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: ENST00000259008
Querying Taster for transcript #2: ENST00000577598
MT speed 2.04 s - this script 4.028499 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BRIP1	disease_causing	0.999999770142051	simple_aae				P47A	single base exchange	rs28903098		show file
BRIP1	disease_causing	0.999999770142051	simple_aae				P47A	single base exchange	rs28903098		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999770142051 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014756)
known disease mutation at this position (HGMD CM1617603)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:59937223G>CN/A show variant in all transcripts IGV

HGNC symbol

BRIP1

Ensembl transcript ID

ENST00000259008

Genbank transcript ID

NM_032043

UniProt peptide

Q9BX63

alteration type

single base exchange

alteration region

CDS

DNA changes

c.139C>G
cDNA.407C>G
g.3660C>G

AA changes

P47A Score: 27 explain score(s)

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

frameshift

known variant

Reference ID: rs28903098

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	1	27	28

known disease mutation at this position, please check HGMD for details (HGMD ID CM1617603)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1617603)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014756)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1617603)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014756)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014756)

regulatory features

H2AZ, Histone, Histone 2A variant Z
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.839	1
	4.839	1
(flanking)	0.15	0.997

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 marginally increased	3664	wt: 0.9345 / mu: 0.9703 (marginal change - not scored)	wt: TCCCACAGGAAGTGG mu: TGCCACAGGAAGTGG	CCAC\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000009493

Mmulatta

all identical

ENSMMUG00000009027

Fcatus

no alignment

ENSFCAG00000018470

n/a

Mmusculus

all identical

ENSMUSG00000034329

Ggallus

all identical

ENSGALG00000005279

Trubripes

no homologue

Drerio

all identical

ENSDARG00000074410

Dmelanogaster

no homologue

Celegans

all identical

F33H2.1

114

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
11	442	DOMAIN	Helicase ATP-binding.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3750 / 3750

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

1250 / 1250

position of stopcodon in wt / mu cDNA

4018 / 4018

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

269 / 269

chromosome

strand

-1

last intron/exon boundary

3174

theoretical NMD boundary in CDS

2855

length of CDS

3750

coding sequence (CDS) position

139

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

407

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

3660

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

59937223

original gDNA sequence snippet

AACATTGTTTGTTGGAGAGTCCCACAGGAAGTGGAAAAAGC

altered gDNA sequence snippet

AACATTGTTTGTTGGAGAGTGCCACAGGAAGTGGAAAAAGC

original cDNA sequence snippet

AACATTGTTTGTTGGAGAGTCCCACAGGAAGTGGAAAAAGC

altered cDNA sequence snippet

AACATTGTTTGTTGGAGAGTGCCACAGGAAGTGGAAAAAGC

wildtype AA sequence

MSSMWSEYTI GGVKIYFPYK AYPSQLAMMN SILRGLNSKQ HCLLESPTGS GKSLALLCSA
LAWQQSLSGK PADEGVSEKA EVQLSCCCAC HSKDFTNNDM NQGTSRHFNY PSTPPSERNG
TSSTCQDSPE KTTLAAKLSA KKQASIYRDE NDDFQVEKKR IRPLETTQQI RKRHCFGTEV
HNLDAKVDSG KTVKLNSPLE KINSFSPQKP PGHCSRCCCS TKQGNSQESS NTIKKDHTGK
SKIPKIYFGT RTHKQIAQIT RELRRTAYSG VPMTILSSRD HTCVHPEVVG NFNRNEKCME
LLDGKNGKSC YFYHGVHKIS DQHTLQTFQG MCKAWDIEEL VSLGKKLKAC PYYTARELIQ
DADIIFCPYN YLLDAQIRES MDLNLKEQVV ILDEAHNIED CARESASYSV TEVQLRFARD
ELDSMVNNNI RKKDHEPLRA VCCSLINWLE ANAEYLVERD YESACKIWSG NEMLLTLHKM
GITTATFPIL QGHFSAVLQK EEKISPIYGK EEAREVPVIS ASTQIMLKGL FMVLDYLFRQ
NSRFADDYKI AIQQTYSWTN QIDISDKNGL LVLPKNKKRS RQKTAVHVLN FWCLNPAVAF
SDINGKVQTI VLTSGTLSPM KSFSSELGVT FTIQLEANHI IKNSQVWVGT IGSGPKGRNL
CATFQNTETF EFQDEVGALL LSVCQTVSQG ILCFLPSYKL LEKLKERWLS TGLWHNLELV
KTVIVEPQGG EKTNFDELLQ VYYDAIKYKG EKDGALLVAV CRGKVSEGLD FSDDNARAVI
TIGIPFPNVK DLQVELKRQY NDHHSKLRGL LPGRQWYEIQ AYRALNQALG RCIRHRNDWG
ALILVDDRFR NNPSRYISGL SKWVRQQIQH HSTFESALES LAEFSKKHQK VLNVSIKDRT
NIQDNESTLE VTSLKYSTSP YLLEAASHLS PENFVEDEAK ICVQELQCPK IITKNSPLPS
SIISRKEKND PVFLEEAGKA EKIVISRSTS PTFNKQTKRV SWSSFNSLGQ YFTGKIPKAT
PELGSSENSA SSPPRFKTEK MESKTVLPFT DKCESSNLTV NTSFGSCPQS ETIISSLKID
ATLTRKNHSE HPLCSEEALD PDIELSLVSE EDKQSTSNRD FETEAEDESI YFTPELYDPE
DTDEEKNDLA ETDRGNRLAN NSDCILAKDL FEIRTIKEVD SAREVKAEDC IDTKLNGILH
IEESKIDDID GNVKTTWINE LELGKTHEIE IKNFKPSPSK NKGMFPGFK*

mutated AA sequence

MSSMWSEYTI GGVKIYFPYK AYPSQLAMMN SILRGLNSKQ HCLLESATGS GKSLALLCSA
LAWQQSLSGK PADEGVSEKA EVQLSCCCAC HSKDFTNNDM NQGTSRHFNY PSTPPSERNG
TSSTCQDSPE KTTLAAKLSA KKQASIYRDE NDDFQVEKKR IRPLETTQQI RKRHCFGTEV
HNLDAKVDSG KTVKLNSPLE KINSFSPQKP PGHCSRCCCS TKQGNSQESS NTIKKDHTGK
SKIPKIYFGT RTHKQIAQIT RELRRTAYSG VPMTILSSRD HTCVHPEVVG NFNRNEKCME
LLDGKNGKSC YFYHGVHKIS DQHTLQTFQG MCKAWDIEEL VSLGKKLKAC PYYTARELIQ
DADIIFCPYN YLLDAQIRES MDLNLKEQVV ILDEAHNIED CARESASYSV TEVQLRFARD
ELDSMVNNNI RKKDHEPLRA VCCSLINWLE ANAEYLVERD YESACKIWSG NEMLLTLHKM
GITTATFPIL QGHFSAVLQK EEKISPIYGK EEAREVPVIS ASTQIMLKGL FMVLDYLFRQ
NSRFADDYKI AIQQTYSWTN QIDISDKNGL LVLPKNKKRS RQKTAVHVLN FWCLNPAVAF
SDINGKVQTI VLTSGTLSPM KSFSSELGVT FTIQLEANHI IKNSQVWVGT IGSGPKGRNL
CATFQNTETF EFQDEVGALL LSVCQTVSQG ILCFLPSYKL LEKLKERWLS TGLWHNLELV
KTVIVEPQGG EKTNFDELLQ VYYDAIKYKG EKDGALLVAV CRGKVSEGLD FSDDNARAVI
TIGIPFPNVK DLQVELKRQY NDHHSKLRGL LPGRQWYEIQ AYRALNQALG RCIRHRNDWG
ALILVDDRFR NNPSRYISGL SKWVRQQIQH HSTFESALES LAEFSKKHQK VLNVSIKDRT
NIQDNESTLE VTSLKYSTSP YLLEAASHLS PENFVEDEAK ICVQELQCPK IITKNSPLPS
SIISRKEKND PVFLEEAGKA EKIVISRSTS PTFNKQTKRV SWSSFNSLGQ YFTGKIPKAT
PELGSSENSA SSPPRFKTEK MESKTVLPFT DKCESSNLTV NTSFGSCPQS ETIISSLKID
ATLTRKNHSE HPLCSEEALD PDIELSLVSE EDKQSTSNRD FETEAEDESI YFTPELYDPE
DTDEEKNDLA ETDRGNRLAN NSDCILAKDL FEIRTIKEVD SAREVKAEDC IDTKLNGILH
IEESKIDDID GNVKTTWINE LELGKTHEIE IKNFKPSPSK NKGMFPGFK*

speed

1.07 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

disease causing

Model: simple_aae, prob: 0.999999770142051 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014756)
known disease mutation at this position (HGMD CM1617603)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:59937223G>CN/A show variant in all transcripts IGV

HGNC symbol

BRIP1

Ensembl transcript ID

ENST00000577598

Genbank transcript ID

N/A

UniProt peptide

Q9BX63

alteration type

single base exchange

alteration region

CDS

DNA changes

c.139C>G
cDNA.139C>G
g.3660C>G

AA changes

P47A Score: 27 explain score(s)

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

frameshift

known variant

Reference ID: rs28903098

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	1	27	28

regulatory features

H2AZ, Histone, Histone 2A variant Z
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.839	1
	4.839	1
(flanking)	0.15	0.997

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 marginally increased	3664	wt: 0.9345 / mu: 0.9703 (marginal change - not scored)	wt: TCCCACAGGAAGTGG mu: TGCCACAGGAAGTGG	CCAC\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000009493

Mmulatta

all identical

ENSMMUG00000009027

Fcatus

no alignment

ENSFCAG00000018470

n/a

Mmusculus

all identical

ENSMUSG00000034329

Ggallus

all identical

ENSGALG00000005279

Trubripes

no homologue

Drerio

all identical

ENSDARG00000074410

Dmelanogaster

no homologue

Celegans

all identical

F33H2.1

114

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
11	442	DOMAIN	Helicase ATP-binding.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2985 / 2985

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

995 / 995

position of stopcodon in wt / mu cDNA

2985 / 2985

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

2576

theoretical NMD boundary in CDS

2525

length of CDS

2985

coding sequence (CDS) position

139

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

139

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

3660

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

59937223

original gDNA sequence snippet

AACATTGTTTGTTGGAGAGTCCCACAGGAAGTGGAAAAAGC

altered gDNA sequence snippet

AACATTGTTTGTTGGAGAGTGCCACAGGAAGTGGAAAAAGC

original cDNA sequence snippet

AACATTGTTTGTTGGAGAGTCCCACAGGAAGTGGAAAAAGC

altered cDNA sequence snippet

AACATTGTTTGTTGGAGAGTGCCACAGGAAGTGGAAAAAGC

wildtype AA sequence

mutated AA sequence

speed

0.97 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems