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: ENST00000361070
Querying Taster for transcript #2: ENST00000571750
MT speed 1.51 s - this script 3.498927 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RFWD3	polymorphism_automatic	0.907545471643751	simple_aae		affected		I564V	single base exchange	rs7193541		show file
RFWD3	polymorphism_automatic	0.907545471643751	simple_aae		affected		I564V	single base exchange	rs7193541		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0924545283562487 (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)

chr16:74664743T>CN/A show variant in all transcripts IGV

HGNC symbol

RFWD3

Ensembl transcript ID

ENST00000571750

Genbank transcript ID

N/A

UniProt peptide

Q6PCD5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1690A>G
cDNA.1899A>G
g.36037A>G

AA changes

I564V Score: 29 explain score(s)

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

564

frameshift

known variant

Reference ID: rs7193541

database	homozygous (C/C)	heterozygous	allele carriers
1000G	429	1109	1538
ExAC	9367	14033	23400

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.69	0.99
	1.585	0.93
(flanking)	-0.986	0.23

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	36042	wt: 0.46 / mu: 0.55	wt: CTGGCCAATGGTTCAATTCTGGTATATGACGTGCGAAACAC mu: CTGGCCAATGGTTCAGTTCTGGTATATGACGTGCGAAACAC	tctg\|GTAT
Acc increased	36046	wt: 0.33 / mu: 0.49	wt: CCAATGGTTCAATTCTGGTATATGACGTGCGAAACACGAGC mu: CCAATGGTTCAGTTCTGGTATATGACGTGCGAAACACGAGC	gtat\|ATGA
Acc marginally increased	36048	wt: 0.7956 / mu: 0.8360 (marginal change - not scored)	wt: AATGGTTCAATTCTGGTATATGACGTGCGAAACACGAGCAG mu: AATGGTTCAGTTCTGGTATATGACGTGCGAAACACGAGCAG	atat\|GACG
Donor gained	36031	0.90	mu: CCAATGGTTCAGTTC	AATG\|gttc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

564

mutated

all conserved

564

Ptroglodytes

all identical

ENSPTRG00000008348

563

Mmulatta

all identical

ENSMMUG00000008375

559

Fcatus

not conserved

ENSFCAG00000015146

547

Mmusculus

all identical

ENSMUSG00000033596

564

Ggallus

all identical

ENSGALG00000002755

414

Trubripes

all conserved

ENSTRUG00000016541

306

Drerio

all conserved

ENSDARG00000087752

420

Dmelanogaster

all conserved

FBgn0036660

402

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000007674

432

protein features

start (aa)	end (aa)	feature	details
539	577	REPEAT	WD 2.	lost
583	628	REPEAT	WD 3.	might get lost (downstream of altered splice site)
597	597	CONFLICT	A -> V (in Ref. 1; BAA91662).	might get lost (downstream of altered splice site)
741	741	CONFLICT	Q -> R (in Ref. 1; BAB14169).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2325 / 2325

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

775 / 775

position of stopcodon in wt / mu cDNA

2534 / 2534

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

210 / 210

chromosome

strand

-1

last intron/exon boundary

2391

theoretical NMD boundary in CDS

2131

length of CDS

2325

coding sequence (CDS) position

1690

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

1899

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

36037

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

74664743

original gDNA sequence snippet

CTGGACTGGCCAATGGTTCAATTCTGGTATATGACGTGCGA

altered gDNA sequence snippet

CTGGACTGGCCAATGGTTCAGTTCTGGTATATGACGTGCGA

original cDNA sequence snippet

CTGGACTGGCCAATGGTTCAATTCTGGTATATGACGTGCGA

altered cDNA sequence snippet

CTGGACTGGCCAATGGTTCAGTTCTGGTATATGACGTGCGA

wildtype AA sequence

MAHEAMEYDV QVQLNHAEQQ PAPAGMASSQ GGPALLQPVP ADVVSSQGVP SILQPAPAEV
ISSQATPPLL QPAPQLSVDL TEVEVLGEDT VENINPRTSE QHRQGSDGNH TIPASSLHSM
TNFISGLQRL HGMLEFLRPS SSNHSVGPMR TRRRVSASRR ARAGGSQRTD SARLRAPLDA
YFQVSRTQPD LPATTYDSET RNPVSEELQV SSSSDSDSDS SAEYGGVVDQ AEESGAVILE
EQLAGVSAEQ EVTCIDGGKT LPKQPSPQKS EPLLPSASMD EEEGDTCTIC LEQWTNAGDH
RLSALRCGHL FGYRCISTWL KGQVRKCPQC NKKARHSDIV VLYARTLRAL DTSEQERMKS
SLLKEQMLRK QAELESAQCR LQLQVLTDKC TRLQRRVQDL QKLTSHQSQN LQQPRGSQAW
VLSCSPSSQG QHKHKYHFQK TFTVSQAGNC RIMAYCDALS CLVISQPSPQ ASFLPGFGVK
MLSTANMKSS QYIPMHGKQI RGLAFSSYLR GLLLSASLDN TIKLTSLETN TVVQTYNAGR
PVWSCCWCLD EANYIYAGLA NGSILVYDVR NTSSHVQELV AQKARCPLVS LSYMPRAASA
AFPYGGVLAG TLEDASFWEQ KMDFSHWPHV LPLEPGGCID FQTENSSRHC LVTYRPDKNH
TTIRSVLMEM SYRLDDTGNP ICSCQPVHTF FGGPTCKLLT KNAIFQSPEN DGNILVCTGD
EAANSALLWD AASGSLLQDL QTDQPVLDIC PFEVNRNSYL ATLTEKMVHI YKWE*

mutated AA sequence

MAHEAMEYDV QVQLNHAEQQ PAPAGMASSQ GGPALLQPVP ADVVSSQGVP SILQPAPAEV
ISSQATPPLL QPAPQLSVDL TEVEVLGEDT VENINPRTSE QHRQGSDGNH TIPASSLHSM
TNFISGLQRL HGMLEFLRPS SSNHSVGPMR TRRRVSASRR ARAGGSQRTD SARLRAPLDA
YFQVSRTQPD LPATTYDSET RNPVSEELQV SSSSDSDSDS SAEYGGVVDQ AEESGAVILE
EQLAGVSAEQ EVTCIDGGKT LPKQPSPQKS EPLLPSASMD EEEGDTCTIC LEQWTNAGDH
RLSALRCGHL FGYRCISTWL KGQVRKCPQC NKKARHSDIV VLYARTLRAL DTSEQERMKS
SLLKEQMLRK QAELESAQCR LQLQVLTDKC TRLQRRVQDL QKLTSHQSQN LQQPRGSQAW
VLSCSPSSQG QHKHKYHFQK TFTVSQAGNC RIMAYCDALS CLVISQPSPQ ASFLPGFGVK
MLSTANMKSS QYIPMHGKQI RGLAFSSYLR GLLLSASLDN TIKLTSLETN TVVQTYNAGR
PVWSCCWCLD EANYIYAGLA NGSVLVYDVR NTSSHVQELV AQKARCPLVS LSYMPRAASA
AFPYGGVLAG TLEDASFWEQ KMDFSHWPHV LPLEPGGCID FQTENSSRHC LVTYRPDKNH
TTIRSVLMEM SYRLDDTGNP ICSCQPVHTF FGGPTCKLLT KNAIFQSPEN DGNILVCTGD
EAANSALLWD AASGSLLQDL QTDQPVLDIC PFEVNRNSYL ATLTEKMVHI YKWE*

speed

0.87 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: 0.0924545283562486 (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)

chr16:74664743T>CN/A show variant in all transcripts IGV

HGNC symbol

RFWD3

Ensembl transcript ID

ENST00000361070

Genbank transcript ID

NM_018124

UniProt peptide

Q6PCD5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1690A>G
cDNA.1788A>G
g.36037A>G

AA changes

I564V Score: 29 explain score(s)

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

564

frameshift

known variant

Reference ID: rs7193541

database	homozygous (C/C)	heterozygous	allele carriers
1000G	429	1109	1538
ExAC	9367	14033	23400

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.69	0.99
	1.585	0.93
(flanking)	-0.986	0.23

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	36042	wt: 0.46 / mu: 0.55	wt: CTGGCCAATGGTTCAATTCTGGTATATGACGTGCGAAACAC mu: CTGGCCAATGGTTCAGTTCTGGTATATGACGTGCGAAACAC	tctg\|GTAT
Acc increased	36046	wt: 0.33 / mu: 0.49	wt: CCAATGGTTCAATTCTGGTATATGACGTGCGAAACACGAGC mu: CCAATGGTTCAGTTCTGGTATATGACGTGCGAAACACGAGC	gtat\|ATGA
Acc marginally increased	36048	wt: 0.7956 / mu: 0.8360 (marginal change - not scored)	wt: AATGGTTCAATTCTGGTATATGACGTGCGAAACACGAGCAG mu: AATGGTTCAGTTCTGGTATATGACGTGCGAAACACGAGCAG	atat\|GACG
Donor gained	36031	0.90	mu: CCAATGGTTCAGTTC	AATG\|gttc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

564

mutated

all conserved

564

Ptroglodytes

all identical

ENSPTRG00000008348

563

Mmulatta

all identical

ENSMMUG00000008375

559

Fcatus

not conserved

ENSFCAG00000015146

547

Mmusculus

all identical

ENSMUSG00000033596

564

Ggallus

all identical

ENSGALG00000002755

414

Trubripes

all conserved

ENSTRUG00000016541

306

Drerio

all conserved

ENSDARG00000087752

420

Dmelanogaster

all conserved

FBgn0036660

402

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000007674

432

protein features

start (aa)	end (aa)	feature	details
539	577	REPEAT	WD 2.	lost
583	628	REPEAT	WD 3.	might get lost (downstream of altered splice site)
597	597	CONFLICT	A -> V (in Ref. 1; BAA91662).	might get lost (downstream of altered splice site)
741	741	CONFLICT	Q -> R (in Ref. 1; BAB14169).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2325 / 2325

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

775 / 775

position of stopcodon in wt / mu cDNA

2423 / 2423

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

99 / 99

chromosome

strand

-1

last intron/exon boundary

2280

theoretical NMD boundary in CDS

2131

length of CDS

2325

coding sequence (CDS) position

1690

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

1788

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

36037

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

74664743

original gDNA sequence snippet

CTGGACTGGCCAATGGTTCAATTCTGGTATATGACGTGCGA

altered gDNA sequence snippet

CTGGACTGGCCAATGGTTCAGTTCTGGTATATGACGTGCGA

original cDNA sequence snippet

CTGGACTGGCCAATGGTTCAATTCTGGTATATGACGTGCGA

altered cDNA sequence snippet

CTGGACTGGCCAATGGTTCAGTTCTGGTATATGACGTGCGA

wildtype AA sequence

mutated AA sequence

MAHEAMEYDV QVQLNHAEQQ PAPAGMASSQ GGPALLQPVP ADVVSSQGVP SILQPAPAEV
ISSQATPPLL QPAPQLSVDL TEVEVLGEDT VENINPRTSE QHRQGSDGNH TIPASSLHSM
TNFISGLQRL HGMLEFLRPS SSNHSVGPMR TRRRVSASRR ARAGGSQRTD SARLRAPLDA
YFQVSRTQPD LPATTYDSET RNPVSEELQV SSSSDSDSDS SAEYGGVVDQ AEESGAVILE
EQLAGVSAEQ EVTCIDGGKT LPKQPSPQKS EPLLPSASMD EEEGDTCTIC LEQWTNAGDH
RLSALRCGHL FGYRCISTWL KGQVRKCPQC NKKARHSDIV VLYARTLRAL DTSEQERMKS
SLLKEQMLRK QAELESAQCR LQLQVLTDKC TRLQRRVQDL QKLTSHQSQN LQQPRGSQAW
VLSCSPSSQG QHKHKYHFQK TFTVSQAGNC RIMAYCDALS CLVISQPSPQ ASFLPGFGVK
MLSTANMKSS QYIPMHGKQI RGLAFSSYLR GLLLSASLDN TIKLTSLETN TVVQTYNAGR
PVWSCCWCLD EANYIYAGLA NGSVLVYDVR NTSSHVQELV AQKARCPLVS LSYMPRAASA
AFPYGGVLAG TLEDASFWEQ KMDFSHWPHV LPLEPGGCID FQTENSSRHC LVTYRPDKNH
TTIRSVLMEM SYRLDDTGNP ICSCQPVHTF FGGPTCKLLT KNAIFQSPEN DGNILVCTGD
EAANSALLWD AASGSLLQDL QTDQPVLDIC PFEVNRNSYL ATLTEKMVHI YKWE*

speed

0.64 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems