mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999959044 (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)

chr19:54725798G>TN/A show variant in all transcripts IGV

HGNC symbol

LILRB3

Ensembl transcript ID

ENST00000346401

Genbank transcript ID

N/A

UniProt peptide

O75022

alteration type

single base exchange

alteration region

CDS

DNA changes

c.560C>A
cDNA.623C>A
g.20805C>A

AA changes

T187N Score: 65 explain score(s)

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

187

frameshift

known variant

Reference ID: rs75069054

database	homozygous (T/T)	heterozygous	allele carriers
1000G	684	1284	1968
ExAC	5680	10429	16109

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.259	0.001
	-0.368	0.001
(flanking)	1.641	0.003

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	20804	wt: 0.33 / mu: 0.60	wt: TGTTCCCTGTGGGCCCCGTGACCCCCAGCCACAGGTGGAGG mu: TGTTCCCTGTGGGCCCCGTGAACCCCAGCCACAGGTGGAGG	gtga\|CCCC
Donor increased	20800	wt: 0.39 / mu: 0.99	wt: GGCCCCGTGACCCCC mu: GGCCCCGTGAACCCC	CCCC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

187

mutated

not conserved

187

Ptroglodytes

all identical

ENSPTRG00000011451

187

Mmulatta

all identical

ENSMMUG00000021880

187

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
24	443	TOPO_DOM	Extracellular (Potential).	lost
111	229	DOMAIN	Ig-like C2-type 2.	lost
187	187	CONFLICT	T -> N (in Ref. 1; AAB68668, 2; AAB87667 and 3; AAP30716).	lost
196	196	DISULFID	By similarity.	might get lost (downstream of altered splice site)
201	201	CONFLICT	T -> M (in Ref. 1; AAB68668 and 2; AAB87667).	might get lost (downstream of altered splice site)
205	205	CONFLICT	W -> R (in Ref. 2; AAB87667).	might get lost (downstream of altered splice site)
225	314	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
245	245	DISULFID	Potential.	might get lost (downstream of altered splice site)
252	252	CONFLICT	N -> D (in Ref. 1; AAB68668 and 2; AAB87667).	might get lost (downstream of altered splice site)
263	263	CONFLICT	D -> A (in Ref. 3; AAP30716).	might get lost (downstream of altered splice site)
268	268	CONFLICT	P -> S (in Ref. 3; AAP30716).	might get lost (downstream of altered splice site)
280	280	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
290	290	CONFLICT	N -> H (in Ref. 1; AAB68668).	might get lost (downstream of altered splice site)
296	296	DISULFID	Potential.	might get lost (downstream of altered splice site)
301	301	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
338	419	DOMAIN	Ig-like C2-type 4.	might get lost (downstream of altered splice site)
340	340	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
345	345	DISULFID	Potential.	might get lost (downstream of altered splice site)
396	396	DISULFID	Potential.	might get lost (downstream of altered splice site)
409	409	CONFLICT	H -> F (in Ref. 1; AAB68668).	might get lost (downstream of altered splice site)
417	417	CONFLICT	V -> M (in Ref. 1; AAB68668).	might get lost (downstream of altered splice site)
444	464	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
465	631	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
480	480	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
512	517	MOTIF	ITIM motif 1.	might get lost (downstream of altered splice site)
525	525	CONFLICT	R -> G (in Ref. 2; AAB87667).	might get lost (downstream of altered splice site)
561	561	CONFLICT	S -> P (in Ref. 2; AAB87667).	might get lost (downstream of altered splice site)
593	598	MOTIF	ITIM motif 2.	might get lost (downstream of altered splice site)
595	595	MOD_RES	Phosphotyrosine; by LYN (By similarity).	might get lost (downstream of altered splice site)
623	628	MOTIF	ITIM motif 3.	might get lost (downstream of altered splice site)
625	625	MOD_RES	Phosphotyrosine; by LYN (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1932 / 1932

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

644 / 644

position of stopcodon in wt / mu cDNA

1995 / 1995

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

64 / 64

chromosome

strand

-1

last intron/exon boundary

1849

theoretical NMD boundary in CDS

1735

length of CDS

1932

coding sequence (CDS) position

560

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

623

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

20805

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

54725798

original gDNA sequence snippet

GTTCCCTGTGGGCCCCGTGACCCCCAGCCACAGGTGGAGGT

altered gDNA sequence snippet

GTTCCCTGTGGGCCCCGTGAACCCCAGCCACAGGTGGAGGT

original cDNA sequence snippet

GTTCCCTGTGGGCCCCGTGACCCCCAGCCACAGGTGGAGGT

altered cDNA sequence snippet

GTTCCCTGTGGGCCCCGTGAACCCCAGCCACAGGTGGAGGT

wildtype AA sequence

MTPALTALLC LGLSLGPRTR VQAGPFPKPT LWAEPGSVIS WGSPVTIWCQ GSQEAQEYRL
HKEGSPEPLD RNNPLEPKNK ARFSIPSMTE HHAGRYRCHY YSSAGWSEPS DPLEMVMTGA
YSKPTLSALP SPVVASGGNM TLRCGSQKGY HHFVLMKEGE HQLPRTLDSQ QLHSRGFQAL
FPVGPVTPSH RWRFTCYYYY TNTPWVWSHP SDPLEILPSG VSRKPSLLTL QGPVLAPGQS
LTLQCGSDVG YNRFVLYKEG ERDFLQRPGQ QPQAGLSQAN FTLGPVSPSN GGQYRCYGAH
NLSSEWSAPS DPLNILMAGQ IYDTVSLSAQ PGPTVASGEN VTLLCQSWWQ FDTFLLTKEG
AAHPPLRLRS MYGAHKYQAE FPMSPVTSAH AGTYRCYGSY SSNPHLLSHP SEPLELVVSG
PEDQPLNPPG SGPQNPPGLG SGAGTRAAGL GRYLEVLIGV SVAFVLLLFL LLFLLLRRQR
HSKHRTSDQR KTDFQRPAGA AETEPKDRGL LRRSSPAADV QEENLYAAVK DTQSEDRVEL
DSQSPHDEDP QAVTYAPVKH SSPRREMASP PSSLSGEFLD TKDRQVEEDR QMDTEAAASE
ASQDVTYAQL HSLTLRRKAT EPPPSQEGEP PAEPSIYATL AIH*

mutated AA sequence

MTPALTALLC LGLSLGPRTR VQAGPFPKPT LWAEPGSVIS WGSPVTIWCQ GSQEAQEYRL
HKEGSPEPLD RNNPLEPKNK ARFSIPSMTE HHAGRYRCHY YSSAGWSEPS DPLEMVMTGA
YSKPTLSALP SPVVASGGNM TLRCGSQKGY HHFVLMKEGE HQLPRTLDSQ QLHSRGFQAL
FPVGPVNPSH RWRFTCYYYY TNTPWVWSHP SDPLEILPSG VSRKPSLLTL QGPVLAPGQS
LTLQCGSDVG YNRFVLYKEG ERDFLQRPGQ QPQAGLSQAN FTLGPVSPSN GGQYRCYGAH
NLSSEWSAPS DPLNILMAGQ IYDTVSLSAQ PGPTVASGEN VTLLCQSWWQ FDTFLLTKEG
AAHPPLRLRS MYGAHKYQAE FPMSPVTSAH AGTYRCYGSY SSNPHLLSHP SEPLELVVSG
PEDQPLNPPG SGPQNPPGLG SGAGTRAAGL GRYLEVLIGV SVAFVLLLFL LLFLLLRRQR
HSKHRTSDQR KTDFQRPAGA AETEPKDRGL LRRSSPAADV QEENLYAAVK DTQSEDRVEL
DSQSPHDEDP QAVTYAPVKH SSPRREMASP PSSLSGEFLD TKDRQVEEDR QMDTEAAASE
ASQDVTYAQL HSLTLRRKAT EPPPSQEGEP PAEPSIYATL AIH*

speed

0.88 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