mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM060825)
known disease mutation at this position (HGMD CM940062)
known disease mutation: rs11975 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49459656C>TN/A show variant in all transcripts IGV

HGNC symbol

AMT

Ensembl transcript ID

ENST00000538581

Genbank transcript ID

NM_001164711

UniProt peptide

P48728

alteration type

single base exchange

alteration region

intron

DNA changes

g.531G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121964982

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

known disease mutation: rs11975 (pathogenic for Non-ketotic hyperglycinemia|Inborn genetic diseases) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.76	1
	5.412	1
(flanking)	-1.765	0.355

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	532	wt: 0.4473 / mu: 0.4763 (marginal change - not scored)	wt: CTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCGG mu: CTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCGG	gcgg\|GAAA
Acc marginally increased	522	wt: 0.2275 / mu: 0.2275 (marginal change - not scored)	wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG mu: CGCTCTATGACTTCCACCTGGCCCACGGCAGGAAAATGGTG	ctgg\|CCCA
Donor increased	532	wt: 0.43 / mu: 0.87	wt: CGGCGGGAAAATGGT mu: CGGCAGGAAAATGGT	GCGG\|gaaa
Donor increased	531	wt: 0.66 / mu: 0.97	wt: ACGGCGGGAAAATGG mu: ACGGCAGGAAAATGG	GGCG\|ggaa
Donor gained	527	0.69	mu: GCCCACGGCAGGAAA	CCAC\|ggca

distance from splice site

138

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
39	44	HELIX		might get lost (downstream of altered splice site)
48	52	STRAND		might get lost (downstream of altered splice site)
55	60	STRAND		might get lost (downstream of altered splice site)
65	74	HELIX		might get lost (downstream of altered splice site)
75	80	STRAND		might get lost (downstream of altered splice site)
84	91	STRAND		might get lost (downstream of altered splice site)
94	101	HELIX		might get lost (downstream of altered splice site)
95	95	CONFLICT	V -> C (in Ref. 2; BAA03512).	might get lost (downstream of altered splice site)
102	104	STRAND		might get lost (downstream of altered splice site)
113	120	STRAND		might get lost (downstream of altered splice site)
126	134	STRAND		might get lost (downstream of altered splice site)
138	144	STRAND		might get lost (downstream of altered splice site)
146	148	HELIX		might get lost (downstream of altered splice site)
149	165	HELIX		might get lost (downstream of altered splice site)
171	174	STRAND		might get lost (downstream of altered splice site)
178	184	STRAND		might get lost (downstream of altered splice site)
187	192	HELIX		might get lost (downstream of altered splice site)
199	201	HELIX		might get lost (downstream of altered splice site)
206	212	STRAND		might get lost (downstream of altered splice site)
215	222	STRAND		might get lost (downstream of altered splice site)
225	235	STRAND		might get lost (downstream of altered splice site)
232	232	BINDING	Substrate.	might get lost (downstream of altered splice site)
237	248	HELIX		might get lost (downstream of altered splice site)
253	255	STRAND		might get lost (downstream of altered splice site)
258	267	HELIX		might get lost (downstream of altered splice site)
261	261	BINDING	Substrate.	might get lost (downstream of altered splice site)
273	275	TURN		might get lost (downstream of altered splice site)
283	287	TURN		might get lost (downstream of altered splice site)
289	291	HELIX		might get lost (downstream of altered splice site)
294	299	HELIX		might get lost (downstream of altered splice site)
305	312	HELIX		might get lost (downstream of altered splice site)
319	328	STRAND		might get lost (downstream of altered splice site)
335	337	STRAND		might get lost (downstream of altered splice site)
343	353	STRAND		might get lost (downstream of altered splice site)
354	357	TURN		might get lost (downstream of altered splice site)
358	365	STRAND		might get lost (downstream of altered splice site)
367	369	HELIX		might get lost (downstream of altered splice site)
375	380	STRAND		might get lost (downstream of altered splice site)
383	390	STRAND		might get lost (downstream of altered splice site)
399	399	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

229 / 229

chromosome

strand

-1

last intron/exon boundary

1094

theoretical NMD boundary in CDS

815

length of CDS

1044

coding sequence (CDS) position

N/A

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

N/A

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

531

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

49459656

original gDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered gDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ TKILGSDRVK LMESLVVGDI AELRPNQGTL
SLFTNEAGGI LDDLIVTNTS EGHLYVVSNA GCWEKDLALM QDKVRELQNQ GRDVGLEVLD
NALLALQGPT AAQVLQAGVA DDLRKLPFMT SAVMEVFGVS GCRVTRCGYT GEDGVEISVP
VAGAVHLATA ILKNPEVKLA GLAARDSLRL EAGLCLYGND IDEHTTPVEG SLSWTLGKRR
RAAMDFPGAK VIVPQLKGRV QRRRVGLMCE GAPMRAHSPI LNMEGTKIGT VTSGCPSPSL
KKNVAMGYVP CEYSRPGTML LVEVRRKQQM AVVSKMPFVP TNYYTLK*

mutated AA sequence

N/A

speed

1.04 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