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: ENST00000375679
Querying Taster for transcript #2: ENST00000375667
MT speed 0 s - this script 3.679075 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CLCNKB	polymorphism_automatic	7.41812560267618e-08	simple_aae				K578E	single base exchange	rs2275166		show file
CLCNKB	polymorphism_automatic	1.00074029951713e-07	simple_aae				K409E	single base exchange	rs2275166		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999925818744 (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 CM1514575)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:16380243A>GN/A show variant in all transcripts IGV

HGNC symbol

CLCNKB

Ensembl transcript ID

ENST00000375679

Genbank transcript ID

NM_000085

UniProt peptide

P51801

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1732A>G
cDNA.1843A>G
g.9972A>G

AA changes

K578E Score: 56 explain score(s)

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

578

frameshift

known variant

Reference ID: rs2275166

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1285	944	2229
ExAC	26455	-20143	6312

known disease mutation at this position, please check HGMD for details (HGMD ID CM1514575)

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.363	0.015
	0.152	0.163
(flanking)	1.797	0.893

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

578

mutated

all conserved

578

Ptroglodytes

all conserved

ENSPTRG00000000217

577

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000010168

579

Mmusculus

all conserved

ENSMUSG00000033770

578

Ggallus

all conserved

ENSGALG00000003713

576

Trubripes

all conserved

ENSTRUG00000001694

586

Drerio

all conserved

ENSDARG00000022560

594

Dmelanogaster

not conserved

FBgn0051116

691

Celegans

not conserved

E04F6.11

588

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
551	609	DOMAIN	CBS 1.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2064 / 2064

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

688 / 688

position of stopcodon in wt / mu cDNA

2175 / 2175

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

112 / 112

chromosome

strand

last intron/exon boundary

2128

theoretical NMD boundary in CDS

1966

length of CDS

2064

coding sequence (CDS) position

1732

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

1843

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

9972

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

16380243

original gDNA sequence snippet

TGACCTCCACAGACGTGGCCAAGTATCCCCTGGTGGAGAGC

altered gDNA sequence snippet

TGACCTCCACAGACGTGGCCGAGTATCCCCTGGTGGAGAGC

original cDNA sequence snippet

TGACCTCCACAGACGTGGCCAAGTATCCCCTGGTGGAGAGC

altered cDNA sequence snippet

TGACCTCCACAGACGTGGCCGAGTATCCCCTGGTGGAGAGC

wildtype AA sequence

MEEFVGLREG SSGNPVTLQE LWGPCPRIRR GIRGGLEWLK QKLFRLGEDW YFLMTLGVLM
ALVSCAMDLA VESVVRAHQW LYREIGDSHL LRYLSWTVYP VALVSFSSGF SQSITPSSGG
SGIPEVKTML AGVVLEDYLD IKNFGAKVVG LSCTLACGST LFLGKVGPFV HLSVMMAAYL
GRVRTTTIGE PENKSKQNEM LVAAAAVGVA TVFAAPFSGV LFSIEVMSSH FSVWDYWRGF
FAATCGAFMF RLLAVFNSEQ ETITSLYKTS FRVDVPFDLP EIFFFVALGG LCGILGSAYL
FCQRIFFGFI RNNRFSSKLL ATSKPVYSAL ATLVLASITY PPSAGRFLAS RLSMKQHLDS
LFDNHSWALM TQNSSPPWPE ELDPQHLWWE WYHPRFTIFG TLAFFLVMKF WMLILATTIP
MPAGYFMPIF VYGAAIGRLF GETLSFIFPE GIVAGGITNP IMPGGYALAG AAAFSGAVTH
TISTALLAFE VTGQIVHALP VLMAVLAANA IAQSCQPSFY DGTVIVKKLP YLPRILGRNI
GSHRVRVEHF MNHSITTLAK DMPLEEVVKV VTSTDVAKYP LVESTESQIL VGIVRRAQLV
QALKAEPPSW APGHQQCLQD ILAAGCPTEP VTLKLSPETS LHEAHNLFEL LNLHSLFVTS
RGRAVGCVSW VEMKKAISNL TNPPAPK*

mutated AA sequence

MEEFVGLREG SSGNPVTLQE LWGPCPRIRR GIRGGLEWLK QKLFRLGEDW YFLMTLGVLM
ALVSCAMDLA VESVVRAHQW LYREIGDSHL LRYLSWTVYP VALVSFSSGF SQSITPSSGG
SGIPEVKTML AGVVLEDYLD IKNFGAKVVG LSCTLACGST LFLGKVGPFV HLSVMMAAYL
GRVRTTTIGE PENKSKQNEM LVAAAAVGVA TVFAAPFSGV LFSIEVMSSH FSVWDYWRGF
FAATCGAFMF RLLAVFNSEQ ETITSLYKTS FRVDVPFDLP EIFFFVALGG LCGILGSAYL
FCQRIFFGFI RNNRFSSKLL ATSKPVYSAL ATLVLASITY PPSAGRFLAS RLSMKQHLDS
LFDNHSWALM TQNSSPPWPE ELDPQHLWWE WYHPRFTIFG TLAFFLVMKF WMLILATTIP
MPAGYFMPIF VYGAAIGRLF GETLSFIFPE GIVAGGITNP IMPGGYALAG AAAFSGAVTH
TISTALLAFE VTGQIVHALP VLMAVLAANA IAQSCQPSFY DGTVIVKKLP YLPRILGRNI
GSHRVRVEHF MNHSITTLAK DMPLEEVVKV VTSTDVAEYP LVESTESQIL VGIVRRAQLV
QALKAEPPSW APGHQQCLQD ILAAGCPTEP VTLKLSPETS LHEAHNLFEL LNLHSLFVTS
RGRAVGCVSW VEMKKAISNL TNPPAPK*

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

polymorphism

Model: simple_aae, prob: 0.99999989992597 (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 CM1514575)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:16380243A>GN/A show variant in all transcripts IGV

HGNC symbol

CLCNKB

Ensembl transcript ID

ENST00000375667

Genbank transcript ID

NM_001165945

UniProt peptide

P51801

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1225A>G
cDNA.1408A>G
g.9972A>G

AA changes

K409E Score: 56 explain score(s)

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

409

frameshift

known variant

Reference ID: rs2275166

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1285	944	2229
ExAC	26455	-20143	6312

known disease mutation at this position, please check HGMD for details (HGMD ID CM1514575)

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.363	0.015
	0.152	0.163
(flanking)	1.797	0.893

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

409

mutated

all conserved

409

Ptroglodytes

all conserved

ENSPTRG00000000217

577

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000010168

579

Mmusculus

all conserved

ENSMUSG00000033770

578

Ggallus

all conserved

ENSGALG00000003713

576

Trubripes

all conserved

ENSTRUG00000001694

586

Drerio

all conserved

ENSDARG00000022560

594

Dmelanogaster

not conserved

FBgn0051116

691

Celegans

not conserved

E04F6.11

587

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
396	416	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1554 / 1554

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

518 / 518

position of stopcodon in wt / mu cDNA

1737 / 1737

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

184 / 184

chromosome

strand

last intron/exon boundary

1690

theoretical NMD boundary in CDS

1456

length of CDS

1554

coding sequence (CDS) position

1225

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

1408

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

9972

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

16380243

original gDNA sequence snippet

TGACCTCCACAGACGTGGCCAAGTATCCCCTGGTGGAGAGC

altered gDNA sequence snippet

TGACCTCCACAGACGTGGCCGAGTATCCCCTGGTGGAGAGC

original cDNA sequence snippet

TGACCTCCACAGACGTGGCCAAGTATCCCCTGGTGGAGAGC

altered cDNA sequence snippet

TGACCTCCACAGACGTGGCCGAGTATCCCCTGGTGGAGAGC

wildtype AA sequence

MPCPPLLSVP VRAAGEQDRW VREEVTWGGG PTVTGGWGWR AHLRSVSPPG VLFSIEVMSS
HFSVWDYWRG FFAATCGAFM FRLLAVFNSE QETITSLYKT SFRVDVPFDL PEIFFFVALG
GLCGILGSAY LFCQRIFFGF IRNNRFSSKL LATSKPVYSA LATLVLASIT YPPSAGRFLA
SRLSMKQHLD SLFDNHSWAL MTQNSSPPWP EELDPQHLWW EWYHPRFTIF GTLAFFLVMK
FWMLILATTI PMPAGYFMPI FVYGAAIGRL FGETLSFIFP EGIVAGGITN PIMPGGYALA
GAAAFSGAVT HTISTALLAF EVTGQIVHAL PVLMAVLAAN AIAQSCQPSF YDGTVIVKKL
PYLPRILGRN IGSHRVRVEH FMNHSITTLA KDMPLEEVVK VVTSTDVAKY PLVESTESQI
LVGIVRRAQL VQALKAEPPS WAPGHQCLQD ILAAGCPTEP VTLKLSPETS LHEAHNLFEL
LNLHSLFVTS RGRAVGCVSW VEMKKAISNL TNPPAPK*

mutated AA sequence

MPCPPLLSVP VRAAGEQDRW VREEVTWGGG PTVTGGWGWR AHLRSVSPPG VLFSIEVMSS
HFSVWDYWRG FFAATCGAFM FRLLAVFNSE QETITSLYKT SFRVDVPFDL PEIFFFVALG
GLCGILGSAY LFCQRIFFGF IRNNRFSSKL LATSKPVYSA LATLVLASIT YPPSAGRFLA
SRLSMKQHLD SLFDNHSWAL MTQNSSPPWP EELDPQHLWW EWYHPRFTIF GTLAFFLVMK
FWMLILATTI PMPAGYFMPI FVYGAAIGRL FGETLSFIFP EGIVAGGITN PIMPGGYALA
GAAAFSGAVT HTISTALLAF EVTGQIVHAL PVLMAVLAAN AIAQSCQPSF YDGTVIVKKL
PYLPRILGRN IGSHRVRVEH FMNHSITTLA KDMPLEEVVK VVTSTDVAEY PLVESTESQI
LVGIVRRAQL VQALKAEPPS WAPGHQCLQD ILAAGCPTEP VTLKLSPETS LHEAHNLFEL
LNLHSLFVTS RGRAVGCVSW VEMKKAISNL TNPPAPK*

speed

0.95 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems