mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 4.16040332391115e-48 (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)

chr15:57925836C>TN/A show variant in all transcripts IGV

HGNC symbol

POLR2M

Ensembl transcript ID

ENST00000380563

Genbank transcript ID

N/A

UniProt peptide

P0CAP2

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.739C>T
g.41606C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs16977629

database	homozygous (T/T)	heterozygous	allele carriers
1000G	126	677	803
ExAC	1081	11177	12258

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.272	1
	4.81	0.998
(flanking)	-4.248	0.002

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

splice sites

splice site change before start ATG (at aa -554) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	41608	wt: 0.9805 / mu: 0.9843 (marginal change - not scored)	wt: AAGCGATTGAAGAAG mu: AAGTGATTGAAGAAG	GCGA\|ttga
Donor increased	41599	wt: 0.40 / mu: 0.93	wt: GTTTTCTGAAAGCGA mu: GTTTTCTGAAAGTGA	TTTC\|tgaa
Donor marginally increased	41604	wt: 0.6055 / mu: 0.6524 (marginal change - not scored)	wt: CTGAAAGCGATTGAA mu: CTGAAAGTGATTGAA	GAAA\|gcga

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
171	171	CONFLICT	H -> D (in Ref. 7; CAB43263).	might get lost (downstream of altered splice site)
185	185	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
270	270	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
301	335	COILED	Potential.	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

2396 / 2396

chromosome

strand

last intron/exon boundary

3359

theoretical NMD boundary in CDS

913

length of CDS

1092

coding sequence (CDS) position

N/A

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

739

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

41606

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

57925836

original gDNA sequence snippet

AACCAATAGTTTTCTGAAAGCGATTGAAGAAGCCAATAAAA

altered gDNA sequence snippet

AACCAATAGTTTTCTGAAAGTGATTGAAGAAGCCAATAAAA

original cDNA sequence snippet

AACCAATAGTTTTCTGAAAGCGATTGAAGAAGCCAATAAAA

altered cDNA sequence snippet

AACCAATAGTTTTCTGAAAGTGATTGAAGAAGCCAATAAAA

wildtype AA sequence

MCSLPRGFEP QAPEDLAQRS LVELREMLKR QERLLRNEKF ICKLPDKGKK IFDSFAKLKA
AIAECEEVRR KSELFNPVSL DCKLRQKAIA EVDVGTDKAQ NSDPILDTSS LVPGCSSVDN
IKSSQTSQNQ GLGRPTLEGD EETSEVEYTV NKGPASSNRD RVPPSSEASE HHPRHRVSSQ
AEDTSSSFDN LFIDRLQRIT IADQGEQQSE ENASTKNLTG LSSGTEKKPH YMEVLEMRAK
NPVPQLRKFK TNVLPFRQND SSSHCQKSGS PISSEERRRR DKQHLDDITA ARLLPLHHMP
TQLLSIEESL ALQKQQKQNY EERPFYSPQY RSSMNLLSLA AAAKDTRGSK SGKMGSLALL
TKL*

mutated AA sequence

N/A

speed

0.60 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