mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.982449390232502 (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)

chr4:129100643G>AN/A show variant in all transcripts IGV

HGNC symbol

LARP1B

Ensembl transcript ID

ENST00000354456

Genbank transcript ID

N/A

UniProt peptide

Q659C4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.236G>A
cDNA.2110G>A
g.118221G>A

AA changes

R79H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs12645577

database	homozygous (A/A)	heterozygous	allele carriers
1000G	885	1082	1967
ExAC	26108	-19449	6659

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.884	1
	2.591	0.998
(flanking)	-0.447	0.897

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
Donor marginally increased	118214	wt: 0.7969 / mu: 0.7970 (marginal change - not scored)	wt: ATTCCAGAGACCGTG mu: ATTCCAGAGACCATG	TCCA\|gaga
Donor increased	118224	wt: 0.81 / mu: 0.93	wt: CCGTGGGCCAGGAAC mu: CCATGGGCCAGGAAC	GTGG\|gcca

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

not conserved

ENSMMUG00000021347

659

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000037814

n/a

Ggallus

not conserved

ENSGALG00000010207

594

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0261618

1296

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000022512

734

protein features

start (aa)	end (aa)	feature	details
114	167	COMPBIAS	Arg-rich.	might get lost (downstream of altered splice site)
209	299	DOMAIN	HTH La-type RNA-binding.	might get lost (downstream of altered splice site)
272	272	CONFLICT	A -> V (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
289	289	CONFLICT	K -> E (in Ref. 1; BAA91576).	might get lost (downstream of altered splice site)
291	291	CONFLICT	E -> T (in Ref. 1; BAC05306).	might get lost (downstream of altered splice site)
340	340	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
343	343	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
363	363	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
432	432	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
454	454	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
473	473	CONFLICT	R -> Q (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
639	639	CONFLICT	T -> A (in Ref. 2; CAD97908).	might get lost (downstream of altered splice site)
671	671	CONFLICT	N -> S (in Ref. 4; AAH62606).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

846 / 846

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

282 / 282

position of stopcodon in wt / mu cDNA

2720 / 2720

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

1875 / 1875

chromosome

strand

last intron/exon boundary

2679

theoretical NMD boundary in CDS

754

length of CDS

846

coding sequence (CDS) position

236

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

2110

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

118221

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

129100643

original gDNA sequence snippet

GGTAATGGATTCCAGAGACCGTGGGCCAGGAACATCCTCTG

altered gDNA sequence snippet

GGTAATGGATTCCAGAGACCATGGGCCAGGAACATCCTCTG

original cDNA sequence snippet

GGTAATGGATTCCAGAGACCGTGGGCCAGGAACATCCTCTG

altered cDNA sequence snippet

GGTAATGGATTCCAGAGACCATGGGCCAGGAACATCCTCTG

wildtype AA sequence

MVHSLPTAVP ESPRIHPTRT PKTPRTPRLQ DPNKTPRFYP VVKEPKAIDV KSPRKRKTRH
STNPPLECHV GWVMDSRDRG PGTSSVSTSN ASPSEGAPLA GSYGCTPHSF PKFQHPSHEL
LKENGFTQQV YHKYRRRCLS ERKRLGIGQS QEMNTLFRFW SFFLRDHFNK KMYEEFRQLA
WEDAKENYRY GLECLFRFYS YGLEKKFRRE IFQDFQEETK KDYESGQLYG LEKFWAYLKY
SQSKTQSIDP KLQEYLCSFK RLEDFRVDNH HDRLLLLIIN I*

mutated AA sequence

MVHSLPTAVP ESPRIHPTRT PKTPRTPRLQ DPNKTPRFYP VVKEPKAIDV KSPRKRKTRH
STNPPLECHV GWVMDSRDHG PGTSSVSTSN ASPSEGAPLA GSYGCTPHSF PKFQHPSHEL
LKENGFTQQV YHKYRRRCLS ERKRLGIGQS QEMNTLFRFW SFFLRDHFNK KMYEEFRQLA
WEDAKENYRY GLECLFRFYS YGLEKKFRRE IFQDFQEETK KDYESGQLYG LEKFWAYLKY
SQSKTQSIDP KLQEYLCSFK RLEDFRVDNH HDRLLLLIIN I*

speed

0.85 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