MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000329956
Querying Taster for transcript #2: ENST00000563189
Querying Taster for transcript #3: ENST00000435835
Querying Taster for transcript #4: ENST00000541146
MT speed 0 s - this script 3.713463 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LRRC36	polymorphism_automatic	5.23230347937442e-11	simple_aae				R101P	single base exchange	rs9922085		show file
LRRC36	polymorphism_automatic	5.23230347937442e-11	simple_aae				R101P	single base exchange	rs9922085		show file
LRRC36	polymorphism_automatic	5.23230347937442e-11	simple_aae				R222P	single base exchange	rs9922085		show file
LRRC36	polymorphism_automatic	0.00132617468393903	without_aae					single base exchange	rs9922085		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999947677 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:67397580G>CN/A show variant in all transcripts IGV

HGNC symbol

LRRC36

Ensembl transcript ID

ENST00000563189

Genbank transcript ID

NM_001161575

UniProt peptide

Q1X8D7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.302G>C
cDNA.393G>C
g.36880G>C

AA changes

R101P Score: 103 explain score(s)

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

101

frameshift

known variant

Reference ID: rs9922085

database	homozygous (C/C)	heterozygous	allele carriers
1000G	286	460	746
ExAC	1628	7649	9277

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOXA2, Transcription Factor, FOXA2 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
USF1, Transcription Factor, USF1 Transcription Factor Binding (-1)
USF1, Transcription Factor, USF1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding (1)

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.116	0.012
	0.721	0.189
(flanking)	0.046	0.295

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	36884	wt: 0.2758 / mu: 0.3062 (marginal change - not scored)	wt: CGTGATCAGAAATTA mu: CCTGATCAGAAATTA	TGAT\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

101

mutated

not conserved

101

Ptroglodytes

not conserved

ENSPTRG00000008227

222

Mmulatta

not conserved

ENSMMUG00000009821

222

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054320

222

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000057934

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1902 / 1902

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

634 / 634

position of stopcodon in wt / mu cDNA

1993 / 1993

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

92 / 92

chromosome

strand

last intron/exon boundary

1774

theoretical NMD boundary in CDS

1632

length of CDS

1902

coding sequence (CDS) position

302

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

393

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

36880

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

67397580

original gDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered gDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

original cDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered cDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

wildtype AA sequence

MLRPRFLPPD DRTVREGERK AAKLHFSQLG NSENFLLEVE KSSREKTMKN CVTGESSASK
VSANVDSRIE MDSNKGLFIP FPNREIKDSL STSATQGNGT RDQKLDTFPL GTQTQEVARR
EMPSDNHQED EFRHYSPRQS TVRSPEKMTR EGYQVSFLDN KSSGSSPEKE LIPKPDTFHL
THDASLSKCL DVGDSSQIHP YQLPSDVGLE NYDSCYSQTL SLHGSLGKRP QRSKNYQEYS
IKPSNDIKTT ASHSCGDLLT SLSNPDSSTG RLLKLSSDLY ATTHFNSDPA VLVNVEQQLS
TSLDDLTPAH GSVPNNAVLG NRTTPLRTLL LSPGTSEHRK IFTKRSLSPS KRGFKWKDNI
LANLNLKHGF QDATGSEPLS SDLGSLHGLA GNHSPPISAR TPHVATVLRQ LLELVDKHWN
GSGSLLLNKK FLGPARDLLL SLVVPAPSQP RCCSHPEDTM KAFCRRELEL KEAAQLVPND
MESLKQKLVR VLEENLILSE KIQQLEEGAA ISIVSGQQSH TYDDLLHKNQ QLTMQVACLN
QELAQLKKLE KTVAILHESQ RSLVVTNEYL LQQLNKEPKG YSGKALLPPE KGHHLGRSSP
FGKSTLSSSS PVAHETGQYL IQSVLDAAPE PGL*

mutated AA sequence

MLRPRFLPPD DRTVREGERK AAKLHFSQLG NSENFLLEVE KSSREKTMKN CVTGESSASK
VSANVDSRIE MDSNKGLFIP FPNREIKDSL STSATQGNGT PDQKLDTFPL GTQTQEVARR
EMPSDNHQED EFRHYSPRQS TVRSPEKMTR EGYQVSFLDN KSSGSSPEKE LIPKPDTFHL
THDASLSKCL DVGDSSQIHP YQLPSDVGLE NYDSCYSQTL SLHGSLGKRP QRSKNYQEYS
IKPSNDIKTT ASHSCGDLLT SLSNPDSSTG RLLKLSSDLY ATTHFNSDPA VLVNVEQQLS
TSLDDLTPAH GSVPNNAVLG NRTTPLRTLL LSPGTSEHRK IFTKRSLSPS KRGFKWKDNI
LANLNLKHGF QDATGSEPLS SDLGSLHGLA GNHSPPISAR TPHVATVLRQ LLELVDKHWN
GSGSLLLNKK FLGPARDLLL SLVVPAPSQP RCCSHPEDTM KAFCRRELEL KEAAQLVPND
MESLKQKLVR VLEENLILSE KIQQLEEGAA ISIVSGQQSH TYDDLLHKNQ QLTMQVACLN
QELAQLKKLE KTVAILHESQ RSLVVTNEYL LQQLNKEPKG YSGKALLPPE KGHHLGRSSP
FGKSTLSSSS PVAHETGQYL IQSVLDAAPE PGL*

speed

0.33 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: 0.999999999947677 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:67397580G>CN/A show variant in all transcripts IGV

HGNC symbol

LRRC36

Ensembl transcript ID

ENST00000435835

Genbank transcript ID

N/A

UniProt peptide

Q1X8D7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.302G>C
cDNA.366G>C
g.36880G>C

AA changes

R101P Score: 103 explain score(s)

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

101

frameshift

known variant

Reference ID: rs9922085

database	homozygous (C/C)	heterozygous	allele carriers
1000G	286	460	746
ExAC	1628	7649	9277

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.116	0.012
	0.721	0.189
(flanking)	0.046	0.295

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	36884	wt: 0.2758 / mu: 0.3062 (marginal change - not scored)	wt: CGTGATCAGAAATTA mu: CCTGATCAGAAATTA	TGAT\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

101

mutated

not conserved

101

Ptroglodytes

not conserved

ENSPTRG00000008227

222

Mmulatta

not conserved

ENSMMUG00000009821

222

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054320

222

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000057934

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1590 / 1590

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

530 / 530

position of stopcodon in wt / mu cDNA

1654 / 1654

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

65 / 65

chromosome

strand

last intron/exon boundary

1435

theoretical NMD boundary in CDS

1320

length of CDS

1590

coding sequence (CDS) position

302

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

366

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

36880

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

67397580

original gDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered gDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

original cDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered cDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

wildtype AA sequence

MLRPRFLPPD DRTVREGERK AAKLHFSQLG NSENFLLEVE KSSREKTMKN CVTGESSASK
VSANVDSRIE MDSNKGLFIP FPNREIKDSL STSATQGNGT RDQKLDTFPL GTQTQEVARR
EMPSDNHQED EFRHYSPRQS TVRSPEKMTR EGYQVSFLDN KSSGSSPEKE LIPKPDTFHL
THDASLSKCL DVGDSSQIHP YQLPSDVGLE NYDSCYSQTL SLHGSLGKRP QRSKNYQEYS
IKPSNDIKTT ASHSCGDLLT SLSNPDSSTG RLLKLSSDLY ATTHFNSDPA VLVNVEQQLS
TSLDDLTPAH GSVPNNAVLG NRTTPLRTLL LSPGTSEHRK IFTKRSLSPS KRGFKWKDNI
LANLNLKHGF QDATGSEESL KQKLVRVLEE NLILSEKIQQ LEEGAAISIV SGQQSHTYDD
LLHKNQQLTM QVACLNQELA QLKKLEKTVA ILHESQRSLV VTNEYLLQQL NKEPKGYSGK
ALLPPEKGHH LGRSSPFGKS TLSSSSPVAH ETGQYLIQSV LDAAPEPGL*

mutated AA sequence

MLRPRFLPPD DRTVREGERK AAKLHFSQLG NSENFLLEVE KSSREKTMKN CVTGESSASK
VSANVDSRIE MDSNKGLFIP FPNREIKDSL STSATQGNGT PDQKLDTFPL GTQTQEVARR
EMPSDNHQED EFRHYSPRQS TVRSPEKMTR EGYQVSFLDN KSSGSSPEKE LIPKPDTFHL
THDASLSKCL DVGDSSQIHP YQLPSDVGLE NYDSCYSQTL SLHGSLGKRP QRSKNYQEYS
IKPSNDIKTT ASHSCGDLLT SLSNPDSSTG RLLKLSSDLY ATTHFNSDPA VLVNVEQQLS
TSLDDLTPAH GSVPNNAVLG NRTTPLRTLL LSPGTSEHRK IFTKRSLSPS KRGFKWKDNI
LANLNLKHGF QDATGSEESL KQKLVRVLEE NLILSEKIQQ LEEGAAISIV SGQQSHTYDD
LLHKNQQLTM QVACLNQELA QLKKLEKTVA ILHESQRSLV VTNEYLLQQL NKEPKGYSGK
ALLPPEKGHH LGRSSPFGKS TLSSSSPVAH ETGQYLIQSV LDAAPEPGL*

speed

0.27 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999947677 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:67397580G>CN/A show variant in all transcripts IGV

HGNC symbol

LRRC36

Ensembl transcript ID

ENST00000329956

Genbank transcript ID

NM_018296

UniProt peptide

Q1X8D7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.665G>C
cDNA.684G>C
g.36880G>C

AA changes

R222P Score: 103 explain score(s)

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

222

frameshift

known variant

Reference ID: rs9922085

database	homozygous (C/C)	heterozygous	allele carriers
1000G	286	460	746
ExAC	1628	7649	9277

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.116	0.012
	0.721	0.189
(flanking)	0.046	0.295

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	36884	wt: 0.2758 / mu: 0.3062 (marginal change - not scored)	wt: CGTGATCAGAAATTA mu: CCTGATCAGAAATTA	TGAT\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

222

mutated

not conserved

222

Ptroglodytes

not conserved

ENSPTRG00000008227

222

Mmulatta

not conserved

ENSMMUG00000009821

222

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054320

222

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000057934

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2265 / 2265

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

755 / 755

position of stopcodon in wt / mu cDNA

2284 / 2284

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

20 / 20

chromosome

strand

last intron/exon boundary

2065

theoretical NMD boundary in CDS

1995

length of CDS

2265

coding sequence (CDS) position

665

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

684

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

36880

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

67397580

original gDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered gDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

original cDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered cDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

wildtype AA sequence

MAEQWELDEE GIRRLGALTL EQPELVESLS LQGSYAGKIH SIGDAFRNFK NLRSLDLSRN
LITSLKGIQY LCSLQDLNLY YNNIPSLVEV SRLQPLPFLK ELDLRLNPVV RKDTDYRLFA
VYTLQTLEKL DDRTVREGER KAAKLHFSQL GNSENFLLEV EKSSREKTMK NCVTGESSAS
KVSANVDSRI EMDSNKGLFI PFPNREIKDS LSTSATQGNG TRDQKLDTFP LGTQTQEVAR
REMPSDNHQE DEFRHYSPRQ STVRSPEKMT REGYQVSFLD NKSSGSSPEK ELIPKPDTFH
LTHDASLSKC LDVGDSSQIH PYQLPSDVGL ENYDSCYSQT LSLHGSLGKR PQRSKNYQEY
SIKPSNDIKT TASHSCGDLL TSLSNPDSST GRLLKLSSDL YATTHFNSDP AVLVNVEQQL
STSLDDLTPA HGSVPNNAVL GNRTTPLRTL LLSPGTSEHR KIFTKRSLSP SKRGFKWKDN
ILANLNLKHG FQDATGSEPL SSDLGSLHGL AGNHSPPISA RTPHVATVLR QLLELVDKHW
NGSGSLLLNK KFLGPARDLL LSLVVPAPSQ PRCCSHPEDT MKAFCRRELE LKEAAQLVPN
DMESLKQKLV RVLEENLILS EKIQQLEEGA AISIVSGQQS HTYDDLLHKN QQLTMQVACL
NQELAQLKKL EKTVAILHES QRSLVVTNEY LLQQLNKEPK GYSGKALLPP EKGHHLGRSS
PFGKSTLSSS SPVAHETGQY LIQSVLDAAP EPGL*

mutated AA sequence

MAEQWELDEE GIRRLGALTL EQPELVESLS LQGSYAGKIH SIGDAFRNFK NLRSLDLSRN
LITSLKGIQY LCSLQDLNLY YNNIPSLVEV SRLQPLPFLK ELDLRLNPVV RKDTDYRLFA
VYTLQTLEKL DDRTVREGER KAAKLHFSQL GNSENFLLEV EKSSREKTMK NCVTGESSAS
KVSANVDSRI EMDSNKGLFI PFPNREIKDS LSTSATQGNG TPDQKLDTFP LGTQTQEVAR
REMPSDNHQE DEFRHYSPRQ STVRSPEKMT REGYQVSFLD NKSSGSSPEK ELIPKPDTFH
LTHDASLSKC LDVGDSSQIH PYQLPSDVGL ENYDSCYSQT LSLHGSLGKR PQRSKNYQEY
SIKPSNDIKT TASHSCGDLL TSLSNPDSST GRLLKLSSDL YATTHFNSDP AVLVNVEQQL
STSLDDLTPA HGSVPNNAVL GNRTTPLRTL LLSPGTSEHR KIFTKRSLSP SKRGFKWKDN
ILANLNLKHG FQDATGSEPL SSDLGSLHGL AGNHSPPISA RTPHVATVLR QLLELVDKHW
NGSGSLLLNK KFLGPARDLL LSLVVPAPSQ PRCCSHPEDT MKAFCRRELE LKEAAQLVPN
DMESLKQKLV RVLEENLILS EKIQQLEEGA AISIVSGQQS HTYDDLLHKN QQLTMQVACL
NQELAQLKKL EKTVAILHES QRSLVVTNEY LLQQLNKEPK GYSGKALLPP EKGHHLGRSS
PFGKSTLSSS SPVAHETGQY LIQSVLDAAP EPGL*

speed

0.80 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.998673825316061 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:67397580G>CN/A show variant in all transcripts IGV

HGNC symbol

LRRC36

Ensembl transcript ID

ENST00000541146

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.401G>C
g.36880G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs9922085

database	homozygous (C/C)	heterozygous	allele carriers
1000G	286	460	746
ExAC	1628	7649	9277

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.116	0.012
	0.721	0.189
(flanking)	0.046	0.295

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	36884	wt: 0.2758 / mu: 0.3062 (marginal change - not scored)	wt: CGTGATCAGAAATTA mu: CCTGATCAGAAATTA	TGAT\|caga

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

671 / 671

chromosome

strand

last intron/exon boundary

1132

theoretical NMD boundary in CDS

411

length of CDS

681

coding sequence (CDS) position

N/A

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

401

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

36880

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

67397580

original gDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered gDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

original cDNA sequence snippet

AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT

altered cDNA sequence snippet

AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT

wildtype AA sequence

MEGQYPCQPE SKAWFPRCYR QRVTWVVCTV WLETTVPPSL PEPPMWPLSS DSSWSLWIST
GMAPAPSSST RSFSESLKQK LVRVLEENLI LSEKIQQLEE GAAISIVSGQ QSHTYDDLLH
KNQQLTMQVA CLNQELAQLK KLEKTVAILH ESQRSLVVTN EYLLQQLNKE PKGYSGKALL
PPEKGHHLGR SSPFGKSTLS SSSPVAHETG QYLIQSVLDA APEPGL*

mutated AA sequence

N/A

speed

0.64 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems