MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000568104
Querying Taster for transcript #2: ENST00000245157
MT speed 0 s - this script 2.511866 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BBS2	disease_causing_automatic	0.999999999999994	simple_aae		affected	0	G139V	single base exchange	rs121908181		show file
BBS2	disease_causing_automatic	0.999999999999994	simple_aae		affected	0	G139V	single base exchange	rs121908181		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999994 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM064993)
known disease mutation: rs4584 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:56545126C>AN/A show variant in all transcripts IGV

HGNC symbol

BBS2

Ensembl transcript ID

ENST00000568104

Genbank transcript ID

N/A

UniProt peptide

Q9BXC9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.416G>T
cDNA.595G>T
g.9070G>T

AA changes

G139V Score: 109 explain score(s)

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

139

frameshift

known variant

Reference ID: rs121908181
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4584 (pathogenic for Bardet-Biedl syndrome 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM064993)

known disease mutation at this position, please check HGMD for details (HGMD ID CM064993)
known disease mutation at this position, please check HGMD for details (HGMD ID CM064993)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.306	1
	6.182	1
(flanking)	6.182	1

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 marginally increased	9065	wt: 0.3290 / mu: 0.3545 (marginal change - not scored)	wt: ATTTCTTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCT mu: ATTTCTTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCT	gatt\|ATTG
Acc increased	9068	wt: 0.26 / mu: 0.58	wt: TCTTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCTGCA mu: TCTTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCA	tatt\|GGTG
Acc gained	9072	0.65	mu: CCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCAAGGT	gttg\|GCAA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

139

mutated

not conserved

139

Ptroglodytes

all identical

ENSPTRG00000008133

139

Mmulatta

all identical

ENSMMUG00000013268

139

Fcatus

not conserved

ENSFCAG00000008671

139

Mmusculus

all identical

ENSMUSG00000031755

139

Ggallus

all identical

ENSGALG00000003043

140

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041621

139

Dmelanogaster

no homologue

Celegans

all identical

F20D12.3

144

Xtropicalis

all identical

ENSXETG00000020021

139

protein features

start (aa)	end (aa)	feature	details
169	169	CONFLICT	C -> R (in Ref. 2; BAB55252).	might get lost (downstream of altered splice site)
325	369	COILED	Potential.	might get lost (downstream of altered splice site)
457	457	CONFLICT	L -> S (in Ref. 2; BAB55252).	might get lost (downstream of altered splice site)
648	648	CONFLICT	Y -> H (in Ref. 2; BAB55252).	might get lost (downstream of altered splice site)

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

2207 / 2207

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

180 / 180

chromosome

strand

-1

last intron/exon boundary

2101

theoretical NMD boundary in CDS

1871

length of CDS

2028

coding sequence (CDS) position

416

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

595

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

9070

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

56545126

original gDNA sequence snippet

TTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCTGCAAG

altered gDNA sequence snippet

TTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCAAG

original cDNA sequence snippet

TTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCTGCAAG

altered cDNA sequence snippet

TTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCAAG

wildtype AA sequence

MLLPVFTLKL RHKISPRMVA IGRYDGTHPC LAAATQTGKV FIHNPHTRNQ HVSASRVFQS
PLESDVSLLS INQAVSCLTA GVLNPELGYD ALLVGTQTNL LAYDVYNNSD LFYREVADGA
NAIVLGTLGD ISSPLAIIGG NCALQGFNHE GSDLFWTVTG DNVNSLALCD FDGDGKKELL
VGSEDFDIRV FKEDEIVAEM TETEIVTSLC PMYGSRFGYA LSNGTVGVYD KTSRYWRIKS
KNHAMSIHAF DLNSDGVNEL ITGWSNGKVD ARSDRTGEVI FKDNFSSAIA GVVEGDYRMD
GHIQLICCSV DGEIRGYLPG TAEMRGNLMD TSAEQDLIRE LSQKKQNLLL ELRNYEENAK
AELASPLNEA DGHRGIIPAN TRLHTTLSVS LGNETQTAHT ELRISTSNDT IIRAVLIFAE
GIFTGESHVV HPSIHNLSSS ICIPIVPPKD VPVDLHLKAF VGYRSSTQFH VFESTRQLPR
FSMYALTSLD PASEPISYVN FTIAERAQRV VVWLGQNFLL PEDTHIQNAP FQVCFTSLRN
GGHLHIKIKL SGEVDEYHSV HQKLSADMAD HSNLIRSLLV GAEDARLMRD MKTMKSRYME
LYDLNRDLLN GYKIRCNNHT ELLGNLKAVN QAIQRAGRLR VGKPKNQVIT ACRDAIRSNN
INTLFKIMRV GTASS*

mutated AA sequence

MLLPVFTLKL RHKISPRMVA IGRYDGTHPC LAAATQTGKV FIHNPHTRNQ HVSASRVFQS
PLESDVSLLS INQAVSCLTA GVLNPELGYD ALLVGTQTNL LAYDVYNNSD LFYREVADGA
NAIVLGTLGD ISSPLAIIVG NCALQGFNHE GSDLFWTVTG DNVNSLALCD FDGDGKKELL
VGSEDFDIRV FKEDEIVAEM TETEIVTSLC PMYGSRFGYA LSNGTVGVYD KTSRYWRIKS
KNHAMSIHAF DLNSDGVNEL ITGWSNGKVD ARSDRTGEVI FKDNFSSAIA GVVEGDYRMD
GHIQLICCSV DGEIRGYLPG TAEMRGNLMD TSAEQDLIRE LSQKKQNLLL ELRNYEENAK
AELASPLNEA DGHRGIIPAN TRLHTTLSVS LGNETQTAHT ELRISTSNDT IIRAVLIFAE
GIFTGESHVV HPSIHNLSSS ICIPIVPPKD VPVDLHLKAF VGYRSSTQFH VFESTRQLPR
FSMYALTSLD PASEPISYVN FTIAERAQRV VVWLGQNFLL PEDTHIQNAP FQVCFTSLRN
GGHLHIKIKL SGEVDEYHSV HQKLSADMAD HSNLIRSLLV GAEDARLMRD MKTMKSRYME
LYDLNRDLLN GYKIRCNNHT ELLGNLKAVN QAIQRAGRLR VGKPKNQVIT ACRDAIRSNN
INTLFKIMRV GTASS*

speed

0.29 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: 0.999999999999994 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM064993)
known disease mutation: rs4584 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:56545126C>AN/A show variant in all transcripts IGV

HGNC symbol

BBS2

Ensembl transcript ID

ENST00000245157

Genbank transcript ID

NM_031885

UniProt peptide

Q9BXC9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.416G>T
cDNA.837G>T
g.9070G>T

AA changes

G139V Score: 109 explain score(s)

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

139

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.306	1
	6.182	1
(flanking)	6.182	1

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 marginally increased	9065	wt: 0.3290 / mu: 0.3545 (marginal change - not scored)	wt: ATTTCTTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCT mu: ATTTCTTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCT	gatt\|ATTG
Acc increased	9068	wt: 0.26 / mu: 0.58	wt: TCTTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCTGCA mu: TCTTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCA	tatt\|GGTG
Acc gained	9072	0.65	mu: CCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCAAGGT	gttg\|GCAA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

139

mutated

not conserved

139

Ptroglodytes

all identical

ENSPTRG00000008133

139

Mmulatta

all identical

ENSMMUG00000013268

139

Fcatus

not conserved

ENSFCAG00000008671

139

Mmusculus

all identical

ENSMUSG00000031755

139

Ggallus

all identical

ENSGALG00000003043

140

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041621

139

Dmelanogaster

no homologue

Celegans

all identical

F20D12.3

144

Xtropicalis

all identical

ENSXETG00000020021

139

protein features

start (aa)	end (aa)	feature	details
169	169	CONFLICT	C -> R (in Ref. 2; BAB55252).	might get lost (downstream of altered splice site)
325	369	COILED	Potential.	might get lost (downstream of altered splice site)
457	457	CONFLICT	L -> S (in Ref. 2; BAB55252).	might get lost (downstream of altered splice site)
648	648	CONFLICT	Y -> H (in Ref. 2; BAB55252).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2166 / 2166

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

722 / 722

position of stopcodon in wt / mu cDNA

2587 / 2587

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

422 / 422

chromosome

strand

-1

last intron/exon boundary

2481

theoretical NMD boundary in CDS

2009

length of CDS

2166

coding sequence (CDS) position

416

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

837

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

9070

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

56545126

original gDNA sequence snippet

TTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCTGCAAG

altered gDNA sequence snippet

TTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCAAG

original cDNA sequence snippet

TTCCCCTCTTGCGATTATTGGTGGCAATTGTGCTCTGCAAG

altered cDNA sequence snippet

TTCCCCTCTTGCGATTATTGTTGGCAATTGTGCTCTGCAAG

wildtype AA sequence

MLLPVFTLKL RHKISPRMVA IGRYDGTHPC LAAATQTGKV FIHNPHTRNQ HVSASRVFQS
PLESDVSLLS INQAVSCLTA GVLNPELGYD ALLVGTQTNL LAYDVYNNSD LFYREVADGA
NAIVLGTLGD ISSPLAIIGG NCALQGFNHE GSDLFWTVTG DNVNSLALCD FDGDGKKELL
VGSEDFDIRV FKEDEIVAEM TETEIVTSLC PMYGSRFGYA LSNGTVGVYD KTSRYWRIKS
KNHAMSIHAF DLNSDGVNEL ITGWSNGKVD ARSDRTGEVI FKDNFSSAIA GVVEGDYRMD
GHIQLICCSV DGEIRGYLPG TAEMRGNLMD TSAEQDLIRE LSQKKQNLLL ELRNYEENAK
AELASPLNEA DGHRGIIPAN TRLHTTLSVS LGNETQTAHT ELRISTSNDT IIRAVLIFAE
GIFTGESHVV HPSIHNLSSS ICIPIVPPKD VPVDLHLKAF VGYRSSTQFH VFESTRQLPR
FSMYALTSLD PASEPISYVN FTIAERAQRV VVWLGQNFLL PEDTHIQNAP FQVCFTSLRN
GGHLHIKIKL SGEITINTDD IDLAGDIIQS MASFFAIEDL QVEADFPVYF EELRKVLVKV
DEYHSVHQKL SADMADHSNL IRSLLVGAED ARLMRDMKTM KSRYMELYDL NRDLLNGYKI
RCNNHTELLG NLKAVNQAIQ RAGRLRVGKP KNQVITACRD AIRSNNINTL FKIMRVGTAS
S*

mutated AA sequence

MLLPVFTLKL RHKISPRMVA IGRYDGTHPC LAAATQTGKV FIHNPHTRNQ HVSASRVFQS
PLESDVSLLS INQAVSCLTA GVLNPELGYD ALLVGTQTNL LAYDVYNNSD LFYREVADGA
NAIVLGTLGD ISSPLAIIVG NCALQGFNHE GSDLFWTVTG DNVNSLALCD FDGDGKKELL
VGSEDFDIRV FKEDEIVAEM TETEIVTSLC PMYGSRFGYA LSNGTVGVYD KTSRYWRIKS
KNHAMSIHAF DLNSDGVNEL ITGWSNGKVD ARSDRTGEVI FKDNFSSAIA GVVEGDYRMD
GHIQLICCSV DGEIRGYLPG TAEMRGNLMD TSAEQDLIRE LSQKKQNLLL ELRNYEENAK
AELASPLNEA DGHRGIIPAN TRLHTTLSVS LGNETQTAHT ELRISTSNDT IIRAVLIFAE
GIFTGESHVV HPSIHNLSSS ICIPIVPPKD VPVDLHLKAF VGYRSSTQFH VFESTRQLPR
FSMYALTSLD PASEPISYVN FTIAERAQRV VVWLGQNFLL PEDTHIQNAP FQVCFTSLRN
GGHLHIKIKL SGEITINTDD IDLAGDIIQS MASFFAIEDL QVEADFPVYF EELRKVLVKV
DEYHSVHQKL SADMADHSNL IRSLLVGAED ARLMRDMKTM KSRYMELYDL NRDLLNGYKI
RCNNHTELLG NLKAVNQAIQ RAGRLRVGKP KNQVITACRD AIRSNNINTL FKIMRVGTAS
S*

speed

0.27 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems