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: ENST00000301407
Querying Taster for transcript #2: ENST00000391869
MT speed 0 s - this script 3.832193 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CGB1	polymorphism_automatic	1.97342998498051e-06	simple_aae		affected		R4G	single base exchange	rs62126040		show file
CGB1	polymorphism_automatic	4.66634635298835e-06	simple_aae		affected		R4G	single base exchange	rs62126040		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999998026570015 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:49539560T>CN/A show variant in all transcripts IGV

HGNC symbol

CGB1

Ensembl transcript ID

ENST00000391869

Genbank transcript ID

N/A

UniProt peptide

A6NKQ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.10A>G
cDNA.26A>G
g.12447A>G

AA changes

R4G Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs62126040

database	homozygous (C/C)	heterozygous	allele carriers
1000G	152	837	989
ExAC	2248	20326	22574

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.327	0.997
	0.338	0.998
(flanking)	1.327	0.999

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	12446.5	sequence motif lost	-	wt: ccca\|GAGG mu: ccca.GGGG
Acc marginally increased	12445	wt: 0.2684 / mu: 0.3475 (marginal change - not scored)	wt: TGAAGCAGTGTCCTTGCCCCAGAGGCTGCTGCTGTTGCTGC mu: TGAAGCAGTGTCCTTGCCCCAGGGGCTGCTGCTGTTGCTGC	ccca\|GAGG

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

not conserved

ENSPTRG00000034144

Mmulatta

no alignment

ENSMMUG00000003917

n/a

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000038194

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000035709

n/a

Dmelanogaster

no alignment

FBgn0063368

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000021249

protein features

start (aa)	end (aa)	feature	details
1	50	SIGNAL	Potential.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

468 / 468

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

156 / 156

position of stopcodon in wt / mu cDNA

484 / 484

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

17 / 17

chromosome

strand

-1

last intron/exon boundary

194

theoretical NMD boundary in CDS

127

length of CDS

468

coding sequence (CDS) position

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

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

12447

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

49539560

original gDNA sequence snippet

AAGCAGTGTCCTTGCCCCAGAGGCTGCTGCTGTTGCTGCTG

altered gDNA sequence snippet

AAGCAGTGTCCTTGCCCCAGGGGCTGCTGCTGTTGCTGCTG

original cDNA sequence snippet

CAAGGATGGAGATGTTCCAGAGGCTGCTGCTGTTGCTGCTG

altered cDNA sequence snippet

CAAGGATGGAGATGTTCCAGGGGCTGCTGCTGTTGCTGCTG

wildtype AA sequence

MFQRLLLLLL LSMGGTWASK EPLRPRCRPI NATLAVEKEG CPVCITVNTT ICAGYCPTMT
RVLQGVLPAL PQVVCNYRDV RFESIRLPGC PRGVNPVVSY AVALSCQCAL CRRSTTDCGG
PKDHPLTCDD PRFQDSSSSK APPPSLPSPS RLPGP*

mutated AA sequence

MFQGLLLLLL LSMGGTWASK EPLRPRCRPI NATLAVEKEG CPVCITVNTT ICAGYCPTMT
RVLQGVLPAL PQVVCNYRDV RFESIRLPGC PRGVNPVVSY AVALSCQCAL CRRSTTDCGG
PKDHPLTCDD PRFQDSSSSK APPPSLPSPS RLPGP*

speed

1.37 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

polymorphism

Model: simple_aae, prob: 0.999995333653647 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:49539560T>CN/A show variant in all transcripts IGV

HGNC symbol

CGB1

Ensembl transcript ID

ENST00000301407

Genbank transcript ID

NM_033377

UniProt peptide

A6NKQ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.10A>G
cDNA.115A>G
g.12447A>G

AA changes

R4G Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs62126040

database	homozygous (C/C)	heterozygous	allele carriers
1000G	152	837	989
ExAC	2248	20326	22574

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.327	0.997
	0.338	0.998
(flanking)	1.327	0.999

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	12446.5	sequence motif lost	-	wt: ccca\|GAGG mu: ccca.GGGG
Acc marginally increased	12445	wt: 0.2684 / mu: 0.3475 (marginal change - not scored)	wt: TGAAGCAGTGTCCTTGCCCCAGAGGCTGCTGCTGTTGCTGC mu: TGAAGCAGTGTCCTTGCCCCAGGGGCTGCTGCTGTTGCTGC	ccca\|GAGG

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

not conserved

ENSPTRG00000034144

Mmulatta

no alignment

ENSMMUG00000003917

n/a

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000038194

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000035709

n/a

Dmelanogaster

no alignment

FBgn0063368

n/a

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000021249

n/a

protein features

start (aa)	end (aa)	feature	details
1	50	SIGNAL	Potential.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

468 / 468

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

156 / 156

position of stopcodon in wt / mu cDNA

573 / 573

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

106 / 106

chromosome

strand

-1

last intron/exon boundary

283

theoretical NMD boundary in CDS

127

length of CDS

468

coding sequence (CDS) position

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

115

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

12447

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

49539560

original gDNA sequence snippet

AAGCAGTGTCCTTGCCCCAGAGGCTGCTGCTGTTGCTGCTG

altered gDNA sequence snippet

AAGCAGTGTCCTTGCCCCAGGGGCTGCTGCTGTTGCTGCTG

original cDNA sequence snippet

AAGAGAGAGACATGTCAAAGAGGCTGCTGCTGTTGCTGCTG

altered cDNA sequence snippet

AAGAGAGAGACATGTCAAAGGGGCTGCTGCTGTTGCTGCTG

wildtype AA sequence

MSKRLLLLLL LSMGGTWASK EPLRPRCRPI NATLAVEKEG CPVCITVNTT ICAGYCPTMT
RVLQGVLPAL PQVVCNYRDV RFESIRLPGC PRGVNPVVSY AVALSCQCAL CRRSTTDCGG
PKDHPLTCDD PRFQDSSSSK APPPSLPSPS RLPGP*

mutated AA sequence

MSKGLLLLLL LSMGGTWASK EPLRPRCRPI NATLAVEKEG CPVCITVNTT ICAGYCPTMT
RVLQGVLPAL PQVVCNYRDV RFESIRLPGC PRGVNPVVSY AVALSCQCAL CRRSTTDCGG
PKDHPLTCDD PRFQDSSSSK APPPSLPSPS RLPGP*

speed

0.45 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems