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 1.45 s - this script 3.634296 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BBS2	disease_causing	0.99999999818434	simple_aae		affected		R315W	single base exchange	rs121908178		show file
BBS2	disease_causing	0.99999999818434	simple_aae		affected		R315W	single base exchange	rs121908178		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999818434 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs4573 (probable pathogenic)
known disease mutation at this position (HGMD CM012905)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:56536366G>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.943C>T
cDNA.1364C>T
g.17830C>T

AA changes

R315W Score: 101 explain score(s)

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

315

frameshift

known variant

Reference ID: rs121908178

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known as potential disease variant: rs4573 (probable pathogenic for Bardet-Biedl syndrome 2|Bardet-Biedl syndrome|Autosomal recessive retinitis pigmentosa|Bardet-biedl syndrome 2/4, digenic) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012905)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012905)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012905)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.191	1
	4.521	1
(flanking)	0.224	0.997

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	17827.5	sequence motif lost	-	wt: ttca\|GTCC mu: ttca.GTCT
Acc marginally increased	17830	wt: 0.9870 / mu: 0.9880 (marginal change - not scored)	wt: TTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCACG mu: TTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCACG	gtcc\|GGGG
Acc marginally increased	17826	wt: 0.9953 / mu: 0.9960 (marginal change - not scored)	wt: GCGGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGG mu: GCGGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGG	ttca\|GTCC
Acc marginally increased	17832	wt: 0.9208 / mu: 0.9407 (marginal change - not scored)	wt: TTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCACGGC mu: TTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCACGGC	ccgg\|GGCT
Acc increased	17828	wt: 0.29 / mu: 0.60	wt: GGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCA mu: GGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCA	cagt\|CCGG
Acc marginally increased	17820	wt: 0.9407 / mu: 0.9452 (marginal change - not scored)	wt: ATACTTGCGGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCT mu: ATACTTGCGGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCT	cttc\|TGTT
Acc marginally increased	17823	wt: 0.9942 / mu: 0.9945 (marginal change - not scored)	wt: CTTGCGGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCC mu: CTTGCGGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCC	ctgt\|TCAG
Acc increased	17840	wt: 0.65 / mu: 0.78	wt: CTGTTCAGTCCGGGGCTACCTGCCTGGCACGGCTGAGATGA mu: CTGTTCAGTCTGGGGCTACCTGCCTGGCACGGCTGAGATGA	acct\|GCCT
Donor marginally increased	17833	wt: 0.2931 / mu: 0.3194 (marginal change - not scored)	wt: TCCGGGGCTACCTGC mu: TCTGGGGCTACCTGC	CGGG\|gcta
Donor increased	17826	wt: 0.56 / mu: 0.76	wt: TGTTCAGTCCGGGGC mu: TGTTCAGTCTGGGGC	TTCA\|gtcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

315

mutated

not conserved

315

Ptroglodytes

all identical

ENSPTRG00000008133

315

Mmulatta

all identical

ENSMMUG00000013268

315

Fcatus

all identical

ENSFCAG00000008671

315

Mmusculus

all identical

ENSMUSG00000031755

315

Ggallus

all identical

ENSGALG00000003043

315

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041621

315

Dmelanogaster

no homologue

Celegans

all conserved

F20D12.3

314

Xtropicalis

all identical

ENSXETG00000020021

315

protein features

start (aa)	end (aa)	feature	details
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

943

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

1364

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

17830

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

56536366

original gDNA sequence snippet

TTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCACG

altered gDNA sequence snippet

TTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCACG

original cDNA sequence snippet

GCTCAGTGGATGGGGAAATCCGGGGCTACCTGCCTGGCACG

altered cDNA sequence snippet

GCTCAGTGGATGGGGAAATCTGGGGCTACCTGCCTGGCACG

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 ISSPLAIIGG NCALQGFNHE GSDLFWTVTG DNVNSLALCD FDGDGKKELL
VGSEDFDIRV FKEDEIVAEM TETEIVTSLC PMYGSRFGYA LSNGTVGVYD KTSRYWRIKS
KNHAMSIHAF DLNSDGVNEL ITGWSNGKVD ARSDRTGEVI FKDNFSSAIA GVVEGDYRMD
GHIQLICCSV DGEIWGYLPG 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

0.75 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

disease causing

Model: simple_aae, prob: 0.99999999818434 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs4573 (probable pathogenic)
known disease mutation at this position (HGMD CM012905)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:56536366G>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.943C>T
cDNA.1122C>T
g.17830C>T

AA changes

R315W Score: 101 explain score(s)

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

315

frameshift

known variant

Reference ID: rs121908178

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.191	1
	4.521	1
(flanking)	0.224	0.997

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	17827.5	sequence motif lost	-	wt: ttca\|GTCC mu: ttca.GTCT
Acc marginally increased	17830	wt: 0.9870 / mu: 0.9880 (marginal change - not scored)	wt: TTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCACG mu: TTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCACG	gtcc\|GGGG
Acc marginally increased	17826	wt: 0.9953 / mu: 0.9960 (marginal change - not scored)	wt: GCGGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGG mu: GCGGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGG	ttca\|GTCC
Acc marginally increased	17832	wt: 0.9208 / mu: 0.9407 (marginal change - not scored)	wt: TTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCACGGC mu: TTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCACGGC	ccgg\|GGCT
Acc increased	17828	wt: 0.29 / mu: 0.60	wt: GGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCA mu: GGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCA	cagt\|CCGG
Acc marginally increased	17820	wt: 0.9407 / mu: 0.9452 (marginal change - not scored)	wt: ATACTTGCGGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCT mu: ATACTTGCGGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCT	cttc\|TGTT
Acc marginally increased	17823	wt: 0.9942 / mu: 0.9945 (marginal change - not scored)	wt: CTTGCGGTTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCC mu: CTTGCGGTTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCC	ctgt\|TCAG
Acc increased	17840	wt: 0.65 / mu: 0.78	wt: CTGTTCAGTCCGGGGCTACCTGCCTGGCACGGCTGAGATGA mu: CTGTTCAGTCTGGGGCTACCTGCCTGGCACGGCTGAGATGA	acct\|GCCT
Donor marginally increased	17833	wt: 0.2931 / mu: 0.3194 (marginal change - not scored)	wt: TCCGGGGCTACCTGC mu: TCTGGGGCTACCTGC	CGGG\|gcta
Donor increased	17826	wt: 0.56 / mu: 0.76	wt: TGTTCAGTCCGGGGC mu: TGTTCAGTCTGGGGC	TTCA\|gtcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

315

mutated

not conserved

315

Ptroglodytes

all identical

ENSPTRG00000008133

315

Mmulatta

all identical

ENSMMUG00000013268

315

Fcatus

all identical

ENSFCAG00000008671

315

Mmusculus

all identical

ENSMUSG00000031755

315

Ggallus

all identical

ENSGALG00000003043

315

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041621

315

Dmelanogaster

no homologue

Celegans

all conserved

F20D12.3

314

Xtropicalis

all identical

ENSXETG00000020021

315

protein features

start (aa)	end (aa)	feature	details
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

943

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

1122

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

17830

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

56536366

original gDNA sequence snippet

TTTTTTCCTTCTGTTCAGTCCGGGGCTACCTGCCTGGCACG

altered gDNA sequence snippet

TTTTTTCCTTCTGTTCAGTCTGGGGCTACCTGCCTGGCACG

original cDNA sequence snippet

GCTCAGTGGATGGGGAAATCCGGGGCTACCTGCCTGGCACG

altered cDNA sequence snippet

GCTCAGTGGATGGGGAAATCTGGGGCTACCTGCCTGGCACG

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 ISSPLAIIGG NCALQGFNHE GSDLFWTVTG DNVNSLALCD FDGDGKKELL
VGSEDFDIRV FKEDEIVAEM TETEIVTSLC PMYGSRFGYA LSNGTVGVYD KTSRYWRIKS
KNHAMSIHAF DLNSDGVNEL ITGWSNGKVD ARSDRTGEVI FKDNFSSAIA GVVEGDYRMD
GHIQLICCSV DGEIWGYLPG 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

0.70 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems