mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.0114318291217216 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116446576A>GN/A show variant in all transcripts IGV

HGNC symbol

NT5DC1

Ensembl transcript ID

ENST00000319550

Genbank transcript ID

NM_152729

UniProt peptide

Q5TFE4

alteration type

single base exchange

alteration region

intron

DNA changes

g.24565A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1064583

database	homozygous (G/G)	heterozygous	allele carriers
1000G	600	1031	1631
ExAC	9789	13189	22978

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.835	0.142
	1.351	0.574
(flanking)	0.84	0.634

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	24558	wt: 0.7780 / mu: 0.8055 (marginal change - not scored)	wt: GGTAGTGGGCCTTTTATGCCTGTGGGCATTTGGTATCGTTC mu: GGTAGTGGGCCTTTTATGCCTGTGGGCGTTTGGTATCGTTC	gcct\|GTGG
Acc increased	24556	wt: 0.47 / mu: 0.58	wt: TGGGTAGTGGGCCTTTTATGCCTGTGGGCATTTGGTATCGT mu: TGGGTAGTGGGCCTTTTATGCCTGTGGGCGTTTGGTATCGT	atgc\|CTGT

distance from splice site

7468

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
313	313	METAL	Magnesium (By similarity).	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

83 / 83

chromosome

strand

last intron/exon boundary

1335

theoretical NMD boundary in CDS

1202

length of CDS

1368

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)

24565

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

116446576

original gDNA sequence snippet

GGCCTTTTATGCCTGTGGGCATTTGGTATCGTTCAGCGTAA

altered gDNA sequence snippet

GGCCTTTTATGCCTGTGGGCGTTTGGTATCGTTCAGCGTAA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAQHFSLAAC DVVGFDLDHT LCRYNLPESA PLIYNSFAQF LVKEKGYDKE LLNVTPEDWD
FCCKGLALDL EDGNFLKLAN NGTVLRASHG TKMMTPEVLA EAYGKKEWKH FLSDTGMACR
SGKYYFYDNY FDLPGALLCA RVVDYLTKLN NGQKTFDFWK DIVAAIQHNY KMSAFKENCG
IYFPEIKRDP GRYLHSCPES VKKWLRQLKN AGKILLLITS SHSDYCRLLC EYILGNDFTD
LFDIVITNAL KPGFFSHLPS QRPFRTLEND EEQEALPSLD KPGWYSQGNA VHLYELLKKM
TGKPEPKVVY FGDSMHSDIF PARHYSNWET VLILEELRGD EGTRSQRPEE SEPLEKKGKY
EGPKAKPLNT SSKKWGSFFI DSVLGLENTE DSLVYTWSCK RISTYSTIAI PSIEAIAELP
LDYKFTRFSS SNSKTAGYYP NPPLVLSSDE TLISK*

mutated AA sequence

N/A

speed

0.15 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