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: ENST00000337801
Querying Taster for transcript #2: ENST00000429564
MT speed 0 s - this script 3.936757 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AQP12A	polymorphism_automatic	0.988173939272163	simple_aae		affected		L28R	single base exchange	rs71428454		show file
AQP12A	polymorphism_automatic	0.999363000720716	simple_aae		affected		L28R	single base exchange	rs71428454		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0118260607278369 (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)

chr2:241631413T>GN/A show variant in all transcripts IGV

HGNC symbol

AQP12A

Ensembl transcript ID

ENST00000429564

Genbank transcript ID

N/A

UniProt peptide

Q8IXF9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.83T>G
cDNA.146T>G
g.152T>G

AA changes

L28R Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs71428454

database	homozygous (G/G)	heterozygous	allele carriers
1000G	212	577	789
ExAC	6791	18504	25295

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.381	0.873
	2.581	0.987
(flanking)	0.481	0.993

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	146	0.70	mu: CTCCAAGGCCCGGCT	CCAA\|ggcc

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

no homologue

Mmulatta

all identical

ENSMMUG00000031103

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000045091

Ggallus

all identical

ENSGALG00000006436

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000043279

Dmelanogaster

all identical

FBgn0033807

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
55	75	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
81	83	MOTIF	NPA 1.	might get lost (downstream of altered splice site)
100	126	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
146	166	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
179	199	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
200	202	MOTIF	NPA 2.	might get lost (downstream of altered splice site)
216	236	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

924 / 924

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

308 / 308

position of stopcodon in wt / mu cDNA

987 / 987

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

64 / 64

chromosome

strand

last intron/exon boundary

788

theoretical NMD boundary in CDS

674

length of CDS

924

coding sequence (CDS) position

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

146

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

152

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

241631413

original gDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCTGCTCCCAGTGGGCGCCTATG

altered gDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCGGCTCCCAGTGGGCGCCTATG

original cDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCTGCTCCCAGTGGGCGCCTATG

altered cDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCGGCTCCCAGTGGGCGCCTATG

wildtype AA sequence

MAGLNVSLSF FFATFALCEA ARRASKALLP VGAYEVFARE AVGAVQLGPC CLEMRTLVEL
GPWAGDFGPD LLLTLLFLLF LAHGVTLDGA SANPTVSLQE FLMAEQSLPG TLLKLAAQGL
GMQAACTLMR LCWAWELSDL HLLQSLMAQS CSSALRTSVP HGALVEAACA FCFHLTLLHL
RHSPPAYSGP AVALLVTVTA YTAGPFTSAF FNPALAASVT FACSGHTLLE YVQVYWLGPL
TGMVLAVLLH QGRLPHLFQR NLFYGQKNKY RAPRGKPAPA SGDTQTPAKG SSVREPGRSG
VEGPHSS*

mutated AA sequence

MAGLNVSLSF FFATFALCEA ARRASKARLP VGAYEVFARE AVGAVQLGPC CLEMRTLVEL
GPWAGDFGPD LLLTLLFLLF LAHGVTLDGA SANPTVSLQE FLMAEQSLPG TLLKLAAQGL
GMQAACTLMR LCWAWELSDL HLLQSLMAQS CSSALRTSVP HGALVEAACA FCFHLTLLHL
RHSPPAYSGP AVALLVTVTA YTAGPFTSAF FNPALAASVT FACSGHTLLE YVQVYWLGPL
TGMVLAVLLH QGRLPHLFQR NLFYGQKNKY RAPRGKPAPA SGDTQTPAKG SSVREPGRSG
VEGPHSS*

speed

1.44 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: 0.000636999279283632 (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)

chr2:241631413T>GN/A show variant in all transcripts IGV

HGNC symbol

AQP12A

Ensembl transcript ID

ENST00000337801

Genbank transcript ID

NM_198998

UniProt peptide

Q8IXF9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.83T>G
cDNA.152T>G
g.152T>G

AA changes

L28R Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs71428454

database	homozygous (G/G)	heterozygous	allele carriers
1000G	212	577	789
ExAC	6791	18504	25295

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.381	0.873
	2.581	0.987
(flanking)	0.481	0.993

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	146	0.70	mu: CTCCAAGGCCCGGCT	CCAA\|ggcc

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

no homologue

Mmulatta

all identical

ENSMMUG00000031103

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000045091

Ggallus

all identical

ENSGALG00000006436

Trubripes

no homologue

Drerio

all identical

ENSDARG00000043279

RLLLR

Dmelanogaster

all identical

FBgn0033807

RRLVTRE

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
55	75	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
81	83	MOTIF	NPA 1.	might get lost (downstream of altered splice site)
100	126	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
146	166	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
179	199	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
200	202	MOTIF	NPA 2.	might get lost (downstream of altered splice site)
216	236	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

888 / 888

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

296 / 296

position of stopcodon in wt / mu cDNA

957 / 957

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

70 / 70

chromosome

strand

last intron/exon boundary

758

theoretical NMD boundary in CDS

638

length of CDS

888

coding sequence (CDS) position

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

152

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

152

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

241631413

original gDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCTGCTCCCAGTGGGCGCCTATG

altered gDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCGGCTCCCAGTGGGCGCCTATG

original cDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCTGCTCCCAGTGGGCGCCTATG

altered cDNA sequence snippet

CAGGCGGGCCTCCAAGGCCCGGCTCCCAGTGGGCGCCTATG

wildtype AA sequence

MAGLNVSLSF FFATFALCEA ARRASKALLP VGAYEVFARE AMRTLVELGP WAGDFGPDLL
LTLLFLLFLA HGVTLDGASA NPTVSLQEFL MAEQSLPGTL LKLAAQGLGM QAACTLMRLC
WAWELSDLHL LQSLMAQSCS SALRTSVPHG ALVEAACAFC FHLTLLHLRH SPPAYSGPAV
ALLVTVTAYT AGPFTSAFFN PALAASVTFA CSGHTLLEYV QVYWLGPLTG MVLAVLLHQG
RLPHLFQRNL FYGQKNKYRA PRGKPAPASG DTQTPAKGSS VREPGRSGVE GPHSS*

mutated AA sequence

MAGLNVSLSF FFATFALCEA ARRASKARLP VGAYEVFARE AMRTLVELGP WAGDFGPDLL
LTLLFLLFLA HGVTLDGASA NPTVSLQEFL MAEQSLPGTL LKLAAQGLGM QAACTLMRLC
WAWELSDLHL LQSLMAQSCS SALRTSVPHG ALVEAACAFC FHLTLLHLRH SPPAYSGPAV
ALLVTVTAYT AGPFTSAFFN PALAASVTFA CSGHTLLEYV QVYWLGPLTG MVLAVLLHQG
RLPHLFQRNL FYGQKNKYRA PRGKPAPASG DTQTPAKGSS VREPGRSGVE GPHSS*

speed

0.49 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems