mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999470567 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CD097041)
known disease mutation at this position (HGMD CM035618)
known disease mutation at this position (HGMD CM096932)
known disease mutation at this position (HGMD CM096933)
known disease mutation: rs21076 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:44185216G>AN/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.1130C>T
cDNA.1415C>T
g.52554C>T

AA changes

A377V Score: 64 explain score(s)

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

377

frameshift

known variant

Reference ID: rs193929374
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs21076 (pathogenic for Permanent neonatal diabetes mellitus) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)

known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)

known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)

known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096933)

known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096933)
known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)

known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096933)
known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)

known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096933)
known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)

known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096933)
known disease mutation at this position, please check HGMD for details (HGMD ID CD097041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035618)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096932)
known disease mutation at this position, please check HGMD for details (HGMD ID CM096933)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.859	0.499
	5.851	1
(flanking)	2.622	0.999

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
Acc increased	52565	wt: 0.62 / mu: 0.71	wt: CTACGCGCGCTGCGCACATGTGCTCGGCGGGGCTGGCGGGC mu: CTACGCGCGTTGCGCACATGTGCTCGGCGGGGCTGGCGGGC	atgt\|GCTC
Acc marginally increased	52563	wt: 0.5349 / mu: 0.5398 (marginal change - not scored)	wt: GTCTACGCGCGCTGCGCACATGTGCTCGGCGGGGCTGGCGG mu: GTCTACGCGCGTTGCGCACATGTGCTCGGCGGGGCTGGCGG	acat\|GTGC
Donor increased	52558	wt: 0.80 / mu: 0.88	wt: GCTGCGCACATGTGC mu: GTTGCGCACATGTGC	TGCG\|caca
Donor gained	52547	0.65	mu: TGTCTACGCGCGTTG	TCTA\|cgcg

distance from splice site

114

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

377

mutated

not conserved

377

Ptroglodytes

all identical

ENSPTRG00000019140

377

Mmulatta

all identical

ENSMMUG00000002427

379

Fcatus

all identical

ENSFCAG00000014361

363

Mmusculus

all identical

ENSMUSG00000041798

378

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000068006

389

Dmelanogaster

all identical

FBgn0001186

458

Celegans

all identical

F14B4.2

407

Xtropicalis

all identical

ENSXETG00000019003

378

protein features

start (aa)	end (aa)	feature	details
361	396	HELIX		lost
400	409	STRAND		might get lost (downstream of altered splice site)
411	415	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)
411	415	HELIX		might get lost (downstream of altered splice site)
414	414	MUTAGEN	K->A: Small change in activity.	might get lost (downstream of altered splice site)
416	418	STRAND		might get lost (downstream of altered splice site)
419	430	HELIX		might get lost (downstream of altered splice site)
434	440	STRAND		might get lost (downstream of altered splice site)
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

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

1130

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

1415

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

52554

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

44185216

original gDNA sequence snippet

CGAGAGCGTGTCTACGCGCGCTGCGCACATGTGCTCGGCGG

altered gDNA sequence snippet

CGAGAGCGTGTCTACGCGCGTTGCGCACATGTGCTCGGCGG

original cDNA sequence snippet

CGAGAGCGTGTCTACGCGCGCTGCGCACATGTGCTCGGCGG

altered cDNA sequence snippet

CGAGAGCGTGTCTACGCGCGTTGCGCACATGTGCTCGGCGG

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

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 ESVSTRVAHM CSAGLAGVIN RMRESRSEDV MRITVGVDGS VYKLHPSFKE
RFHASVRRLT PSCEITFIES EEGSGRGAAL VSAVACKKAC MLGQ*

speed

1.00 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