mutation t@sting

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

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

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

1.02 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