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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000447370
Querying Taster for transcript #2: ENST00000458019
MT speed 1.76 s - this script 3.792923 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SIGLEC11	polymorphism_automatic	8.79100126027765e-11	simple_aae		affected		E96A	single base exchange	rs9676436		show file
SIGLEC11	polymorphism_automatic	8.79100126027765e-11	simple_aae		affected		E96A	single base exchange	rs9676436		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999991209 (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)

chr19:50463982T>GN/A show variant in all transcripts IGV

HGNC symbol

SIGLEC11

Ensembl transcript ID

ENST00000447370

Genbank transcript ID

NM_052884

UniProt peptide

Q96RL6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.287A>C
cDNA.378A>C
g.448A>C

AA changes

E96A Score: 107 explain score(s)

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

frameshift

known variant

Reference ID: rs9676436

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	5474	21819	27293

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.305	0
	-0.343	0
(flanking)	-2.01	0

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 increased	446	wt: 0.39 / mu: 0.50	wt: GAGGTGGAAATGAGC mu: GAGGTGGCAATGAGC	GGTG\|gaaa

distance from splice site

174

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000011328

Mmulatta

all identical

ENSMMUG00000006385

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000030468

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000089404

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
28	561	TOPO_DOM	Extracellular (Potential).	lost
31	134	DOMAIN	Ig-like V-type.	lost
96	96	CONFLICT	E -> A (in Ref. 3; AAQ88502).	lost
114	114	DISULFID	By similarity.	might get lost (downstream of altered splice site)
132	132	BINDING	Sialic acid (By similarity).	might get lost (downstream of altered splice site)
159	244	DOMAIN	Ig-like C2-type 1.	might get lost (downstream of altered splice site)
177	177	DISULFID	By similarity.	might get lost (downstream of altered splice site)
186	186	DISULFID	By similarity.	might get lost (downstream of altered splice site)
228	228	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	350	DOMAIN	Ig-like C2-type 2.	might get lost (downstream of altered splice site)
262	262	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
287	287	DISULFID	By similarity.	might get lost (downstream of altered splice site)
334	334	DISULFID	By similarity.	might get lost (downstream of altered splice site)
355	452	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
365	365	CONFLICT	A -> G (in Ref. 3; AAQ88502).	might get lost (downstream of altered splice site)
366	366	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
375	375	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
391	391	DISULFID	By similarity.	might get lost (downstream of altered splice site)
436	436	DISULFID	By similarity.	might get lost (downstream of altered splice site)
497	497	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
515	515	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
562	584	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
585	698	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
642	647	MOTIF	ITIM motif.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2097 / 2097

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

699 / 699

position of stopcodon in wt / mu cDNA

2188 / 2188

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

-1

last intron/exon boundary

1922

theoretical NMD boundary in CDS

1780

length of CDS

2097

coding sequence (CDS) position

287

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

378

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

448

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

50463982

original gDNA sequence snippet

CAACCAGAGTCGAGAGGTGGAAATGAGCACCCGGGACCGAT

altered gDNA sequence snippet

CAACCAGAGTCGAGAGGTGGCAATGAGCACCCGGGACCGAT

original cDNA sequence snippet

CAACCAGAGTCGAGAGGTGGAAATGAGCACCCGGGACCGAT

altered cDNA sequence snippet

CAACCAGAGTCGAGAGGTGGCAATGAGCACCCGGGACCGAT

wildtype AA sequence

MVPGQAQPQS PEMLLLPLLL PVLGAGSLNK DPSYSLQVQR QVPVPEGLCV IVSCNLSYPR
DGWDESTAAY GYWFKGRTSP KTGAPVATNN QSREVEMSTR DRFQLTGDPG KGSCSLVIRD
AQREDEAWYF FRVERGSRVR HSFLSNAFFL KVTALTKKPD VYIPETLEPG QPVTVICVFN
WAFKKCPAPS FSWTGAALSP RRTRPSTSHF SVLSFTPSPQ DHDTDLTCHV DFSRKGVSAQ
RTVRLRVAYA PKDLIISISH DNTSALELQG NVIYLEVQKG QFLRLLCAAD SQPPATLSWV
LQDRVLSSSH PWGPRTLGLE LRGVRAGDSG RYTCRAENRL GSQQQALDLS VQYPPENLRV
MVSQANRTVL ENLGNGTSLP VLEGQSLRLV CVTHSSPPAR LSWTRWGQTV GPSQPSDPGV
LELPPIQMEH EGEFTCHAQH PLGSQHVSLS LSVHYPPQLL GPSCSWEAEG LHCSCSSQAS
PAPSLRWWLG EELLEGNSSQ GSFEVTPSSA GPWANSSLSL HGGLSSGLRL RCKAWNVHGA
QSGSVFQLLP GKLEHGGGLG LGAALGAGVA ALLAFCSCLV VFRVKICRKE ARKRAAAEQD
VPSTLGPISQ GHQHECSAGS SQDHPPPGAA TYTPGKGEEQ ELHYASLSFQ GLRLWEPADQ
EAPSTTEYSE IKIHTGQPLR GPGFGLQLER EMSGMVPK*

mutated AA sequence

MVPGQAQPQS PEMLLLPLLL PVLGAGSLNK DPSYSLQVQR QVPVPEGLCV IVSCNLSYPR
DGWDESTAAY GYWFKGRTSP KTGAPVATNN QSREVAMSTR DRFQLTGDPG KGSCSLVIRD
AQREDEAWYF FRVERGSRVR HSFLSNAFFL KVTALTKKPD VYIPETLEPG QPVTVICVFN
WAFKKCPAPS FSWTGAALSP RRTRPSTSHF SVLSFTPSPQ DHDTDLTCHV DFSRKGVSAQ
RTVRLRVAYA PKDLIISISH DNTSALELQG NVIYLEVQKG QFLRLLCAAD SQPPATLSWV
LQDRVLSSSH PWGPRTLGLE LRGVRAGDSG RYTCRAENRL GSQQQALDLS VQYPPENLRV
MVSQANRTVL ENLGNGTSLP VLEGQSLRLV CVTHSSPPAR LSWTRWGQTV GPSQPSDPGV
LELPPIQMEH EGEFTCHAQH PLGSQHVSLS LSVHYPPQLL GPSCSWEAEG LHCSCSSQAS
PAPSLRWWLG EELLEGNSSQ GSFEVTPSSA GPWANSSLSL HGGLSSGLRL RCKAWNVHGA
QSGSVFQLLP GKLEHGGGLG LGAALGAGVA ALLAFCSCLV VFRVKICRKE ARKRAAAEQD
VPSTLGPISQ GHQHECSAGS SQDHPPPGAA TYTPGKGEEQ ELHYASLSFQ GLRLWEPADQ
EAPSTTEYSE IKIHTGQPLR GPGFGLQLER EMSGMVPK*

speed

0.99 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: 0.99999999991209 (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)

chr19:50463982T>GN/A show variant in all transcripts IGV

HGNC symbol

SIGLEC11

Ensembl transcript ID

ENST00000458019

Genbank transcript ID

N/A

UniProt peptide

Q96RL6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.287A>C
cDNA.378A>C
g.448A>C

AA changes

E96A Score: 107 explain score(s)

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

frameshift

known variant

Reference ID: rs9676436

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	5474	21819	27293

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.305	0
	-0.343	0
(flanking)	-2.01	0

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 increased	446	wt: 0.39 / mu: 0.50	wt: GAGGTGGAAATGAGC mu: GAGGTGGCAATGAGC	GGTG\|gaaa

distance from splice site

174

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000011328

Mmulatta

all identical

ENSMMUG00000006385

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000030468

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000089404

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
28	561	TOPO_DOM	Extracellular (Potential).	lost
31	134	DOMAIN	Ig-like V-type.	lost
96	96	CONFLICT	E -> A (in Ref. 3; AAQ88502).	lost
114	114	DISULFID	By similarity.	might get lost (downstream of altered splice site)
132	132	BINDING	Sialic acid (By similarity).	might get lost (downstream of altered splice site)
159	244	DOMAIN	Ig-like C2-type 1.	might get lost (downstream of altered splice site)
177	177	DISULFID	By similarity.	might get lost (downstream of altered splice site)
186	186	DISULFID	By similarity.	might get lost (downstream of altered splice site)
228	228	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	350	DOMAIN	Ig-like C2-type 2.	might get lost (downstream of altered splice site)
262	262	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
287	287	DISULFID	By similarity.	might get lost (downstream of altered splice site)
334	334	DISULFID	By similarity.	might get lost (downstream of altered splice site)
355	452	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
365	365	CONFLICT	A -> G (in Ref. 3; AAQ88502).	might get lost (downstream of altered splice site)
366	366	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
375	375	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
391	391	DISULFID	By similarity.	might get lost (downstream of altered splice site)
436	436	DISULFID	By similarity.	might get lost (downstream of altered splice site)
497	497	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
515	515	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
562	584	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
585	698	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
642	647	MOTIF	ITIM motif.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1809 / 1809

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

603 / 603

position of stopcodon in wt / mu cDNA

1900 / 1900

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

-1

last intron/exon boundary

1634

theoretical NMD boundary in CDS

1492

length of CDS

1809

coding sequence (CDS) position

287

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

378

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

448

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

50463982

original gDNA sequence snippet

CAACCAGAGTCGAGAGGTGGAAATGAGCACCCGGGACCGAT

altered gDNA sequence snippet

CAACCAGAGTCGAGAGGTGGCAATGAGCACCCGGGACCGAT

original cDNA sequence snippet

CAACCAGAGTCGAGAGGTGGAAATGAGCACCCGGGACCGAT

altered cDNA sequence snippet

CAACCAGAGTCGAGAGGTGGCAATGAGCACCCGGGACCGAT

wildtype AA sequence

MVPGQAQPQS PEMLLLPLLL PVLGAGSLNK DPSYSLQVQR QVPVPEGLCV IVSCNLSYPR
DGWDESTAAY GYWFKGRTSP KTGAPVATNN QSREVEMSTR DRFQLTGDPG KGSCSLVIRD
AQREDEAWYF FRVERGSRVR HSFLSNAFFL KVTALTKKPD VYIPETLEPG QPVTVICVFN
WAFKKCPAPS FSWTGAALSP RRTRPSTSHF SVLSFTPSPQ DHDTDLTCHV DFSRKGVSAQ
RTVRLRVAYA PKDLIISISH DNTSALELQG NVIYLEVQKG QFLRLLCAAD SQPPATLSWV
LQDRVLSSSH PWGPRTLGLE LRGVRAGDSG RYTCRAENRL GSQQQALDLS VQYPPENLRV
MVSQANRTVL ENLGNGTSLP VLEGQSLRLV CVTHSSPPAR LSWTRWGQTV GPSQPSDPGV
LELPPIQMEH EGEFTCHAQH PLGSQHVSLS LSVHWKLEHG GGLGLGAALG AGVAALLAFC
SCLVVFRVKI CRKEARKRAA AEQDVPSTLG PISQGHQHEC SAGSSQDHPP PGAATYTPGK
GEEQELHYAS LSFQGLRLWE PADQEAPSTT EYSEIKIHTG QPLRGPGFGL QLEREMSGMV
PK*

mutated AA sequence

MVPGQAQPQS PEMLLLPLLL PVLGAGSLNK DPSYSLQVQR QVPVPEGLCV IVSCNLSYPR
DGWDESTAAY GYWFKGRTSP KTGAPVATNN QSREVAMSTR DRFQLTGDPG KGSCSLVIRD
AQREDEAWYF FRVERGSRVR HSFLSNAFFL KVTALTKKPD VYIPETLEPG QPVTVICVFN
WAFKKCPAPS FSWTGAALSP RRTRPSTSHF SVLSFTPSPQ DHDTDLTCHV DFSRKGVSAQ
RTVRLRVAYA PKDLIISISH DNTSALELQG NVIYLEVQKG QFLRLLCAAD SQPPATLSWV
LQDRVLSSSH PWGPRTLGLE LRGVRAGDSG RYTCRAENRL GSQQQALDLS VQYPPENLRV
MVSQANRTVL ENLGNGTSLP VLEGQSLRLV CVTHSSPPAR LSWTRWGQTV GPSQPSDPGV
LELPPIQMEH EGEFTCHAQH PLGSQHVSLS LSVHWKLEHG GGLGLGAALG AGVAALLAFC
SCLVVFRVKI CRKEARKRAA AEQDVPSTLG PISQGHQHEC SAGSSQDHPP PGAATYTPGK
GEEQELHYAS LSFQGLRLWE PADQEAPSTT EYSEIKIHTG QPLRGPGFGL QLEREMSGMV
PK*

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems