mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999877 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs11978 (probable pathogenic)
known disease mutation at this position (HGMD CM983428)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49456455C>GN/A show variant in all transcripts IGV

HGNC symbol

AMT

Ensembl transcript ID

ENST00000458307

Genbank transcript ID

NM_001164710

UniProt peptide

P48728

alteration type

single base exchange

alteration region

CDS

DNA changes

c.694G>C
cDNA.713G>C
g.3732G>C

AA changes

D232H Score: 81 explain score(s)

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

232

frameshift

known variant

Reference ID: rs121964984

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known as potential disease variant: rs11978 (probable pathogenic for Non-ketotic hyperglycinemia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

regulatory features

Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.496	1
	5.441	1
(flanking)	0.031	0.991

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 marginally increased	3727	wt: 0.7803 / mu: 0.8233 (marginal change - not scored)	wt: GGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACA mu: GGCAGGCCTCTGCCTGTATGGGAATCACATTGATGAACACA	atgg\|GAAT
Donor marginally increased	3725	wt: 0.9342 / mu: 0.9539 (marginal change - not scored)	wt: CTGTATGGGAATGAC mu: CTGTATGGGAATCAC	GTAT\|ggga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

232

mutated

not conserved

232

Ptroglodytes

all identical

ENSPTRG00000014924

276

Mmulatta

all identical

ENSMMUG00000005452

276

Fcatus

all identical

ENSFCAG00000009856

276

Mmusculus

all identical

ENSMUSG00000032607

276

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

286

Drerio

all identical

ENSDARG00000010862

283

Dmelanogaster

all identical

FBgn0032287

274

Celegans

all identical

F25B4.1

272

Xtropicalis

all identical

ENSXETG00000005937

276

protein features

start (aa)	end (aa)	feature	details
225	235	STRAND		lost
232	232	BINDING	Substrate.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1080 / 1080

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

360 / 360

position of stopcodon in wt / mu cDNA

1099 / 1099

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

20 / 20

chromosome

strand

-1

last intron/exon boundary

921

theoretical NMD boundary in CDS

851

length of CDS

1080

coding sequence (CDS) position

694

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

713

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

3732

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

49456455

original gDNA sequence snippet

GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA

altered gDNA sequence snippet

GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA

original cDNA sequence snippet

GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA

altered cDNA sequence snippet

GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA

wildtype AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEAGLCLYG NDIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRRVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*

mutated AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEAGLCLYG NHIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRRVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*

speed

0.70 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