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: ENST00000314218
Querying Taster for transcript #2: ENST00000542236
MT speed 0 s - this script 4.223322 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BBS12	disease_causing	0.999990560649164	simple_aae		affected		A289P	single base exchange	rs121918328		show file
BBS12	disease_causing	0.999990560649164	simple_aae		affected		A289P	single base exchange	rs121918328		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999990560649164 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs1150 (probable pathogenic)
known disease mutation at this position (HGMD CM070032)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:123663912G>CN/A show variant in all transcripts IGV

HGNC symbol

BBS12

Ensembl transcript ID

ENST00000314218

Genbank transcript ID

NM_152618

UniProt peptide

Q6ZW61

alteration type

single base exchange

alteration region

CDS

DNA changes

c.865G>C
cDNA.1058G>C
g.10056G>C

AA changes

A289P Score: 27 explain score(s)

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

289

frameshift

known variant

Reference ID: rs121918328
Allele 'C' was neither found in ExAC nor 1000G.
known as potential disease variant: rs1150 (probable pathogenic for Retinal dystrophy|Bardet-Biedl syndrome 12|Bardet-Biedl syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070032)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070032)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070032)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.638	0.474
	4.069	0.99
(flanking)	3.824	0.989

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 increased	10058	wt: 0.84 / mu: 0.96	wt: GAAGCAGTACAGCTG mu: GAACCAGTACAGCTG	AGCA\|gtac
Donor marginally increased	10053	wt: 0.6568 / mu: 0.6639 (marginal change - not scored)	wt: TAGAAGAAGCAGTAC mu: TAGAAGAACCAGTAC	GAAG\|aagc
Donor marginally increased	10047	wt: 0.9506 / mu: 0.9592 (marginal change - not scored)	wt: AGTTAGTAGAAGAAG mu: AGTTAGTAGAAGAAC	TTAG\|taga

distance from splice site

875

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

289

mutated

not conserved

289

Ptroglodytes

all identical

ENSPTRG00000016420

289

Mmulatta

all identical

ENSMMUG00000030171

289

Fcatus

all identical

ENSFCAG00000014537

291

Mmusculus

all identical

ENSMUSG00000051444

289

Ggallus

not conserved

ENSGALG00000011837

Trubripes

no homologue

Drerio

all identical

ENSDARG00000016112

418

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001588

270

protein features

start (aa)	end (aa)	feature	details
462	462	CONFLICT	E -> G (in Ref. 2; CAD98035).	might get lost (downstream of altered splice site)
597	597	CONFLICT	K -> R (in Ref. 1; BAC04006).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2133 / 2133

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

711 / 711

position of stopcodon in wt / mu cDNA

2326 / 2326

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

194 / 194

chromosome

strand

last intron/exon boundary

184

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

2133

coding sequence (CDS) position

865

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

1058

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

10056

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

123663912

original gDNA sequence snippet

GCATGAAGTTAGTAGAAGAAGCAGTACAGCTGCAATATCAG

altered gDNA sequence snippet

GCATGAAGTTAGTAGAAGAACCAGTACAGCTGCAATATCAG

original cDNA sequence snippet

GCATGAAGTTAGTAGAAGAAGCAGTACAGCTGCAATATCAG

altered cDNA sequence snippet

GCATGAAGTTAGTAGAAGAACCAGTACAGCTGCAATATCAG

wildtype AA sequence

MVMACRVVNK RRHMGLQQLS SFAETGRTFL GPLKSSKFII DEECHESVLI SSTVRLLESL
DLTSAVGQLL NEAVQAQNNT YRTGISTLLF LVGAWSSAVE ECLHLGVPIS IIVSVMSEGL
NFCSEEVVSL HVPVHNIFDC MDSTKTFSQL ETFSVSLCPF LQVPSDTDLI EELHGLKDVA
SQTLTISNLS GRPLKSYELF KPQTKVEADN NTSRTLKNSL LADTCCRQSI LIHSRHFNRT
DNTEGVSKPD GFQEHVTATH KTYRCNDLVE LAVGLSHGDH SSMKLVEEAV QLQYQNACVQ
QGNCTKPFMF DISRIFTCCL PGLPETSSCV CPGYITVVSV SNNPVIKELQ NQPVRIVLIE
GDLTENYRHL GFNKSANIKT VLDSMRLQED SSEELWANHV LQVLIQFKVN LVLVQGNVSE
RLIEKCINSK RLVIGSVNGS VMQAFAEAAG AVQVAYITQV NEDCVGDGVC VTFWRSSPLD
VVDRNNRIAI LLKTEGINLV TAVLTNPVTA QMQIKEDRFW TCAYRLYYAL KEEKVFLGGG
AVEFLCLSCL HILAEQSLKK ENHACSGWLH NTSSWLASSL AIYRPTVLKF LANGWQKYLS
TLLYNTANYS SEFEASTYIQ HHLQNATDSG SPSSYILNEY SKLNSRIFNS DISNKLEQIP
RVYDVVTPKI EAWRRALDLV LLVLQTDSEI ITGHGHTQIN SQELTGFLFL *

mutated AA sequence

MVMACRVVNK RRHMGLQQLS SFAETGRTFL GPLKSSKFII DEECHESVLI SSTVRLLESL
DLTSAVGQLL NEAVQAQNNT YRTGISTLLF LVGAWSSAVE ECLHLGVPIS IIVSVMSEGL
NFCSEEVVSL HVPVHNIFDC MDSTKTFSQL ETFSVSLCPF LQVPSDTDLI EELHGLKDVA
SQTLTISNLS GRPLKSYELF KPQTKVEADN NTSRTLKNSL LADTCCRQSI LIHSRHFNRT
DNTEGVSKPD GFQEHVTATH KTYRCNDLVE LAVGLSHGDH SSMKLVEEPV QLQYQNACVQ
QGNCTKPFMF DISRIFTCCL PGLPETSSCV CPGYITVVSV SNNPVIKELQ NQPVRIVLIE
GDLTENYRHL GFNKSANIKT VLDSMRLQED SSEELWANHV LQVLIQFKVN LVLVQGNVSE
RLIEKCINSK RLVIGSVNGS VMQAFAEAAG AVQVAYITQV NEDCVGDGVC VTFWRSSPLD
VVDRNNRIAI LLKTEGINLV TAVLTNPVTA QMQIKEDRFW TCAYRLYYAL KEEKVFLGGG
AVEFLCLSCL HILAEQSLKK ENHACSGWLH NTSSWLASSL AIYRPTVLKF LANGWQKYLS
TLLYNTANYS SEFEASTYIQ HHLQNATDSG SPSSYILNEY SKLNSRIFNS DISNKLEQIP
RVYDVVTPKI EAWRRALDLV LLVLQTDSEI ITGHGHTQIN SQELTGFLFL *

speed

1.16 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: 0.999990560649164 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs1150 (probable pathogenic)
known disease mutation at this position (HGMD CM070032)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:123663912G>CN/A show variant in all transcripts IGV

HGNC symbol

BBS12

Ensembl transcript ID

ENST00000542236

Genbank transcript ID

NM_001178007

UniProt peptide

Q6ZW61

alteration type

single base exchange

alteration region

CDS

DNA changes

c.865G>C
cDNA.1246G>C
g.10056G>C

AA changes

A289P Score: 27 explain score(s)

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

289

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.638	0.474
	4.069	0.99
(flanking)	3.824	0.989

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 increased	10058	wt: 0.84 / mu: 0.96	wt: GAAGCAGTACAGCTG mu: GAACCAGTACAGCTG	AGCA\|gtac
Donor marginally increased	10053	wt: 0.6568 / mu: 0.6639 (marginal change - not scored)	wt: TAGAAGAAGCAGTAC mu: TAGAAGAACCAGTAC	GAAG\|aagc
Donor marginally increased	10047	wt: 0.9506 / mu: 0.9592 (marginal change - not scored)	wt: AGTTAGTAGAAGAAG mu: AGTTAGTAGAAGAAC	TTAG\|taga

distance from splice site

875

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

289

mutated

not conserved

289

Ptroglodytes

all identical

ENSPTRG00000016420

289

Mmulatta

all identical

ENSMMUG00000030171

289

Fcatus

all identical

ENSFCAG00000014537

291

Mmusculus

all identical

ENSMUSG00000051444

289

Ggallus

not conserved

ENSGALG00000011837

Trubripes

no homologue

Drerio

all identical

ENSDARG00000016112

418

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001588

270

protein features

start (aa)	end (aa)	feature	details
462	462	CONFLICT	E -> G (in Ref. 2; CAD98035).	might get lost (downstream of altered splice site)
597	597	CONFLICT	K -> R (in Ref. 1; BAC04006).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2133 / 2133

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

711 / 711

position of stopcodon in wt / mu cDNA

2514 / 2514

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

382 / 382

chromosome

strand

last intron/exon boundary

372

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

2133

coding sequence (CDS) position

865

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

1246

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

10056

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

123663912

original gDNA sequence snippet

GCATGAAGTTAGTAGAAGAAGCAGTACAGCTGCAATATCAG

altered gDNA sequence snippet

GCATGAAGTTAGTAGAAGAACCAGTACAGCTGCAATATCAG

original cDNA sequence snippet

GCATGAAGTTAGTAGAAGAAGCAGTACAGCTGCAATATCAG

altered cDNA sequence snippet

GCATGAAGTTAGTAGAAGAACCAGTACAGCTGCAATATCAG

wildtype AA sequence

mutated AA sequence

MVMACRVVNK RRHMGLQQLS SFAETGRTFL GPLKSSKFII DEECHESVLI SSTVRLLESL
DLTSAVGQLL NEAVQAQNNT YRTGISTLLF LVGAWSSAVE ECLHLGVPIS IIVSVMSEGL
NFCSEEVVSL HVPVHNIFDC MDSTKTFSQL ETFSVSLCPF LQVPSDTDLI EELHGLKDVA
SQTLTISNLS GRPLKSYELF KPQTKVEADN NTSRTLKNSL LADTCCRQSI LIHSRHFNRT
DNTEGVSKPD GFQEHVTATH KTYRCNDLVE LAVGLSHGDH SSMKLVEEPV QLQYQNACVQ
QGNCTKPFMF DISRIFTCCL PGLPETSSCV CPGYITVVSV SNNPVIKELQ NQPVRIVLIE
GDLTENYRHL GFNKSANIKT VLDSMRLQED SSEELWANHV LQVLIQFKVN LVLVQGNVSE
RLIEKCINSK RLVIGSVNGS VMQAFAEAAG AVQVAYITQV NEDCVGDGVC VTFWRSSPLD
VVDRNNRIAI LLKTEGINLV TAVLTNPVTA QMQIKEDRFW TCAYRLYYAL KEEKVFLGGG
AVEFLCLSCL HILAEQSLKK ENHACSGWLH NTSSWLASSL AIYRPTVLKF LANGWQKYLS
TLLYNTANYS SEFEASTYIQ HHLQNATDSG SPSSYILNEY SKLNSRIFNS DISNKLEQIP
RVYDVVTPKI EAWRRALDLV LLVLQTDSEI ITGHGHTQIN SQELTGFLFL *

speed

1.12 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems