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: ENST00000339994
Querying Taster for transcript #2: ENST00000528731
MT speed 0 s - this script 4.376253 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KCNJ11	polymorphism_automatic	6.56001855947608e-07	simple_aae				V337I	single base exchange	rs5215		show file
KCNJ11	polymorphism_automatic	6.56001855947608e-07	simple_aae				V250I	single base exchange	rs5215		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999343998144 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM078157)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:17408630C>TN/A show variant in all transcripts IGV

HGNC symbol

KCNJ11

Ensembl transcript ID

ENST00000339994

Genbank transcript ID

NM_000525

UniProt peptide

Q14654

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1009G>A
cDNA.1577G>A
g.2249G>A

AA changes

V337I Score: 29 explain score(s)

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

337

frameshift

known variant

Reference ID: rs5215

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1377	905	2282
ExAC	25728	-18689	7039

known disease mutation at this position, please check HGMD for details (HGMD ID CM078157)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
CTCF, Transcription Factor, CCCTC-binding factor

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.514	0.973
	-0.594	0.223
(flanking)	0.273	0.331

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 marginally increased	2249	wt: 0.9827 / mu: 0.9923 (marginal change - not scored)	wt: ACACCGTCAAAGTGC mu: ACACCATCAAAGTGC	ACCG\|tcaa

distance from splice site

1225

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

337

mutated

all conserved

337

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000023580

337

Fcatus

all conserved

ENSFCAG00000007305

244

Mmusculus

all conserved

ENSMUSG00000096146

337

Ggallus

all identical

ENSGALG00000020505

235

Trubripes

no homologue

Drerio

all identical

ENSDARG00000051880

336

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
167	390	TOPO_DOM	Cytoplasmic (By similarity).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1173 / 1173

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

391 / 391

position of stopcodon in wt / mu cDNA

1741 / 1741

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

569 / 569

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

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

length of CDS

1173

coding sequence (CDS) position

1009

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

1577

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

2249

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

17408630

original gDNA sequence snippet

ACTCCAAGTTTGGCAACACCGTCAAAGTGCCCACACCACTC

altered gDNA sequence snippet

ACTCCAAGTTTGGCAACACCATCAAAGTGCCCACACCACTC

original cDNA sequence snippet

ACTCCAAGTTTGGCAACACCGTCAAAGTGCCCACACCACTC

altered cDNA sequence snippet

ACTCCAAGTTTGGCAACACCATCAAAGTGCCCACACCACTC

wildtype AA sequence

MLSRKGIIPE EYVLTRLAED PAKPRYRARQ RRARFVSKKG NCNVAHKNIR EQGRFLQDVF
TTLVDLKWPH TLLIFTMSFL CSWLLFAMAW WLIAFAHGDL APSEGTAEPC VTSIHSFSSA
FLFSIEVQVT IGFGGRMVTE ECPLAILILI VQNIVGLMIN AIMLGCIFMK TAQAHRRAET
LIFSKHAVIA LRHGRLCFML RVGDLRKSMI ISATIHMQVV RKTTSPEGEV VPLHQVDIPM
ENGVGGNSIF LVAPLIIYHV IDANSPLYDL APSDLHHHQD LEIIVILEGV VETTGITTQA
RTSYLADEIL WGQRFVPIVA EEDGRYSVDY SKFGNTVKVP TPLCTARQLD EDHSLLEALT
LASARGPLRK RSVPMAKAKP KFSISPDSLS *

mutated AA sequence

MLSRKGIIPE EYVLTRLAED PAKPRYRARQ RRARFVSKKG NCNVAHKNIR EQGRFLQDVF
TTLVDLKWPH TLLIFTMSFL CSWLLFAMAW WLIAFAHGDL APSEGTAEPC VTSIHSFSSA
FLFSIEVQVT IGFGGRMVTE ECPLAILILI VQNIVGLMIN AIMLGCIFMK TAQAHRRAET
LIFSKHAVIA LRHGRLCFML RVGDLRKSMI ISATIHMQVV RKTTSPEGEV VPLHQVDIPM
ENGVGGNSIF LVAPLIIYHV IDANSPLYDL APSDLHHHQD LEIIVILEGV VETTGITTQA
RTSYLADEIL WGQRFVPIVA EEDGRYSVDY SKFGNTIKVP TPLCTARQLD EDHSLLEALT
LASARGPLRK RSVPMAKAKP KFSISPDSLS *

speed

1.19 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: 0.999999343998144 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM078157)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:17408630C>TN/A show variant in all transcripts IGV

HGNC symbol

KCNJ11

Ensembl transcript ID

ENST00000528731

Genbank transcript ID

NM_001166290

UniProt peptide

Q14654

alteration type

single base exchange

alteration region

CDS

DNA changes

c.748G>A
cDNA.922G>A
g.2249G>A

AA changes

V250I Score: 29 explain score(s)

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

250

frameshift

known variant

Reference ID: rs5215

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1377	905	2282
ExAC	25728	-18689	7039

known disease mutation at this position, please check HGMD for details (HGMD ID CM078157)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.514	0.973
	-0.594	0.223
(flanking)	0.273	0.331

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 marginally increased	2249	wt: 0.9827 / mu: 0.9923 (marginal change - not scored)	wt: ACACCGTCAAAGTGC mu: ACACCATCAAAGTGC	ACCG\|tcaa

distance from splice site

764

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

250

mutated

all conserved

250

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000023580

337

Fcatus

all conserved

ENSFCAG00000007305

244

Mmusculus

all conserved

ENSMUSG00000096146

337

Ggallus

all identical

ENSGALG00000020505

235

Trubripes

no homologue

Drerio

all identical

ENSDARG00000051880

336

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
167	390	TOPO_DOM	Cytoplasmic (By similarity).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

912 / 912

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

304 / 304

position of stopcodon in wt / mu cDNA

1086 / 1086

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

175 / 175

chromosome

strand

-1

last intron/exon boundary

159

theoretical NMD boundary in CDS

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

length of CDS

912

coding sequence (CDS) position

748

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

922

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

2249

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

17408630

original gDNA sequence snippet

ACTCCAAGTTTGGCAACACCGTCAAAGTGCCCACACCACTC

altered gDNA sequence snippet

ACTCCAAGTTTGGCAACACCATCAAAGTGCCCACACCACTC

original cDNA sequence snippet

ACTCCAAGTTTGGCAACACCGTCAAAGTGCCCACACCACTC

altered cDNA sequence snippet

ACTCCAAGTTTGGCAACACCATCAAAGTGCCCACACCACTC

wildtype AA sequence

MAWWLIAFAH GDLAPSEGTA EPCVTSIHSF SSAFLFSIEV QVTIGFGGRM VTEECPLAIL
ILIVQNIVGL MINAIMLGCI FMKTAQAHRR AETLIFSKHA VIALRHGRLC FMLRVGDLRK
SMIISATIHM QVVRKTTSPE GEVVPLHQVD IPMENGVGGN SIFLVAPLII YHVIDANSPL
YDLAPSDLHH HQDLEIIVIL EGVVETTGIT TQARTSYLAD EILWGQRFVP IVAEEDGRYS
VDYSKFGNTV KVPTPLCTAR QLDEDHSLLE ALTLASARGP LRKRSVPMAK AKPKFSISPD
SLS*

mutated AA sequence

MAWWLIAFAH GDLAPSEGTA EPCVTSIHSF SSAFLFSIEV QVTIGFGGRM VTEECPLAIL
ILIVQNIVGL MINAIMLGCI FMKTAQAHRR AETLIFSKHA VIALRHGRLC FMLRVGDLRK
SMIISATIHM QVVRKTTSPE GEVVPLHQVD IPMENGVGGN SIFLVAPLII YHVIDANSPL
YDLAPSDLHH HQDLEIIVIL EGVVETTGIT TQARTSYLAD EILWGQRFVP IVAEEDGRYS
VDYSKFGNTI KVPTPLCTAR QLDEDHSLLE ALTLASARGP LRKRSVPMAK AKPKFSISPD
SLS*

speed

1.27 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems