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: ENST00000294309
Querying Taster for transcript #2: ENST00000542467
MT speed 0 s - this script 4.211577 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TPCN2	polymorphism_automatic	0.372051969829163	simple_aae		affected		K376R	single base exchange	rs3750965		show file
TPCN2	polymorphism_automatic	0.372051969829163	simple_aae		affected		K376R	single base exchange	rs3750965		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.627948030170837 (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)

chr11:68840160A>GN/A show variant in all transcripts IGV

HGNC symbol

TPCN2

Ensembl transcript ID

ENST00000294309

Genbank transcript ID

NM_139075

UniProt peptide

Q8NHX9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1127A>G
cDNA.1228A>G
g.23796A>G

AA changes

K376R Score: 26 explain score(s)

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

376

frameshift

known variant

Reference ID: rs3750965

database	homozygous (G/G)	heterozygous	allele carriers
1000G	266	924	1190
ExAC	5679	21409	27088

regulatory features

Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Nrsf, Transcription Factor, Nrsf TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.957	0.685
	0.549	0.448
(flanking)	-0.922	0.171

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	23795	wt: 0.67 / mu: 0.99	wt: CCCACAAACAGGCCA mu: CCCACAGACAGGCCA	CACA\|aaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

376

mutated

all conserved

376

Ptroglodytes

all identical

ENSPTRG00000003992

286

Mmulatta

all identical

ENSMMUG00000010784

376

Fcatus

all identical

ENSFCAG00000002792

338

Mmusculus

all identical

ENSMUSG00000048677

360

Ggallus

all identical

ENSGALG00000007550

361

AIM

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000068381

389

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000967

393

protein features

start (aa)	end (aa)	feature	details
311	436	TOPO_DOM	Cytoplasmic (Potential).	lost
437	459	TRANSMEM	Helical; Name=S1 of repeat II; (Potential).	might get lost (downstream of altered splice site)
460	465	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
466	486	TRANSMEM	Helical; Name=S2 of repeat II; (Potential).	might get lost (downstream of altered splice site)
487	502	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
503	523	TRANSMEM	Helical; Name=S3 of repeat II; (Potential).	might get lost (downstream of altered splice site)
524	554	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
555	575	TRANSMEM	Helical; Name=S4 of repeat II; (Potential).	might get lost (downstream of altered splice site)
576	580	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
581	601	TRANSMEM	Helical; Name=S5 of repeat II; (Potential).	might get lost (downstream of altered splice site)
602	635	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
611	611	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
618	618	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
636	658	INTRAMEM	Helical; Pore-forming; (Potential).	might get lost (downstream of altered splice site)
659	673	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
674	694	TRANSMEM	Helical; Name=S6 of repeat II; (Potential).	might get lost (downstream of altered splice site)
695	752	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2259 / 2259

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

753 / 753

position of stopcodon in wt / mu cDNA

2360 / 2360

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

102 / 102

chromosome

strand

last intron/exon boundary

2282

theoretical NMD boundary in CDS

2130

length of CDS

2259

coding sequence (CDS) position

1127

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

1228

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

23796

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

68840160

original gDNA sequence snippet

CCAGCTGGACAGCTCCCACAAACAGGCCATGATGGAGGTAC

altered gDNA sequence snippet

CCAGCTGGACAGCTCCCACAGACAGGCCATGATGGAGGTAC

original cDNA sequence snippet

CCAGCTGGACAGCTCCCACAAACAGGCCATGATGGAGAAGG

altered cDNA sequence snippet

CCAGCTGGACAGCTCCCACAGACAGGCCATGATGGAGAAGG

wildtype AA sequence

MAEPQAESEP LLGGARGGGG DWPAGLTTYR SIQVGPGAAA RWDLCIDQAV VFIEDAIQYR
SINHRVDASS MWLYRRYYSN VCQRTLSFTI FLILFLAFIE TPSSLTSTAD VRYRAAPWEP
PCGLTESVEV LCLLVFAADL SVKGYLFGWA HFQKNLWLLG YLVVLVVSLV DWTVSLSLVC
HEPLRIRRLL RPFFLLQNSS MMKKTLKCIR WSLPEMASVG LLLAIHLCLF TMFGMLLFAG
GKQDDGQDRE RLTYFQNLPE SLTSLLVLLT TANNPDVMIP AYSKNRAYAI FFIVFTVIGS
LFLMNLLTAI IYSQFRGYLM KSLQTSLFRR RLGTRAAFEV LSSMVGEGGA FPQAVGVKPQ
NLLQVLQKVQ LDSSHKQAMM EKVRSYGSVL LSAEEFQKLF NELDRSVVKE HPPRPEYQSP
FLQSAQFLFG HYYFDYLGNL IALANLVSIC VFLVLDADVL PAERDDFILG ILNCVFIVYY
LLEMLLKVFA LGLRGYLSYP SNVFDGLLTV VLLVLEISTL AVYRLPHPGW RPEMVGLLSL
WDMTRMLNML IVFRFLRIIP SMKLMAVVAS TVLGLVQNMR AFGGILVVVY YVFAIIGINL
FRGVIVALPG NSSLAPANGS APCGSFEQLE YWANNFDDFA AALVTLWNLM VVNNWQVFLD
AYRRYSGPWS KIYFVLWWLV SSVIWVNLFL ALILENFLHK WDPRSHLQPL AGTPEATYQM
TVELLFRDIL EEPGEDELTE RLSQHPHLWL CR*

mutated AA sequence

MAEPQAESEP LLGGARGGGG DWPAGLTTYR SIQVGPGAAA RWDLCIDQAV VFIEDAIQYR
SINHRVDASS MWLYRRYYSN VCQRTLSFTI FLILFLAFIE TPSSLTSTAD VRYRAAPWEP
PCGLTESVEV LCLLVFAADL SVKGYLFGWA HFQKNLWLLG YLVVLVVSLV DWTVSLSLVC
HEPLRIRRLL RPFFLLQNSS MMKKTLKCIR WSLPEMASVG LLLAIHLCLF TMFGMLLFAG
GKQDDGQDRE RLTYFQNLPE SLTSLLVLLT TANNPDVMIP AYSKNRAYAI FFIVFTVIGS
LFLMNLLTAI IYSQFRGYLM KSLQTSLFRR RLGTRAAFEV LSSMVGEGGA FPQAVGVKPQ
NLLQVLQKVQ LDSSHRQAMM EKVRSYGSVL LSAEEFQKLF NELDRSVVKE HPPRPEYQSP
FLQSAQFLFG HYYFDYLGNL IALANLVSIC VFLVLDADVL PAERDDFILG ILNCVFIVYY
LLEMLLKVFA LGLRGYLSYP SNVFDGLLTV VLLVLEISTL AVYRLPHPGW RPEMVGLLSL
WDMTRMLNML IVFRFLRIIP SMKLMAVVAS TVLGLVQNMR AFGGILVVVY YVFAIIGINL
FRGVIVALPG NSSLAPANGS APCGSFEQLE YWANNFDDFA AALVTLWNLM VVNNWQVFLD
AYRRYSGPWS KIYFVLWWLV SSVIWVNLFL ALILENFLHK WDPRSHLQPL AGTPEATYQM
TVELLFRDIL EEPGEDELTE RLSQHPHLWL CR*

speed

1.35 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: 0.627948030170837 (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)

chr11:68840160A>GN/A show variant in all transcripts IGV

HGNC symbol

TPCN2

Ensembl transcript ID

ENST00000542467

Genbank transcript ID

N/A

UniProt peptide

Q8NHX9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1127A>G
cDNA.1164A>G
g.23796A>G

AA changes

K376R Score: 26 explain score(s)

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

376

frameshift

known variant

Reference ID: rs3750965

database	homozygous (G/G)	heterozygous	allele carriers
1000G	266	924	1190
ExAC	5679	21409	27088

regulatory features

Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Nrsf, Transcription Factor, Nrsf TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.957	0.685
	0.549	0.448
(flanking)	-0.922	0.171

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	23795	wt: 0.67 / mu: 0.99	wt: CCCACAAACAGGCCA mu: CCCACAGACAGGCCA	CACA\|aaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

376

mutated

all conserved

376

Ptroglodytes

all identical

ENSPTRG00000003992

286

Mmulatta

all identical

ENSMMUG00000010784

376

Fcatus

all identical

ENSFCAG00000002792

338

Mmusculus

all identical

ENSMUSG00000048677

360

Ggallus

all identical

ENSGALG00000007550

361

AIM

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000068381

389

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000967

393

protein features

start (aa)	end (aa)	feature	details
311	436	TOPO_DOM	Cytoplasmic (Potential).	lost
437	459	TRANSMEM	Helical; Name=S1 of repeat II; (Potential).	might get lost (downstream of altered splice site)
460	465	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
466	486	TRANSMEM	Helical; Name=S2 of repeat II; (Potential).	might get lost (downstream of altered splice site)
487	502	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
503	523	TRANSMEM	Helical; Name=S3 of repeat II; (Potential).	might get lost (downstream of altered splice site)
524	554	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
555	575	TRANSMEM	Helical; Name=S4 of repeat II; (Potential).	might get lost (downstream of altered splice site)
576	580	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
581	601	TRANSMEM	Helical; Name=S5 of repeat II; (Potential).	might get lost (downstream of altered splice site)
602	635	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
611	611	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
618	618	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
636	658	INTRAMEM	Helical; Pore-forming; (Potential).	might get lost (downstream of altered splice site)
659	673	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
674	694	TRANSMEM	Helical; Name=S6 of repeat II; (Potential).	might get lost (downstream of altered splice site)
695	752	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1713 / 1713

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

571 / 571

position of stopcodon in wt / mu cDNA

1750 / 1750

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

38 / 38

chromosome

strand

last intron/exon boundary

1672

theoretical NMD boundary in CDS

1584

length of CDS

1713

coding sequence (CDS) position

1127

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

1164

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

23796

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

68840160

original gDNA sequence snippet

CCAGCTGGACAGCTCCCACAAACAGGCCATGATGGAGGTAC

altered gDNA sequence snippet

CCAGCTGGACAGCTCCCACAGACAGGCCATGATGGAGGTAC

original cDNA sequence snippet

CCAGCTGGACAGCTCCCACAAACAGGCCATGATGGAGAAGG

altered cDNA sequence snippet

CCAGCTGGACAGCTCCCACAGACAGGCCATGATGGAGAAGG

wildtype AA sequence

MAEPQAESEP LLGGARGGGG DWPAGLTTYR SIQVGPGAAA RWDLCIDQAV VFIEDAIQYR
SINHRVDASS MWLYRRYYSN VCQRTLSFTI FLILFLAFIE TPSSLTSTAD VRYRAAPWEP
PCGLTESVEV LCLLVFAADL SVKGYLFGWA HFQKNLWLLG YLVVLVVSLV DWTVSLSLVC
HEPLRIRRLL RPFFLLQNSS MMKKTLKCIR WSLPEMASVG LLLAIHLCLF TMFGMLLFAG
GKQDDGQDRE RLTYFQNLPE SLTSLLVLLT TANNPDVMIP AYSKNRAYAI FFIVFTVIGS
LFLMNLLTAI IYSQFRGYLM KSLQTSLFRR RLGTRAAFEV LSSMVGEGGA FPQAVGVKPQ
NLLQVLQKVQ LDSSHKQAMM EKVRSYGSVL LSAEEFQKLF NELDRSVVKE HPPRPEYQSP
FLQSAQFLFG HYYFDYLGNL IALANLVSIC VFLVLDADVL PAERDDFILG ILNCVFIVYY
LLEMLLKVFA LGLRGYLSYP SNVFDGLLTV VLLNFLHKWD PRSHLQPLAG TPEATYQMTV
ELLFRDILEE PGEDELTERL SQHPHLWLCR *

mutated AA sequence

MAEPQAESEP LLGGARGGGG DWPAGLTTYR SIQVGPGAAA RWDLCIDQAV VFIEDAIQYR
SINHRVDASS MWLYRRYYSN VCQRTLSFTI FLILFLAFIE TPSSLTSTAD VRYRAAPWEP
PCGLTESVEV LCLLVFAADL SVKGYLFGWA HFQKNLWLLG YLVVLVVSLV DWTVSLSLVC
HEPLRIRRLL RPFFLLQNSS MMKKTLKCIR WSLPEMASVG LLLAIHLCLF TMFGMLLFAG
GKQDDGQDRE RLTYFQNLPE SLTSLLVLLT TANNPDVMIP AYSKNRAYAI FFIVFTVIGS
LFLMNLLTAI IYSQFRGYLM KSLQTSLFRR RLGTRAAFEV LSSMVGEGGA FPQAVGVKPQ
NLLQVLQKVQ LDSSHRQAMM EKVRSYGSVL LSAEEFQKLF NELDRSVVKE HPPRPEYQSP
FLQSAQFLFG HYYFDYLGNL IALANLVSIC VFLVLDADVL PAERDDFILG ILNCVFIVYY
LLEMLLKVFA LGLRGYLSYP SNVFDGLLTV VLLNFLHKWD PRSHLQPLAG TPEATYQMTV
ELLFRDILEE PGEDELTERL SQHPHLWLCR *

speed

0.87 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems