MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000403799
Querying Taster for transcript #2: ENST00000395796
Querying Taster for transcript #3: ENST00000345378
Querying Taster for transcript #4: ENST00000437084
MT speed 0 s - this script 4.598154 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GCK	disease_causing_automatic	0.999999999911634	simple_aae		affected	0	V438M	single base exchange	rs104894012		show file
GCK	disease_causing_automatic	0.999999999934332	simple_aae		affected	0	V455M	single base exchange	rs104894012		show file
GCK	disease_causing_automatic	0.999999999934332	simple_aae		affected	0	V454M	single base exchange	rs104894012		show file
GCK	disease_causing_automatic	0.999999999934332	simple_aae		affected	0	V456M	single base exchange	rs104894012		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999911634 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980898)
known disease mutation: rs16140 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:44184770C>TN/A show variant in all transcripts IGV

HGNC symbol

GCK

Ensembl transcript ID

ENST00000437084

Genbank transcript ID

N/A

UniProt peptide

P35557

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1312G>A
cDNA.1346G>A
g.53000G>A

AA changes

V438M Score: 21 explain score(s)

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

438

frameshift

known variant

Reference ID: rs104894012
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16140 (pathogenic for Hyperinsulinism due to glucokinase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980898)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980898)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980898)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Znf263, Transcription Factor, Znf263 TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.055	1
	6.123	1
(flanking)	-3.304	0.002

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	52996	wt: 0.60 / mu: 0.99	wt: GTCTCGGCGGTGGCC mu: GTCTCGGCGATGGCC	CTCG\|gcgg
Donor increased	53005	wt: 0.21 / mu: 0.52	wt: GTGGCCTGTAAGAAG mu: ATGGCCTGTAAGAAG	GGCC\|tgta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

438

mutated

all conserved

438

Ptroglodytes

all identical

ENSPTRG00000019140

454

Mmulatta

all identical

ENSMMUG00000002427

456

Fcatus

all identical

ENSFCAG00000014361

440

Mmusculus

all identical

ENSMUSG00000041798

455

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000068006

466

Dmelanogaster

all identical

FBgn0001186

529

Celegans

all identical

F14B4.2

479

Xtropicalis

all identical

ENSXETG00000019003

455

protein features

start (aa)	end (aa)	feature	details
434	440	STRAND		lost
444	456	HELIX		might get lost (downstream of altered splice site)
457	459	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1347 / 1347

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

449 / 449

position of stopcodon in wt / mu cDNA

1381 / 1381

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

35 / 35

chromosome

strand

-1

last intron/exon boundary

1237

theoretical NMD boundary in CDS

1152

length of CDS

1347

coding sequence (CDS) position

1312

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

1346

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

53000

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

44184770

original gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

original cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

wildtype AA sequence

MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MMKHKKLPLG FTFSFPVRHE DIDKGILLNW TKGFKASGAE GNNVVGLLRD AIKRRGDFEM
DVVAMVNDTV ATMISCYYED HQCEVGMIVG TGCNACYMEE MQNVELVEGD EGRMCVNTEW
GAFGDSGELD EFLLEYDRLV DESSANPGQQ LYEKLIGGKY MGELVRLVLL RLVDENLLFH
GEASEQLRTR GAFETRFVSQ VESDTGDRKQ IYNILSTLGL RPSTTDCDIV RRACESVSTR
AAHMCSAGLA GVINRMRESR SEDVMRITVG VDGSVYKLHP SFKERFHASV RRLTPSCEIT
FIESEEGSGR GAALVSAVAC KKACMLGQ*

mutated AA sequence

speed

0.73 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: 0.999999999934332 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980898)
known disease mutation: rs16140 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:44184770C>TN/A show variant in all transcripts IGV

HGNC symbol

GCK

Ensembl transcript ID

ENST00000403799

Genbank transcript ID

NM_000162

UniProt peptide

P35557

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1363G>A
cDNA.1833G>A
g.53000G>A

AA changes

V455M Score: 21 explain score(s)

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

455

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Znf263, Transcription Factor, Znf263 TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.055	1
	6.123	1
(flanking)	-3.304	0.002

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	52996	wt: 0.60 / mu: 0.99	wt: GTCTCGGCGGTGGCC mu: GTCTCGGCGATGGCC	CTCG\|gcgg
Donor increased	53005	wt: 0.21 / mu: 0.52	wt: GTGGCCTGTAAGAAG mu: ATGGCCTGTAAGAAG	GGCC\|tgta

distance from splice site

110

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

455

mutated

all conserved

455

Ptroglodytes

all identical

ENSPTRG00000019140

454

Mmulatta

all identical

ENSMMUG00000002427

456

Fcatus

all identical

ENSFCAG00000014361

440

Mmusculus

all identical

ENSMUSG00000041798

455

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000068006

466

Dmelanogaster

all identical

FBgn0001186

529

Celegans

all identical

F14B4.2

479

Xtropicalis

all identical

ENSXETG00000019003

455

protein features

start (aa)	end (aa)	feature	details
444	456	HELIX		lost
457	459	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1398 / 1398

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

466 / 466

position of stopcodon in wt / mu cDNA

1868 / 1868

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

471 / 471

chromosome

strand

-1

last intron/exon boundary

1724

theoretical NMD boundary in CDS

1203

length of CDS

1398

coding sequence (CDS) position

1363

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

1833

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

53000

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

44184770

original gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

original cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

wildtype AA sequence

MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN
VVGLLRDAIK RRGDFEMDVV AMVNDTVATM ISCYYEDHQC EVGMIVGTGC NACYMEEMQN
VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES SANPGQQLYE KLIGGKYMGE
LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS
TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK
ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ*

mutated AA sequence

speed

0.70 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999934332 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980898)
known disease mutation: rs16140 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:44184770C>TN/A show variant in all transcripts IGV

HGNC symbol

GCK

Ensembl transcript ID

ENST00000395796

Genbank transcript ID

NM_033508

UniProt peptide

P35557

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1360G>A
cDNA.1645G>A
g.53000G>A

AA changes

V454M Score: 21 explain score(s)

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

454

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Znf263, Transcription Factor, Znf263 TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.055	1
	6.123	1
(flanking)	-3.304	0.002

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	52996	wt: 0.60 / mu: 0.99	wt: GTCTCGGCGGTGGCC mu: GTCTCGGCGATGGCC	CTCG\|gcgg
Donor increased	53005	wt: 0.21 / mu: 0.52	wt: GTGGCCTGTAAGAAG mu: ATGGCCTGTAAGAAG	GGCC\|tgta

distance from splice site

110

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

454

mutated

all conserved

454

Ptroglodytes

all identical

ENSPTRG00000019140

454

Mmulatta

all identical

ENSMMUG00000002427

456

Fcatus

all identical

ENSFCAG00000014361

440

Mmusculus

all identical

ENSMUSG00000041798

455

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000068006

466

Dmelanogaster

all identical

FBgn0001186

529

Celegans

all identical

F14B4.2

479

Xtropicalis

all identical

ENSXETG00000019003

455

protein features

start (aa)	end (aa)	feature	details
444	456	HELIX		lost
457	459	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1395 / 1395

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

465 / 465

position of stopcodon in wt / mu cDNA

1680 / 1680

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

286 / 286

chromosome

strand

-1

last intron/exon boundary

1536

theoretical NMD boundary in CDS

1200

length of CDS

1395

coding sequence (CDS) position

1360

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

1645

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

53000

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

44184770

original gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

original cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

wildtype AA sequence

MPRPRSQLPQ PNSQVEQILA EFQLQEEDLK KVMRRMQKEM DRGLRLETHE EASVKMLPTY
VRSTPEGSEV GDFLSLDLGG TNFRVMLVKV GEGEEGQWSV KTKHQMYSIP EDAMTGTAEM
LFDYISECIS DFLDKHQMKH KKLPLGFTFS FPVRHEDIDK GILLNWTKGF KASGAEGNNV
VGLLRDAIKR RGDFEMDVVA MVNDTVATMI SCYYEDHQCE VGMIVGTGCN ACYMEEMQNV
ELVEGDEGRM CVNTEWGAFG DSGELDEFLL EYDRLVDESS ANPGQQLYEK LIGGKYMGEL
VRLVLLRLVD ENLLFHGEAS EQLRTRGAFE TRFVSQVESD TGDRKQIYNI LSTLGLRPST
TDCDIVRRAC ESVSTRAAHM CSAGLAGVIN RMRESRSEDV MRITVGVDGS VYKLHPSFKE
RFHASVRRLT PSCEITFIES EEGSGRGAAL VSAVACKKAC MLGQ*

mutated AA sequence

speed

0.71 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999934332 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980898)
known disease mutation: rs16140 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:44184770C>TN/A show variant in all transcripts IGV

HGNC symbol

GCK

Ensembl transcript ID

ENST00000345378

Genbank transcript ID

NM_033507

UniProt peptide

P35557

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1366G>A
cDNA.1528G>A
g.53000G>A

AA changes

V456M Score: 21 explain score(s)

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

456

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Znf263, Transcription Factor, Znf263 TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.055	1
	6.123	1
(flanking)	-3.304	0.002

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	52996	wt: 0.60 / mu: 0.99	wt: GTCTCGGCGGTGGCC mu: GTCTCGGCGATGGCC	CTCG\|gcgg
Donor increased	53005	wt: 0.21 / mu: 0.52	wt: GTGGCCTGTAAGAAG mu: ATGGCCTGTAAGAAG	GGCC\|tgta

distance from splice site

110

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

456

mutated

all conserved

456

Ptroglodytes

all identical

ENSPTRG00000019140

454

Mmulatta

all identical

ENSMMUG00000002427

456

Fcatus

all identical

ENSFCAG00000014361

440

Mmusculus

all identical

ENSMUSG00000041798

455

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000068006

466

Dmelanogaster

all identical

FBgn0001186

529

Celegans

all identical

F14B4.2

479

Xtropicalis

all identical

ENSXETG00000019003

455

protein features

start (aa)	end (aa)	feature	details
444	456	HELIX		lost
457	459	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1401 / 1401

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

467 / 467

position of stopcodon in wt / mu cDNA

1563 / 1563

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

163 / 163

chromosome

strand

-1

last intron/exon boundary

1419

theoretical NMD boundary in CDS

1206

length of CDS

1401

coding sequence (CDS) position

1366

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

1528

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

53000

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

44184770

original gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered gDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

original cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT

altered cDNA sequence snippet

GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT

wildtype AA sequence

MAMDVTRSQA QTALTLVEQI LAEFQLQEED LKKVMRRMQK EMDRGLRLET HEEASVKMLP
TYVRSTPEGS EVGDFLSLDL GGTNFRVMLV KVGEGEEGQW SVKTKHQMYS IPEDAMTGTA
EMLFDYISEC ISDFLDKHQM KHKKLPLGFT FSFPVRHEDI DKGILLNWTK GFKASGAEGN
NVVGLLRDAI KRRGDFEMDV VAMVNDTVAT MISCYYEDHQ CEVGMIVGTG CNACYMEEMQ
NVELVEGDEG RMCVNTEWGA FGDSGELDEF LLEYDRLVDE SSANPGQQLY EKLIGGKYMG
ELVRLVLLRL VDENLLFHGE ASEQLRTRGA FETRFVSQVE SDTGDRKQIY NILSTLGLRP
STTDCDIVRR ACESVSTRAA HMCSAGLAGV INRMRESRSE DVMRITVGVD GSVYKLHPSF
KERFHASVRR LTPSCEITFI ESEEGSGRGA ALVSAVACKK ACMLGQ*

mutated AA sequence

speed

1.04 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems