mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999390662 (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)

chr1:236706862G>CN/A show variant in all transcripts IGV

HGNC symbol

LGALS8

Ensembl transcript ID

ENST00000526634

Genbank transcript ID

N/A

UniProt peptide

O00214

alteration type

single base exchange

alteration region

CDS

DNA changes

c.552G>C
cDNA.815G>C
g.25563G>C

AA changes

R184S Score: 110 explain score(s)

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

184

frameshift

known variant

Reference ID: rs2243525

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1169	1056	2225
ExAC	31626	-30485	1141

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.117	0.201
	-1.301	0.105
(flanking)	1.327	0.886

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
Acceptor lost	25560	sequence motif lost	-	wt: tcag\|AGGC mu: tcag.AGCC
Acc increased	25572	wt: 0.42 / mu: 0.70	wt: TCTTTTCAGAGGCTGCCATTCGCTGCAAGGTTGAACACCCC mu: TCTTTTCAGAGCCTGCCATTCGCTGCAAGGTTGAACACCCC	attc\|GCTG
Acc gained	25565	0.35	mu: TGTGGCTTCTTTTCAGAGCCTGCCATTCGCTGCAAGGTTGA	gcct\|GCCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

184

mutated

not conserved

184

Ptroglodytes

not conserved

ENSPTRG00000002140

184

LPSNREGDISKIAPRTVYTKSKDSTVNHTLTCTKIPPMNCVSK

Mmulatta

not conserved

ENSMMUG00000015132

184

LPSNRGDISKIVPRTVYTKSKDSTVNHSLTCTKIPPMNYVSK

Fcatus

not conserved

ENSFCAG00000003385

184

FPSNRGDISKIVPRTVYTKSKGSTANHSLTCAKILPTNCLSK

Mmusculus

not conserved

ENSMUSG00000057554

192

Ggallus

not conserved

ENSGALG00000014371

183

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000037066

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000009015

182

protein features

start (aa)	end (aa)	feature	details
185	193	STRAND		might get lost (downstream of altered splice site)
187	317	DOMAIN	Galectin 2.	might get lost (downstream of altered splice site)
199	199	CONFLICT	R -> G (in Ref. 8; AAL77076).	might get lost (downstream of altered splice site)
200	207	STRAND		might get lost (downstream of altered splice site)
204	204	CONFLICT	K -> Q (in Ref. 1; AAB51605).	might get lost (downstream of altered splice site)
213	220	STRAND		might get lost (downstream of altered splice site)
221	224	TURN		might get lost (downstream of altered splice site)
225	225	CONFLICT	D -> H (in Ref. 8; AAL77076).	might get lost (downstream of altered splice site)
225	233	STRAND		might get lost (downstream of altered splice site)
234	237	TURN		might get lost (downstream of altered splice site)
238	244	STRAND		might get lost (downstream of altered splice site)
246	249	STRAND		might get lost (downstream of altered splice site)
249	255	REGION	Beta-galactoside binding (By similarity).	might get lost (downstream of altered splice site)
256	258	STRAND		might get lost (downstream of altered splice site)
259	259	CONFLICT	F -> L (in Ref. 7; AAK16736).	might get lost (downstream of altered splice site)
266	273	STRAND		might get lost (downstream of altered splice site)
275	282	STRAND		might get lost (downstream of altered splice site)
285	291	STRAND		might get lost (downstream of altered splice site)
297	299	HELIX		might get lost (downstream of altered splice site)
302	315	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

954 / 954

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

318 / 318

position of stopcodon in wt / mu cDNA

1217 / 1217

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

264 / 264

chromosome

strand

last intron/exon boundary

1068

theoretical NMD boundary in CDS

754

length of CDS

954

coding sequence (CDS) position

552

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

815

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

25563

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

236706862

original gDNA sequence snippet

ACTGTGGCTTCTTTTCAGAGGCTGCCATTCGCTGCAAGGTT

altered gDNA sequence snippet

ACTGTGGCTTCTTTTCAGAGCCTGCCATTCGCTGCAAGGTT

original cDNA sequence snippet

TCTGGCACGCCCCAGCTTAGGCTGCCATTCGCTGCAAGGTT

altered cDNA sequence snippet

TCTGGCACGCCCCAGCTTAGCCTGCCATTCGCTGCAAGGTT

wildtype AA sequence

MMLSLNNLQN IIYNPVIPFV GTIPDQLDPG TLIVIRGHVP SDADRFQVDL QNGSSMKPRA
DVAFHFNPRF KRAGCIVCNT LINEKWGREE ITYDTPFKRE KSFEIVIMVL KDKFQVAVNG
KHTLLYGHRI GPEKIDTLGI YGKVNIHSIG FSFSSDLQST QASSLELTEI SRENVPKSGT
PQLRLPFAAR LNTPMGPGRT VVVKGEVNAN AKSFNVDLLA GKSKDIALHL NPRLNIKAFV
RNSFLQESWG EEERNITSFP FSPGMYFEMI IYCDVREFKV AVNGVHSLEY KHRFKELSSI
DTLEINGDIH LLEVRSW*

mutated AA sequence

MMLSLNNLQN IIYNPVIPFV GTIPDQLDPG TLIVIRGHVP SDADRFQVDL QNGSSMKPRA
DVAFHFNPRF KRAGCIVCNT LINEKWGREE ITYDTPFKRE KSFEIVIMVL KDKFQVAVNG
KHTLLYGHRI GPEKIDTLGI YGKVNIHSIG FSFSSDLQST QASSLELTEI SRENVPKSGT
PQLSLPFAAR LNTPMGPGRT VVVKGEVNAN AKSFNVDLLA GKSKDIALHL NPRLNIKAFV
RNSFLQESWG EEERNITSFP FSPGMYFEMI IYCDVREFKV AVNGVHSLEY KHRFKELSSI
DTLEINGDIH LLEVRSW*

speed

1.03 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