MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000372113
Querying Taster for transcript #2: ENST00000538192
MT speed 0 s - this script 2.629392 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LRIT2	polymorphism_automatic	1.79500858621395e-12	simple_aae		affected		T510P	single base exchange	rs6585847		show file
LRIT2	polymorphism_automatic	1.79500858621395e-12	simple_aae		affected		T520P	single base exchange	rs6585847		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998205 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:85981801T>GN/A show variant in all transcripts IGV

HGNC symbol

LRIT2

Ensembl transcript ID

ENST00000372113

Genbank transcript ID

NM_001017924

UniProt peptide

A6NDA9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1528A>C
cDNA.1534A>C
g.3545A>C

AA changes

T510P Score: 38 explain score(s)

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

510

frameshift

known variant

Reference ID: rs6585847

database	homozygous (G/G)	heterozygous	allele carriers
1000G	835	1110	1945
ExAC	15107	2553	17660

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.489	0.059
	1.747	0.059
(flanking)	-0.34	0.009

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	3554	wt: 0.27 / mu: 0.64	wt: CCCCCAGCTGCACCCCTGCAGCCCCGCAGTCCAAGGATGGC mu: CCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGATGGC	gcag\|CCCC
Acc increased	3552	wt: 0.20 / mu: 0.70	wt: AGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCCAAGGATG mu: AGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGATG	ctgc\|AGCC
Acc gained	3550	0.56	mu: AAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGA	ccct\|GCAG

distance from splice site

636

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

510

mutated

not conserved

510

Ptroglodytes

not conserved

ENSPTRG00000029854

520

Mmulatta

not conserved

ENSMMUG00000000659

510

Fcatus

not conserved

ENSFCAG00000001653

510

Mmusculus

not conserved

ENSMUSG00000043418

510

Ggallus

not conserved

ENSGALG00000002307

473

Trubripes

not conserved

ENSTRUG00000011830

471

QGHNLR

Drerio

not conserved

ENSDARG00000030626

509

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005631

516

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1653 / 1653

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

551 / 551

position of stopcodon in wt / mu cDNA

1659 / 1659

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

7 / 7

chromosome

strand

-1

last intron/exon boundary

899

theoretical NMD boundary in CDS

842

length of CDS

1653

coding sequence (CDS) position

1528

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

1534

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

3545

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

85981801

original gDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCC

altered gDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCC

original cDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCC

altered cDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCC

wildtype AA sequence

MASVFHYFLL VLVFLDTHAA QPFCLPGCTC SEESFGRTLQ CTSVSLGKIP GNLSEEFKQV
RIENSPLFEM PQGSFINMST LEYLWLNFNN ISVIHLGALE HLPELRELRL EGNKLCSVPW
TAFRATPLLR VLDLKRNKID ALPELALQFL VSLTYLDLSS NRLTVVSKSV FLNWPAYQKC
RQPDCGAEIL SSLVVALHDN PWVCDCRLRG LVQFVKSITL PVILVNSYLI CQGPLSKAGQ
LFHETELSAC MKPQISTPSA NITIRAGQNV TLRCLAQASP SPSIAWTYPL SMWREFDVLT
SSTGEDTALS ELAIPAAHLV DSGNYTCMAS NSIGKSNLVI SLHVQPAQAL HAPDSLSIPS
EGNAYIDLRV VKQTVHGILL EWLAVADTSK EEWFTLYIAS DEAFRKEVVH IGPGINTYAV
DDLLPGTKYE ACLSLEGQPP HQGQCVAFVT GRDAGGLEAR EHLLHVTVVL CVVLLAVPVG
AYAWAAQGPC SCSKWVLRGC LHRRKAPSCT PAAPQSKDGS FREHPAVCDD GEGHIDTEGD
KEKGGTEDNS *

mutated AA sequence

speed

0.42 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
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998205 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:85981801T>GN/A show variant in all transcripts IGV

HGNC symbol

LRIT2

Ensembl transcript ID

ENST00000538192

Genbank transcript ID

N/A

UniProt peptide

A6NDA9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1558A>C
cDNA.1627A>C
g.3545A>C

AA changes

T520P Score: 38 explain score(s)

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

520

frameshift

known variant

Reference ID: rs6585847

database	homozygous (G/G)	heterozygous	allele carriers
1000G	835	1110	1945
ExAC	15107	2553	17660

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.489	0.059
	1.747	0.059
(flanking)	-0.34	0.009

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	3554	wt: 0.27 / mu: 0.64	wt: CCCCCAGCTGCACCCCTGCAGCCCCGCAGTCCAAGGATGGC mu: CCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGATGGC	gcag\|CCCC
Acc increased	3552	wt: 0.20 / mu: 0.70	wt: AGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCCAAGGATG mu: AGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGATG	ctgc\|AGCC
Acc gained	3550	0.56	mu: AAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGA	ccct\|GCAG

distance from splice site

636

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

520

mutated

not conserved

520

Ptroglodytes

not conserved

ENSPTRG00000029854

520

Mmulatta

not conserved

ENSMMUG00000000659

510

Fcatus

not conserved

ENSFCAG00000001653

510

Mmusculus

not conserved

ENSMUSG00000043418

510

Ggallus

not conserved

ENSGALG00000002307

460

Trubripes

not conserved

ENSTRUG00000011830

471

Drerio

not conserved

ENSDARG00000030626

509

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005631

516

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1683 / 1683

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

561 / 561

position of stopcodon in wt / mu cDNA

1752 / 1752

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

70 / 70

chromosome

strand

-1

last intron/exon boundary

992

theoretical NMD boundary in CDS

872

length of CDS

1683

coding sequence (CDS) position

1558

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

1627

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

3545

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

85981801

original gDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCC

altered gDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCC

original cDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCC

altered cDNA sequence snippet

GCAGGAAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCC

wildtype AA sequence

MASVFHYFLL VLVFLDTHAA QPFCLPGCTC SEESFGRTLQ CTSVSLGKIP GNLSEEFKQV
RIENSPLFEM PQGSFINMST LEYLWLNFNN ISVIHLGALE HLPELRELRL EGNKLCSVPW
TAFRATPLLR VLDLKRNKID ALPELALQFL VSLTYLDLSS NRLTVVSKSV FLNWPAYQKC
RQPDCGAEIL SSLVVALHDN PWVCDCRLRG LVQFVKSITL PVILVNSYLI CQGPLSKAGQ
LFHETELSAC MKPQISTPSA NITIRAGQNV TLRCLAQASP SPSIAWTYPL SMWREFDGLL
GGKHLTPVLT SSTGEDTALS ELAIPAAHLV DSGNYTCMAS NSIGKSNLVI SLHVQPAQAL
HAPDSLSIPS EGNAYIDLRV VKQTVHGILL EWLAVADTSK EEWFTLYIAS DEAFRKEVVH
IGPGINTYAV DDLLPGTKYE ACLSLEGQPP HQGQCVAFVT GRDAGGLEAR EHLLHVTVVL
CVVLLAVPVG AYAWAAQGPC SCSKWVLRGC LHRRKAPSCT PAAPQSKDGS FREHPAVCDD
GEGHIDTEGD KEKGGTEDNS *

mutated AA sequence

MASVFHYFLL VLVFLDTHAA QPFCLPGCTC SEESFGRTLQ CTSVSLGKIP GNLSEEFKQV
RIENSPLFEM PQGSFINMST LEYLWLNFNN ISVIHLGALE HLPELRELRL EGNKLCSVPW
TAFRATPLLR VLDLKRNKID ALPELALQFL VSLTYLDLSS NRLTVVSKSV FLNWPAYQKC
RQPDCGAEIL SSLVVALHDN PWVCDCRLRG LVQFVKSITL PVILVNSYLI CQGPLSKAGQ
LFHETELSAC MKPQISTPSA NITIRAGQNV TLRCLAQASP SPSIAWTYPL SMWREFDGLL
GGKHLTPVLT SSTGEDTALS ELAIPAAHLV DSGNYTCMAS NSIGKSNLVI SLHVQPAQAL
HAPDSLSIPS EGNAYIDLRV VKQTVHGILL EWLAVADTSK EEWFTLYIAS DEAFRKEVVH
IGPGINTYAV DDLLPGTKYE ACLSLEGQPP HQGQCVAFVT GRDAGGLEAR EHLLHVTVVL
CVVLLAVPVG AYAWAAQGPC SCSKWVLRGC LHRRKAPSCP PAAPQSKDGS FREHPAVCDD
GEGHIDTEGD KEKGGTEDNS *

speed

0.23 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems