mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999781949912 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs21077 (probable pathogenic)
known disease mutation at this position (HGMD CM057328)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:44185159C>AN/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.1139G>T
cDNA.1173G>T
g.52611G>T

AA changes

R380L Score: 102 explain score(s)

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

380

frameshift

known variant

Reference ID: rs193929375
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs21077 (probable pathogenic for Permanent neonatal diabetes mellitus|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM057328)

known disease mutation at this position, please check HGMD for details (HGMD ID CM057328)
known disease mutation at this position, please check HGMD for details (HGMD ID CM057328)

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)	1.106	0.998
	4.382	1
(flanking)	3.114	1

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	52613	wt: 0.9656 / mu: 0.9853 (marginal change - not scored)	wt: GCCGCAGCGAGGACG mu: GCCTCAGCGAGGACG	CGCA\|gcga
Donor increased	52616	wt: 0.38 / mu: 0.73	wt: GCAGCGAGGACGTAA mu: TCAGCGAGGACGTAA	AGCG\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

380

mutated

not conserved

380

Ptroglodytes

all identical

ENSPTRG00000019140

396

Mmulatta

all identical

ENSMMUG00000002427

398

Fcatus

all identical

ENSFCAG00000014361

382

Mmusculus

all identical

ENSMUSG00000041798

397

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000068006

408

Dmelanogaster

not conserved

FBgn0001186

476

Celegans

not conserved

F14B4.2

426

Xtropicalis

all identical

ENSXETG00000019003

397

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

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

1139

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

1173

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

52611

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

44185159

original gDNA sequence snippet

CAACCGCATGCGCGAGAGCCGCAGCGAGGACGTAATGCGCA

altered gDNA sequence snippet

CAACCGCATGCGCGAGAGCCTCAGCGAGGACGTAATGCGCA

original cDNA sequence snippet

CAACCGCATGCGCGAGAGCCGCAGCGAGGACGTAATGCGCA

altered cDNA sequence snippet

CAACCGCATGCGCGAGAGCCTCAGCGAGGACGTAATGCGCA

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

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 GVINRMRESL SEDVMRITVG VDGSVYKLHP SFKERFHASV RRLTPSCEIT
FIESEEGSGR GAALVSAVAC KKACMLGQ*

speed

1.12 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