MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #2: ENST00000370888
MT speed 0 s - this script 3.186583 s

Results

genesymbol

pred

model

pred_problem

f_splice

f_known_DM

f_pot_DM

AA_changes

alt_type

snp_id

features_at_a_glance

file

LRRC1

disease causing

0.999999998952445

simple_aae

n/a

201915048

show file

Taster files

mutation t@sting

documentation

Alteration 6:53778661T>G_1_ENST00000370888

Prediction	disease causing	Model: simple_aae, prob: 0.999999998952445 (explain)
Summary	amino acid sequence changed heterozygous in TGP or ExAC protein features (might be) affected	hyperlink

analysed issue

analysis result

name of alteration

6:53778661T>G_1_ENST00000370888

alteration (phys. location)

chr6:53778661T>G show variant in all transcripts IGV

HGNC symbol

LRRC1

ExAC LOF metrics

LOF: 0.57, misssense: 1.15, synonymous: -0.35

Ensembl transcript ID

ENST00000370888

Genbank transcript ID

NM_018214

UniProt peptide

Q9BTT6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1000T>G
g.119367T>G

AA changes

C334G Score: 159
explain score(s)

frameshift

length of protein

normal

known variant

Reference ID: rs201915048

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	554	554

regulatory features

name	class
H3K36me3	Histone	Histone 3 Lysine 36 Tri-Methylation

multicell regulatory features

N/A

external features from FANTOM5 and/or VISTA

N/A

miRNA binding site(s)

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.884	0.564
	4.23	0.998
(flanking)	5.101	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

334

mutated

not conserved

334

Ptroglodytes

all identical

ENSPTRG00000018293

334

Mmulatta

all identical

ENSMMUG00000011049

334

Fcatus

all identical

ENSFCAG00000031982

298

Mmusculus

all identical

ENSMUSG00000032352

334

Ggallus

all identical

ENSGALG00000016304

282

Trubripes

all identical

ENSTRUG00000015250

334

Drerio

no homologue

Dmelanogaster

all identical

FBgn0263289

335

Celegans

all identical

WBGene00002632

334

Xtropicalis

all identical

ENSXETG00000001618

334

protein features

start (aa)	end (aa)	feature	details
311	334	REPEAT	LRR 14.	lost

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1575 / 1575

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

525 / 525

position of stopcodon in wt / mu cDNA

1852 / 1852

poly(A) signal

N/A

position of start ATG in wt / mu cDNA

278 / 278

chromosome

strand

last intron/exon boundary

1693

theoretical NMD boundary in CDS

1365

length of CDS

1575

coding sequence (CDS) position

1000

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

1277

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

119367

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

53778661

original gDNA sequence snippet

TCTCACCATAGATCGGCGGGTGCTGCAGCCTCACTGTGTTC

altered gDNA sequence snippet

TCTCACCATAGATCGGCGGGGGCTGCAGCCTCACTGTGTTC

original cDNA sequence snippet

TACCAAAAGAGATCGGCGGGTGCTGCAGCCTCACTGTGTTC

altered cDNA sequence snippet

TACCAAAAGAGATCGGCGGGGGCTGCAGCCTCACTGTGTTC

wildtype AA sequence

MFHCIPLWRC NRHVESIDKR HCSLVYVPEE IYRYARSLEE LLLDANQLRE LPEQFFQLVK
LRKLGLSDNE IQRLPPEIAN FMQLVELDVS RNEIPEIPES ISFCKALQVA DFSGNPLTRL
PESFPELQNL TCLSVNDISL QSLPENIGNL YNLASLELRE NLLTYLPDSL TQLRRLEELD
LGNNEIYNLP ESIGALLHLK DLWLDGNQLS ELPQEIGNLK NLLCLDVSEN RLERLPEEIS
GLTSLTDLVI SQNLLETIPD GIGKLKKLSI LKVDQNRLTQ LPEAVGECES LTELVLTENQ
LLTLPKSIGK LKKLSNLNAD RNKLVSLPKE IGGCCSLTVF CVRDNRLTRI PAEVSQATEL
HVLDVAGNRL LHLPLSLTAL KLKALWLSDN QSQPLLTFQT DTDYTTGEKI LTCVLLPQLP
SEPTCQENLP RCGALENLVN DVSDEAWNER AVNRVSAIRF VEDEKDEEDN ETRTLLRRAT
PHPGELKHMK KTVENLRNDM NAAKGLDSNK NEVNHAIDRV TTSV*

mutated AA sequence

MFHCIPLWRC NRHVESIDKR HCSLVYVPEE IYRYARSLEE LLLDANQLRE LPEQFFQLVK
LRKLGLSDNE IQRLPPEIAN FMQLVELDVS RNEIPEIPES ISFCKALQVA DFSGNPLTRL
PESFPELQNL TCLSVNDISL QSLPENIGNL YNLASLELRE NLLTYLPDSL TQLRRLEELD
LGNNEIYNLP ESIGALLHLK DLWLDGNQLS ELPQEIGNLK NLLCLDVSEN RLERLPEEIS
GLTSLTDLVI SQNLLETIPD GIGKLKKLSI LKVDQNRLTQ LPEAVGECES LTELVLTENQ
LLTLPKSIGK LKKLSNLNAD RNKLVSLPKE IGGGCSLTVF CVRDNRLTRI PAEVSQATEL
HVLDVAGNRL LHLPLSLTAL KLKALWLSDN QSQPLLTFQT DTDYTTGEKI LTCVLLPQLP
SEPTCQENLP RCGALENLVN DVSDEAWNER AVNRVSAIRF VEDEKDEEDN ETRTLLRRAT
PHPGELKHMK KTVENLRNDM NAAKGLDSNK NEVNHAIDRV TTSV*

version

genome build 37 / Ensembl release 85

speed

0.30 s

for research use only

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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Alteration 6:53778661T>G_1_ENST00000370888

Prediction

disease causing

for research use only

Problems