mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 7.53158629401229e-11 (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)

chr20:1115919A>GN/A show variant in all transcripts IGV

HGNC symbol

PSMF1

Ensembl transcript ID

ENST00000438768

Genbank transcript ID

N/A

UniProt peptide

Q92530

alteration type

single base exchange

alteration region

intron

DNA changes

g.22014A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2235587

database	homozygous (G/G)	heterozygous	allele carriers
1000G	180	650	830
ExAC	2500	16400	18900

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.424	0.915
	0.462	0.91
(flanking)	-0.129	0.906

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 increased	22024	wt: 0.23 / mu: 0.37	wt: ATTCCTCCACACCACCCACACACCAGTCGGCAGCCTCCCTG mu: ATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTCCCTG	acac\|ACCA
Acc increased	22020	wt: 0.41 / mu: 0.46	wt: CCGGATTCCTCCACACCACCCACACACCAGTCGGCAGCCTC mu: CCGGATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTC	accc\|ACAC
Acc marginally increased	22015	wt: 0.9313 / mu: 0.9396 (marginal change - not scored)	wt: CCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGCA mu: CCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGCA	acac\|CACC
Donor gained	22013	0.85	mu: CTCCACGCCACCCAC	CCAC\|gcca
Donor gained	22008	0.41	mu: GATTCCTCCACGCCA	TTCC\|tcca

distance from splice site

7768

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
120	123	HELIX		might get lost (downstream of altered splice site)
127	137	HELIX		might get lost (downstream of altered splice site)
153	153	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
154	271	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
251	251	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
252	252	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

138 / 138

chromosome

strand

last intron/exon boundary

716

theoretical NMD boundary in CDS

528

length of CDS

606

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)

22014

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

1115919

original gDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered gDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRCDPLGPFV VGGEDLDPFG PRRGGMIVDP LRSGFPRALI DPSSGLPNRL PPGAVPPGAR
FDPFGPIGTS PPGPRPDRRG Q*

mutated AA sequence

N/A

speed

0.32 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