mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999995101 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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)

chr2:231072709C>TN/A show variant in all transcripts IGV

HGNC symbol

SP110

Ensembl transcript ID

ENST00000338556

Genbank transcript ID

N/A

UniProt peptide

Q9HB58

alteration type

single base exchange

alteration region

CDS

DNA changes

c.151G>A
cDNA.1135G>A
g.17736G>A

AA changes

G51R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs1365776

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1669	681	2350
ExAC	24440	-16113	8327

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.194	0.004
	-0.237	0.001
(flanking)	0.272	0.001

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	17739	sequence motif lost	-	wt: GGAG\|gtaa mu: AGAG.gtaa
Donor increased	17734	wt: 0.71 / mu: 0.80	wt: CCTCCCAGGAGGTAA mu: CCTCCCAAGAGGTAA	TCCC\|agga
Donor increased	17733	wt: 0.24 / mu: 0.32	wt: GCCTCCCAGGAGGTA mu: GCCTCCCAAGAGGTA	CTCC\|cagg
Donor marginally increased	17738	wt: 0.9793 / mu: 0.9924 (marginal change - not scored)	wt: CCAGGAGGTAAGATG mu: CCAAGAGGTAAGATG	AGGA\|ggta
Donor gained	17731	0.93	mu: AAGCCTCCCAAGAGG	GCCT\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000070034

269

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000055359

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032669

n/a

protein features

start (aa)	end (aa)	feature	details
1	108	DOMAIN	HSR.	lost
167	167	CONFLICT	D -> T (in Ref. 2; AAF99318/AAG09826).	might get lost (downstream of altered splice site)
175	175	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
177	177	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
256	256	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
281	294	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)
428	444	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)
454	535	DOMAIN	SAND.	might get lost (downstream of altered splice site)
464	464	CONFLICT	L -> S (in Ref. 1; AAA18806).	might get lost (downstream of altered splice site)
525	529	REGION	Nuclear hormone receptor interaction (Potential).	might get lost (downstream of altered splice site)
534	580	ZN_FING	PHD-type.	might get lost (downstream of altered splice site)
570	570	CONFLICT	M -> I (in Ref. 3; AK026488).	might get lost (downstream of altered splice site)
581	676	DOMAIN	Bromo.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

756 / 756

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

252 / 252

position of stopcodon in wt / mu cDNA

1740 / 1740

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

985 / 985

chromosome

strand

-1

last intron/exon boundary

1681

theoretical NMD boundary in CDS

646

length of CDS

756

coding sequence (CDS) position

151

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

1135

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

17736

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

231072709

original gDNA sequence snippet

ATAAGAAAAAAAGCCTCCCAGGAGGTAAGATGAGAGTACAA

altered gDNA sequence snippet

ATAAGAAAAAAAGCCTCCCAAGAGGTAAGATGAGAGTACAA

original cDNA sequence snippet

ATAAGAAAAAAAGCCTCCCAGGAGAGATCATTGATGGCACT

altered cDNA sequence snippet

ATAAGAAAAAAAGCCTCCCAAGAGAGATCATTGATGGCACT

wildtype AA sequence

MPEIRDNSPE PNDPEEPQEV SSTPSDKKGK KRKRCIWSTP KRRHKKKSLP GEIIDGTSEM
NEGKRSQKTP STPRRVTQGA ASPGHGIQEK LQVVDKVTQR KDDSTWNSEV MMRVQKARTK
CARKSRLKEK KKEKDICSSS KRRFQKNIHR RGKPKSDTVD FHCSKLPVTC GEAKGILYKK
KMKHGSSVKC IRNEDGTWLT PNEFEVEGKG RNAKNWKRNI RCEGMTLGEL LKSGLLLCPP
RINLKRELNS K*

mutated AA sequence

MPEIRDNSPE PNDPEEPQEV SSTPSDKKGK KRKRCIWSTP KRRHKKKSLP REIIDGTSEM
NEGKRSQKTP STPRRVTQGA ASPGHGIQEK LQVVDKVTQR KDDSTWNSEV MMRVQKARTK
CARKSRLKEK KKEKDICSSS KRRFQKNIHR RGKPKSDTVD FHCSKLPVTC GEAKGILYKK
KMKHGSSVKC IRNEDGTWLT PNEFEVEGKG RNAKNWKRNI RCEGMTLGEL LKSGLLLCPP
RINLKRELNS K*

speed

1.11 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