG00000000223

163

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028919

161

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078853

278

PKPFLNP

EGVND

Dmelanogaster

no alignment

FBgn0261547

n/a

Celegans

no alignment

K07D4.7

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
376	560	DOMAIN	DH.	might get lost (downstream of altered splice site)
592	704	DOMAIN	PH.	might get lost (downstream of altered splice site)
715	776	DOMAIN	SH3.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1509 / 1509

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

503 / 503

position of stopcodon in wt / mu cDNA

1682 / 1682

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

174 / 174

chromosome

strand

-1

last intron/exon boundary

1625

theoretical NMD boundary in CDS

1401

length of CDS

1509

coding sequence (CDS) position

487

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

660

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

4495

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

16534646

original gDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGCAAGAGCAG

altered gDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAGAGCAG

original cDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTGGCCAGGTAGTGCAAGAGCAG

altered cDNA sequence snippet

ACGCTGTCTTCCTAGAGCCTCGCCAGGTAGTGCAAGAGCAG

wildtype AA sequence

mutated AA sequence

speed

1.09 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems