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: ENST00000264499
Querying Taster for transcript #2: ENST00000506636
MT speed 0 s - this script 3.485705 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BBS7	disease_causing_automatic	0.999999999945467	simple_aae		affected	0	T211I	single base exchange	rs119466002		show file
BBS7	disease_causing_automatic	0.999999999945467	simple_aae		affected	0	T211I	single base exchange	rs119466002		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999945467 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM030644)
known disease mutation: rs3016 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:122775945G>AN/A show variant in all transcripts IGV

HGNC symbol

BBS7

Ensembl transcript ID

ENST00000264499

Genbank transcript ID

NM_176824

UniProt peptide

Q8IWZ6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.632C>T
cDNA.816C>T
g.15708C>T

AA changes

T211I Score: 89 explain score(s)

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

211

frameshift

known variant

Reference ID: rs119466002

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs3016 (pathogenic for Bardet-Biedl syndrome|Bardet-Biedl syndrome 1/7, digenic) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030644)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030644)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030644)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.222	0.68
	6.162	1
(flanking)	5.088	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
Donor gained	15712	0.32	mu: ATATCAGACGGAAAA	ATCA\|gacg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

211

mutated

not conserved

211

Ptroglodytes

all identical

ENSPTRG00000016411

198

Mmulatta

all identical

ENSMMUG00000009819

211

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000037325

211

Ggallus

all identical

ENSGALG00000011880

211

Trubripes

all identical

ENSTRUG00000007380

211

Drerio

all identical

ENSDARG00000059911

211

Dmelanogaster

no homologue

Celegans

all identical

Y75B8A.12

214

Xtropicalis

all identical

ENSXETG00000031279

211

protein features

start (aa)	end (aa)	feature	details
469	469	CONFLICT	Q -> L (in Ref. 1; AAO16025/AAO16026 and 2; BAA91767).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2148 / 2148

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

716 / 716

position of stopcodon in wt / mu cDNA

2332 / 2332

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

185 / 185

chromosome

strand

-1

last intron/exon boundary

2199

theoretical NMD boundary in CDS

1964

length of CDS

2148

coding sequence (CDS) position

632

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

816

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

15708

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

122775945

original gDNA sequence snippet

AGAAGACCTTTTGTTTGGGACATCAGACGGAAAACTTGCGC

altered gDNA sequence snippet

AGAAGACCTTTTGTTTGGGATATCAGACGGAAAACTTGCGC

original cDNA sequence snippet

AGAAGACCTTTTGTTTGGGACATCAGACGGAAAACTTGCGC

altered cDNA sequence snippet

AGAAGACCTTTTGTTTGGGATATCAGACGGAAAACTTGCGC

wildtype AA sequence

MDLILNRMDY LQVGVTSQKT MKLIPASRHR ATQKVVIGDH DGVVMCFGMK KGEAAAVFKT
LPGPKIARLE LGGVINTPQE KIFIAAASEI RGFTKRGKQF LSFETNLTES IKAMHISGSD
LFLSASYIYN HYCDCKDQHY YLSGDKINDV ICLPVERLSR ITPVLACQDR VLRVLQGSDV
MYAVEVPGPP TVLALHNGNG GDSGEDLLFG TSDGKLALIQ ITTSKPVRKW EIQNEKKRGG
ILCIDSFDIV GDGVKDLLVG RDDGMVEVYS FDNANEPVLR FDQMLSESVT SIQGGCVGKD
SYDEIVVSTY SGWVTGLTTE PIHKESGPGE ELKINQEMQN KISSLRNELE HLQYKVLQER
ENYQQSSQSS KAKSAVPSFG INDKFTLNKD DASYSLILEV QTAIDNVLIQ SDVPIDLLDV
DKNSAVVSFS SCDSESNDNF LLATYRCQAD TTRLELKIRS IEGQYGTLQA YVTPRIQPKT
CQVRQYHIKP LSLHQRTHFI DHDRPMNTLT LTGQFSFAEV HSWVVFCLPE VPEKPPAGEC
VTFYFQNTFL DTQLESTYRK GEGVFKSDNI STISILKDVL SKEATKRKIN LNISYEINEV
SVKHTLKLIH PKLEYQLLLA KKVQLIDALK ELQIHEGNTN FLIPEYHCIL EEADHLQEEY
KKQPAHLERL YGMITDLFID KFKFKGTNVK TKVPLLLEIL DSYDQNALIS FFDAA*

mutated AA sequence

MDLILNRMDY LQVGVTSQKT MKLIPASRHR ATQKVVIGDH DGVVMCFGMK KGEAAAVFKT
LPGPKIARLE LGGVINTPQE KIFIAAASEI RGFTKRGKQF LSFETNLTES IKAMHISGSD
LFLSASYIYN HYCDCKDQHY YLSGDKINDV ICLPVERLSR ITPVLACQDR VLRVLQGSDV
MYAVEVPGPP TVLALHNGNG GDSGEDLLFG ISDGKLALIQ ITTSKPVRKW EIQNEKKRGG
ILCIDSFDIV GDGVKDLLVG RDDGMVEVYS FDNANEPVLR FDQMLSESVT SIQGGCVGKD
SYDEIVVSTY SGWVTGLTTE PIHKESGPGE ELKINQEMQN KISSLRNELE HLQYKVLQER
ENYQQSSQSS KAKSAVPSFG INDKFTLNKD DASYSLILEV QTAIDNVLIQ SDVPIDLLDV
DKNSAVVSFS SCDSESNDNF LLATYRCQAD TTRLELKIRS IEGQYGTLQA YVTPRIQPKT
CQVRQYHIKP LSLHQRTHFI DHDRPMNTLT LTGQFSFAEV HSWVVFCLPE VPEKPPAGEC
VTFYFQNTFL DTQLESTYRK GEGVFKSDNI STISILKDVL SKEATKRKIN LNISYEINEV
SVKHTLKLIH PKLEYQLLLA KKVQLIDALK ELQIHEGNTN FLIPEYHCIL EEADHLQEEY
KKQPAHLERL YGMITDLFID KFKFKGTNVK TKVPLLLEIL DSYDQNALIS FFDAA*

speed

0.79 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: 0.999999999945467 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM030644)
known disease mutation: rs3016 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:122775945G>AN/A show variant in all transcripts IGV

HGNC symbol

BBS7

Ensembl transcript ID

ENST00000506636

Genbank transcript ID

NM_018190

UniProt peptide

Q8IWZ6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.632C>T
cDNA.769C>T
g.15708C>T

AA changes

T211I Score: 89 explain score(s)

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

211

frameshift

known variant

Reference ID: rs119466002

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.222	0.68
	6.162	1
(flanking)	5.088	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
Donor gained	15712	0.32	mu: ATATCAGACGGAAAA	ATCA\|gacg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

211

mutated

not conserved

211

Ptroglodytes

all identical

ENSPTRG00000016411

198

Mmulatta

all identical

ENSMMUG00000009819

211

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000037325

211

Ggallus

all identical

ENSGALG00000011880

211

Trubripes

all identical

ENSTRUG00000007380

211

Drerio

all identical

ENSDARG00000059911

211

Dmelanogaster

no homologue

Celegans

all identical

Y75B8A.12

214

Xtropicalis

all identical

ENSXETG00000031279

211

protein features

start (aa)	end (aa)	feature	details
469	469	CONFLICT	Q -> L (in Ref. 1; AAO16025/AAO16026 and 2; BAA91767).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2019 / 2019

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

673 / 673

position of stopcodon in wt / mu cDNA

2156 / 2156

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

138 / 138

chromosome

strand

-1

last intron/exon boundary

2028

theoretical NMD boundary in CDS

1840

length of CDS

2019

coding sequence (CDS) position

632

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

769

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

15708

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

122775945

original gDNA sequence snippet

AGAAGACCTTTTGTTTGGGACATCAGACGGAAAACTTGCGC

altered gDNA sequence snippet

AGAAGACCTTTTGTTTGGGATATCAGACGGAAAACTTGCGC

original cDNA sequence snippet

AGAAGACCTTTTGTTTGGGACATCAGACGGAAAACTTGCGC

altered cDNA sequence snippet

AGAAGACCTTTTGTTTGGGATATCAGACGGAAAACTTGCGC

wildtype AA sequence

mutated AA sequence

MDLILNRMDY LQVGVTSQKT MKLIPASRHR ATQKVVIGDH DGVVMCFGMK KGEAAAVFKT
LPGPKIARLE LGGVINTPQE KIFIAAASEI RGFTKRGKQF LSFETNLTES IKAMHISGSD
LFLSASYIYN HYCDCKDQHY YLSGDKINDV ICLPVERLSR ITPVLACQDR VLRVLQGSDV
MYAVEVPGPP TVLALHNGNG GDSGEDLLFG ISDGKLALIQ ITTSKPVRKW EIQNEKKRGG
ILCIDSFDIV GDGVKDLLVG RDDGMVEVYS FDNANEPVLR FDQMLSESVT SIQGGCVGKD
SYDEIVVSTY SGWVTGLTTE PIHKESGPGE ELKINQEMQN KISSLRNELE HLQYKVLQER
ENYQQSSQSS KAKSAVPSFG INDKFTLNKD DASYSLILEV QTAIDNVLIQ SDVPIDLLDV
DKNSAVVSFS SCDSESNDNF LLATYRCQAD TTRLELKIRS IEGQYGTLQA YVTPRIQPKT
CQVRQYHIKP LSLHQRTHFI DHDRPMNTLT LTGQFSFAEV HSWVVFCLPE VPEKPPAGEC
VTFYFQNTFL DTQLESTYRK GEGVFKSDNI STISILKDVL SKEATKRKIN LNISYEINEV
SVKHTLKLIH PKLEYQLLLA KKVQLIDALK ELQIHEGNTN FLIPEYHCIL EEADHLQEEY
KKQPAHLERL YG*

speed

0.75 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems