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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000458385
Querying Taster for transcript #2: ENST00000514798
Querying Taster for transcript #3: ENST00000296775
MT speed 0 s - this script 3.555363 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CFAP97	polymorphism_automatic	2.90401036551202e-12	simple_aae		affected		T238A	single base exchange	rs1133657		show file
CFAP97	polymorphism_automatic	2.90401036551202e-12	simple_aae		affected		T238A	single base exchange	rs1133657		show file
CFAP97	polymorphism_automatic	2.90401036551202e-12	simple_aae		affected		T238A	single base exchange	rs1133657		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997096 (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)

chr4:186111639T>CN/A show variant in all transcripts IGV

HGNC symbol

CFAP97

Ensembl transcript ID

ENST00000458385

Genbank transcript ID

NM_020827

UniProt peptide

Q9P2B7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.712A>G
cDNA.832A>G
g.19020A>G

AA changes

T238A Score: 58 explain score(s)

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

238

frameshift

known variant

Reference ID: rs1133657

database	homozygous (C/C)	heterozygous	allele carriers
1000G	501	1154	1655
ExAC	14167	4433	18600

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.558	0.004
	1.777	0.007
(flanking)	-0.198	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	19014	0.85	mu: CTTCAAGTACTGCAC	TCAA\|gtac

distance from splice site

343

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

all identical

ENSPTRG00000016647

237

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000031631

250

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000056381

218

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000034114

208

protein features

start (aa)	end (aa)	feature	details
170	236	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
374	450	COILED	Potential.	might get lost (downstream of altered splice site)
512	512	CONFLICT	D -> T (in Ref. 4; AAH30535).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1599 / 1599

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

533 / 533

position of stopcodon in wt / mu cDNA

1719 / 1719

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

121 / 121

chromosome

strand

-1

last intron/exon boundary

1592

theoretical NMD boundary in CDS

1421

length of CDS

1599

coding sequence (CDS) position

712

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

832

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

19020

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

186111639

original gDNA sequence snippet

AAACACAGCCTTCAAGTACTACACCAAAATGTGGCCACTAC

altered gDNA sequence snippet

AAACACAGCCTTCAAGTACTGCACCAAAATGTGGCCACTAC

original cDNA sequence snippet

AAACACAGCCTTCAAGTACTACACCAAAATGTGGCCACTAC

altered cDNA sequence snippet

AAACACAGCCTTCAAGTACTGCACCAAAATGTGGCCACTAC

wildtype AA sequence

MDQFGDILEG EVDHSFFDSD FEEGKKCETN SVFDKQNDDP KERIDKDTKN VNSNTGMQTT
ENYLTEKGNE RNVKFPPEHP VENDVTQTVS SFSLPASSRS KKLCDVTTGL KIHVSIPNRI
PKIVKEGEDD YYTDGEESSD DGKKYHVKSK SAKPSTNVKK SIRKKYCKVS SSSSSSLSSS
SSGSGTDCLD AGSDSHLSDS SPSSKSSKKH VSGITLLSPK HKYKSGIKST ETQPSSTTPK
CGHYPEESED TVTDVSPLST PDISPLQSFE LGIANDQKVK IKKQENVSQE IYEDVEDLKN
NSKYLKAAKK GKEKHEPDVS SKSSSVLDSS LDHRHKQKVL HDTMDLNHLL KAFLQLDKKG
PQKHHFDQPS VAPGKNYSFT REEVRQIDRE NQRLLKELSR QAEKPGSKST IPRSADHPPK
LYHSALNRQK EQQRIERENL ALLKRLEAVK PTVGMKRSEQ LMDYHRNMGY LNSSPLSRRA
RSTLGQYSPL RASRTSSATS GLSCRSERSA VDPSSGHPRR RPKPPNVRTA WL*

mutated AA sequence

MDQFGDILEG EVDHSFFDSD FEEGKKCETN SVFDKQNDDP KERIDKDTKN VNSNTGMQTT
ENYLTEKGNE RNVKFPPEHP VENDVTQTVS SFSLPASSRS KKLCDVTTGL KIHVSIPNRI
PKIVKEGEDD YYTDGEESSD DGKKYHVKSK SAKPSTNVKK SIRKKYCKVS SSSSSSLSSS
SSGSGTDCLD AGSDSHLSDS SPSSKSSKKH VSGITLLSPK HKYKSGIKST ETQPSSTAPK
CGHYPEESED TVTDVSPLST PDISPLQSFE LGIANDQKVK IKKQENVSQE IYEDVEDLKN
NSKYLKAAKK GKEKHEPDVS SKSSSVLDSS LDHRHKQKVL HDTMDLNHLL KAFLQLDKKG
PQKHHFDQPS VAPGKNYSFT REEVRQIDRE NQRLLKELSR QAEKPGSKST IPRSADHPPK
LYHSALNRQK EQQRIERENL ALLKRLEAVK PTVGMKRSEQ LMDYHRNMGY LNSSPLSRRA
RSTLGQYSPL RASRTSSATS GLSCRSERSA VDPSSGHPRR RPKPPNVRTA WL*

speed

0.75 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: 0.999999999997096 (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)

chr4:186111639T>CN/A show variant in all transcripts IGV

HGNC symbol

CFAP97

Ensembl transcript ID

ENST00000514798

Genbank transcript ID

N/A

UniProt peptide

Q9P2B7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.712A>G
cDNA.972A>G
g.19020A>G

AA changes

T238A Score: 58 explain score(s)

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

238

frameshift

known variant

Reference ID: rs1133657

database	homozygous (C/C)	heterozygous	allele carriers
1000G	501	1154	1655
ExAC	14167	4433	18600

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.558	0.004
	1.777	0.007
(flanking)	-0.198	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	19014	0.85	mu: CTTCAAGTACTGCAC	TCAA\|gtac

distance from splice site

343

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

all identical

ENSPTRG00000016647

237

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000031631

250

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000056381

218

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000034114

208

protein features

start (aa)	end (aa)	feature	details
170	236	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
374	450	COILED	Potential.	might get lost (downstream of altered splice site)
512	512	CONFLICT	D -> T (in Ref. 4; AAH30535).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1362 / 1362

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

454 / 454

position of stopcodon in wt / mu cDNA

1622 / 1622

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

261 / 261

chromosome

strand

-1

last intron/exon boundary

1581

theoretical NMD boundary in CDS

1270

length of CDS

1362

coding sequence (CDS) position

712

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

972

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

19020

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

186111639

original gDNA sequence snippet

AAACACAGCCTTCAAGTACTACACCAAAATGTGGCCACTAC

altered gDNA sequence snippet

AAACACAGCCTTCAAGTACTGCACCAAAATGTGGCCACTAC

original cDNA sequence snippet

AAACACAGCCTTCAAGTACTACACCAAAATGTGGCCACTAC

altered cDNA sequence snippet

AAACACAGCCTTCAAGTACTGCACCAAAATGTGGCCACTAC

wildtype AA sequence

mutated AA sequence

MDQFGDILEG EVDHSFFDSD FEEGKKCETN SVFDKQNDDP KERIDKDTKN VNSNTGMQTT
ENYLTEKGNE RNVKFPPEHP VENDVTQTVS SFSLPASSRS KKLCDVTTGL KIHVSIPNRI
PKIVKEGEDD YYTDGEESSD DGKKYHVKSK SAKPSTNVKK SIRKKYCKVS SSSSSSLSSS
SSGSGTDCLD AGSDSHLSDS SPSSKSSKKH VSGITLLSPK HKYKSGIKST ETQPSSTAPK
CGHYPEESED TVTDVSPLST PDISPLQSFE LGIANDQKVK IKKQENVSQE IYEDVEDLKN
NSKYLKAAKK GKEKHEPDVS SKSSSVLDSS LDHRHKQKVL HDTMDLNHLL KAFLQLDKKG
PQKHHFDQPS VAPGKNYSFT REEVRQIDRE NQRLLKELSR QAEKPGSKST IPRSADHPPK
LYHSALNRQK EQQRIERENL TISLCHPGWS AVT*

speed

0.68 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997096 (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)

chr4:186111639T>CN/A show variant in all transcripts IGV

HGNC symbol

CFAP97

Ensembl transcript ID

ENST00000296775

Genbank transcript ID

N/A

UniProt peptide

Q9P2B7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.712A>G
cDNA.859A>G
g.19020A>G

AA changes

T238A Score: 58 explain score(s)

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

238

frameshift

known variant

Reference ID: rs1133657

database	homozygous (C/C)	heterozygous	allele carriers
1000G	501	1154	1655
ExAC	14167	4433	18600

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.558	0.004
	1.777	0.007
(flanking)	-0.198	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	19014	0.85	mu: CTTCAAGTACTGCAC	TCAA\|gtac

distance from splice site

343

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

all identical

ENSPTRG00000016647

237

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000031631

250

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000056381

218

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000034114

208

protein features

start (aa)	end (aa)	feature	details
170	236	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
374	450	COILED	Potential.	might get lost (downstream of altered splice site)
512	512	CONFLICT	D -> T (in Ref. 4; AAH30535).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1362 / 1362

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

454 / 454

position of stopcodon in wt / mu cDNA

1509 / 1509

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

148 / 148

chromosome

strand

-1

last intron/exon boundary

1468

theoretical NMD boundary in CDS

1270

length of CDS

1362

coding sequence (CDS) position

712

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

859

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

19020

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

186111639

original gDNA sequence snippet

AAACACAGCCTTCAAGTACTACACCAAAATGTGGCCACTAC

altered gDNA sequence snippet

AAACACAGCCTTCAAGTACTGCACCAAAATGTGGCCACTAC

original cDNA sequence snippet

AAACACAGCCTTCAAGTACTACACCAAAATGTGGCCACTAC

altered cDNA sequence snippet

AAACACAGCCTTCAAGTACTGCACCAAAATGTGGCCACTAC

wildtype AA sequence

mutated AA sequence

MDQFGDILEG EVDHSFFDSD FEEGKKCETN SVFDKQNDDP KERIDKDTKN VNSNTGMQTT
ENYLTEKGNE RNVKFPPEHP VENDVTQTVS SFSLPASSRS KKLCDVTTGL KIHVSIPNRI
PKIVKEGEDD YYTDGEESSD DGKKYHVKSK SAKPSTNVKK SIRKKYCKVS SSSSSSLSSS
SSGSGTDCLD AGSDSHLSDS SPSSKSSKKH VSGITLLSPK HKYKSGIKST ETQPSSTAPK
CGHYPEESED TVTDVSPLST PDISPLQSFE LGIANDQKVK IKKQENVSQE IYEDVEDLKN
NSKYLKAAKK GKEKHEPDVS SKSSSVLDSS LDHRHKQKVL HDTMDLNHLL KAFLQLDKKG
PQKHHFDQPS VAPGKNYSFT REEVRQIDRE NQRLLKELSR QAEKPGSKST IPRSADHPPK
LYHSALNRQK EQQRIERENL TISLCHPGWS AVT*

speed

0.74 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems