mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 1.25470307920951e-16 (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)

chr19:41255500C>GN/A show variant in all transcripts IGV

HGNC symbol

C19orf54

Ensembl transcript ID

ENST00000339153

Genbank transcript ID

N/A

UniProt peptide

Q5BKX5

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.232G>C
g.909G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2254343

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1469	852	2321
ExAC	5631	3998	9629

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.424	0.998
	1.448	1
(flanking)	2.713	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -59) | splice site change before start ATG (at aa -58) | splice site change before start ATG (at aa -57) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	920	wt: 0.9562 / mu: 0.9731 (marginal change - not scored)	wt: CTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAGCTC mu: CTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAGCTC	ttcg\|GCCT
Acc increased	915	wt: 0.63 / mu: 0.85	wt: AGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCC mu: AGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCC	atgt\|CTTC
Acc marginally increased	913	wt: 0.9239 / mu: 0.9767 (marginal change - not scored)	wt: ACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAG mu: ACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAG	tcat\|GTCT
Acc increased	917	wt: 0.21 / mu: 0.42	wt: GGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAG mu: GGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAG	gtct\|TCGG
Acc marginally increased	919	wt: 0.9261 / mu: 0.9608 (marginal change - not scored)	wt: CCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAGCT mu: CCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAGCT	cttc\|GGCC
Acc marginally increased	912	wt: 0.2142 / mu: 0.2476 (marginal change - not scored)	wt: CACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGA mu: CACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGA	gtca\|TGTC
Acc gained	911	0.45	mu: CCACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAG	cctc\|ATGT
Acc gained	914	0.31	mu: CAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGC	catg\|TCTT

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
4	69	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
70	70	CONFLICT	R -> P (in Ref. 3; BC020262).	might get lost (downstream of altered splice site)
316	316	MOD_RES	Phosphoserine.	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

416 / 416

chromosome

strand

-1

last intron/exon boundary

812

theoretical NMD boundary in CDS

346

length of CDS

420

coding sequence (CDS) position

N/A

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

232

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

909

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

41255500

original gDNA sequence snippet

TGCCACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGA

altered gDNA sequence snippet

TGCCACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGA

original cDNA sequence snippet

ACTCAAAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGA

altered cDNA sequence snippet

ACTCAAAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGA

wildtype AA sequence

MRAGGLVDGR YSPVAPQWRP PGETHTGGHG KRLHGPGRDV LSTSYDEDFN HEPCQRKGHK
AHWAVSAGVL LGVRAVPSLG YTEDPELPGL FHPVLGTPCQ PPSLPEEGSP GAVYLLSKQG
KSWHYQLWDY DQGPPLSSH*

mutated AA sequence

N/A

speed

0.91 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