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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000559717
Querying Taster for transcript #2: ENST00000360468
Querying Taster for transcript #3: ENST00000431652
MT speed 0 s - this script 3.96128 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MAN2A2	polymorphism_automatic	5.78695618003167e-06	simple_aae		affected		Q412R	single base exchange	rs2106673		show file
MAN2A2	polymorphism_automatic	5.78695618003167e-06	simple_aae		affected		Q412R	single base exchange	rs2106673		show file
MAN2A2	polymorphism_automatic	0.999999999999703	without_aae		affected			single base exchange	rs2106673		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999421304382 (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)

chr15:91452595A>GN/A show variant in all transcripts IGV

HGNC symbol

MAN2A2

Ensembl transcript ID

ENST00000559717

Genbank transcript ID

N/A

UniProt peptide

P49641

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1235A>G
cDNA.1694A>G
g.7148A>G

AA changes

Q412R Score: 43 explain score(s)

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

412

frameshift

known variant

Reference ID: rs2106673

database	homozygous (G/G)	heterozygous	allele carriers
1000G	816	930	1746
ExAC	12566	7635	20201

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.769	1
	0.96	1
(flanking)	2.769	1

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 gained	7142	0.36	mu: GAAGAAGTCCCGGCT	AGAA\|gtcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

412

mutated

all conserved

412

Ptroglodytes

all conserved

ENSPTRG00000007463

412

Mmulatta

all conserved

ENSMMUG00000005103

411

Fcatus

all conserved

ENSFCAG00000006094

368

Mmusculus

all conserved

ENSMUSG00000038886

412

Ggallus

no alignment

ENSGALG00000008336

n/a

Trubripes

all conserved

ENSTRUG00000000691

412

Drerio

all conserved

ENSDARG00000063101

412

Dmelanogaster

all conserved

FBgn0011740

390

Celegans

all identical

F58H1.1

429

Xtropicalis

all conserved

ENSXETG00000015458

412

protein features

start (aa)	end (aa)	feature	details
27	796	TOPO_DOM	Lumenal (Potential).	lost
569	569	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
1093	1093	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1131	1131	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3453 / 3453

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

1151 / 1151

position of stopcodon in wt / mu cDNA

3912 / 3912

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

460 / 460

chromosome

strand

last intron/exon boundary

3760

theoretical NMD boundary in CDS

3250

length of CDS

3453

coding sequence (CDS) position

1235

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

1694

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

7148

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

91452595

original gDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered gDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

original cDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered cDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

wildtype AA sequence

MKLKKQVTVC GAAIFCVAVF SLYLMLDRVQ HDPTRHQNGG NFPRSQISVL QNRIEQLEQL
LEENHEIISH IKDSVLELTA NAEGPPAMLP YYTVNGSWVV PPEPRPSFFS ISPQDCQFAL
GGRGQKPELQ MLTVSEELPF DNVDGGVWRQ GFDISYDPHD WDAEDLQVFV VPHSHNDPGW
IKTFDKYYTE QTQHILNSMV SKLQEDPRRR FLWAEVSFFA KWWDNINVQK RAAVRRLVGN
GQLEIATGGW VMPDEANSHY FALIDQLIEG HQWLERNLGA TPRSGWAVDP FGYSSTMPYL
LRRANLTSML IQRVHYAIKK HFAATHSLEF MWRQTWDSDS STDIFCHMMP FYSYDVPHTC
GPDPKICCQF DFKRLPGGRI NCPWKVPPRA ITEANVAERA ALLLDQYRKK SQLFRSNVLL
VPLGDDFRYD KPQEWDAQFF NYQRLFDFFN SRPNLHVQAQ FGTLSDYFDA LYKRTGVEPG
ARPPGFPVLS GDFFSYADRE DHYWTGYYTS RPFYKSLDRV LEAHLRGAEV LYSLAAAHAR
RSGLAGRYPL SDFTLLTEAR RTLGLFQHHD AITGTAKEAV VVDYGVRLLR SLVNLKQVII
HAAHYLVLGD KETYHFDPEA PFLQVDDTRL SHDALPERTV IQLDSSPRFV VLFNPLEQER
FSMVSLLVNS PRVRVLSEEG QPLAVQISAH WSSATEAVPD VYQVSVPVRL PALGLGVLQL
QLGLDGHRTL PSSVRIYLHG RQLSVSRHEA FPLRVIDSGT SDFALSNRYM QVWFSGLTGL
LKSIRRVDEE HEQQVDMQVL VYGTRTSKDK SGAYLFLPDG EAKPYVPKEP PVLRVTEGPF
FSEVVAYYEH IHQAVRLYNL PGVEGLSLDI SSLVDIRDYV NKELALHIHT DIDSQGIFFT
DLNGFQVQPR RYLKKLPLQA NFYPMPVMAY IQDAQKRLTL HTAQALGVSS LKDGQLEVIL
DRRLMQDDNR GLGQGLKDNK RTCNRFRLLL ERRTVGSEVQ DSHSTSYPSL LSHLTSMYLN
APALALPVAR MQLPGPGLRS FHPLASSLPC DFHLLNLRTL QAEEDTLPSA ETALILHRKG
FDCGLEAKNL GFNCTTSQGK VALGSLFHGL DVVFLQPTSL TLLYPLASPS NSTDVYLEPM
EIATFRLRLG *

mutated AA sequence

MKLKKQVTVC GAAIFCVAVF SLYLMLDRVQ HDPTRHQNGG NFPRSQISVL QNRIEQLEQL
LEENHEIISH IKDSVLELTA NAEGPPAMLP YYTVNGSWVV PPEPRPSFFS ISPQDCQFAL
GGRGQKPELQ MLTVSEELPF DNVDGGVWRQ GFDISYDPHD WDAEDLQVFV VPHSHNDPGW
IKTFDKYYTE QTQHILNSMV SKLQEDPRRR FLWAEVSFFA KWWDNINVQK RAAVRRLVGN
GQLEIATGGW VMPDEANSHY FALIDQLIEG HQWLERNLGA TPRSGWAVDP FGYSSTMPYL
LRRANLTSML IQRVHYAIKK HFAATHSLEF MWRQTWDSDS STDIFCHMMP FYSYDVPHTC
GPDPKICCQF DFKRLPGGRI NCPWKVPPRA ITEANVAERA ALLLDQYRKK SRLFRSNVLL
VPLGDDFRYD KPQEWDAQFF NYQRLFDFFN SRPNLHVQAQ FGTLSDYFDA LYKRTGVEPG
ARPPGFPVLS GDFFSYADRE DHYWTGYYTS RPFYKSLDRV LEAHLRGAEV LYSLAAAHAR
RSGLAGRYPL SDFTLLTEAR RTLGLFQHHD AITGTAKEAV VVDYGVRLLR SLVNLKQVII
HAAHYLVLGD KETYHFDPEA PFLQVDDTRL SHDALPERTV IQLDSSPRFV VLFNPLEQER
FSMVSLLVNS PRVRVLSEEG QPLAVQISAH WSSATEAVPD VYQVSVPVRL PALGLGVLQL
QLGLDGHRTL PSSVRIYLHG RQLSVSRHEA FPLRVIDSGT SDFALSNRYM QVWFSGLTGL
LKSIRRVDEE HEQQVDMQVL VYGTRTSKDK SGAYLFLPDG EAKPYVPKEP PVLRVTEGPF
FSEVVAYYEH IHQAVRLYNL PGVEGLSLDI SSLVDIRDYV NKELALHIHT DIDSQGIFFT
DLNGFQVQPR RYLKKLPLQA NFYPMPVMAY IQDAQKRLTL HTAQALGVSS LKDGQLEVIL
DRRLMQDDNR GLGQGLKDNK RTCNRFRLLL ERRTVGSEVQ DSHSTSYPSL LSHLTSMYLN
APALALPVAR MQLPGPGLRS FHPLASSLPC DFHLLNLRTL QAEEDTLPSA ETALILHRKG
FDCGLEAKNL GFNCTTSQGK VALGSLFHGL DVVFLQPTSL TLLYPLASPS NSTDVYLEPM
EIATFRLRLG *

speed

1.00 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: 0.99999421304382 (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)

chr15:91452595A>GN/A show variant in all transcripts IGV

HGNC symbol

MAN2A2

Ensembl transcript ID

ENST00000360468

Genbank transcript ID

NM_006122

UniProt peptide

P49641

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1235A>G
cDNA.1253A>G
g.7148A>G

AA changes

Q412R Score: 43 explain score(s)

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

412

frameshift

known variant

Reference ID: rs2106673

database	homozygous (G/G)	heterozygous	allele carriers
1000G	816	930	1746
ExAC	12566	7635	20201

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.769	1
	0.96	1
(flanking)	2.769	1

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 gained	7142	0.36	mu: GAAGAAGTCCCGGCT	AGAA\|gtcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

412

mutated

all conserved

412

Ptroglodytes

all conserved

ENSPTRG00000007463

412

Mmulatta

all conserved

ENSMMUG00000005103

411

Fcatus

all conserved

ENSFCAG00000006094

368

Mmusculus

all conserved

ENSMUSG00000038886

412

Ggallus

no alignment

ENSGALG00000008336

n/a

Trubripes

all conserved

ENSTRUG00000000691

412

Drerio

all conserved

ENSDARG00000063101

412

Dmelanogaster

all conserved

FBgn0011740

390

Celegans

all identical

F58H1.1

429

Xtropicalis

all conserved

ENSXETG00000015458

412

protein features

start (aa)	end (aa)	feature	details
27	796	TOPO_DOM	Lumenal (Potential).	lost
569	569	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
1093	1093	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1131	1131	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3453 / 3453

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

1151 / 1151

position of stopcodon in wt / mu cDNA

3471 / 3471

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

19 / 19

chromosome

strand

last intron/exon boundary

3319

theoretical NMD boundary in CDS

3250

length of CDS

3453

coding sequence (CDS) position

1235

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

1253

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

7148

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

91452595

original gDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered gDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

original cDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered cDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

wildtype AA sequence

mutated AA sequence

MKLKKQVTVC GAAIFCVAVF SLYLMLDRVQ HDPTRHQNGG NFPRSQISVL QNRIEQLEQL
LEENHEIISH IKDSVLELTA NAEGPPAMLP YYTVNGSWVV PPEPRPSFFS ISPQDCQFAL
GGRGQKPELQ MLTVSEELPF DNVDGGVWRQ GFDISYDPHD WDAEDLQVFV VPHSHNDPGW
IKTFDKYYTE QTQHILNSMV SKLQEDPRRR FLWAEVSFFA KWWDNINVQK RAAVRRLVGN
GQLEIATGGW VMPDEANSHY FALIDQLIEG HQWLERNLGA TPRSGWAVDP FGYSSTMPYL
LRRANLTSML IQRVHYAIKK HFAATHSLEF MWRQTWDSDS STDIFCHMMP FYSYDVPHTC
GPDPKICCQF DFKRLPGGRI NCPWKVPPRA ITEANVAERA ALLLDQYRKK SRLFRSNVLL
VPLGDDFRYD KPQEWDAQFF NYQRLFDFFN SRPNLHVQAQ FGTLSDYFDA LYKRTGVEPG
ARPPGFPVLS GDFFSYADRE DHYWTGYYTS RPFYKSLDRV LEAHLRGAEV LYSLAAAHAR
RSGLAGRYPL SDFTLLTEAR RTLGLFQHHD AITGTAKEAV VVDYGVRLLR SLVNLKQVII
HAAHYLVLGD KETYHFDPEA PFLQVDDTRL SHDALPERTV IQLDSSPRFV VLFNPLEQER
FSMVSLLVNS PRVRVLSEEG QPLAVQISAH WSSATEAVPD VYQVSVPVRL PALGLGVLQL
QLGLDGHRTL PSSVRIYLHG RQLSVSRHEA FPLRVIDSGT SDFALSNRYM QVWFSGLTGL
LKSIRRVDEE HEQQVDMQVL VYGTRTSKDK SGAYLFLPDG EAKPYVPKEP PVLRVTEGPF
FSEVVAYYEH IHQAVRLYNL PGVEGLSLDI SSLVDIRDYV NKELALHIHT DIDSQGIFFT
DLNGFQVQPR RYLKKLPLQA NFYPMPVMAY IQDAQKRLTL HTAQALGVSS LKDGQLEVIL
DRRLMQDDNR GLGQGLKDNK RTCNRFRLLL ERRTVGSEVQ DSHSTSYPSL LSHLTSMYLN
APALALPVAR MQLPGPGLRS FHPLASSLPC DFHLLNLRTL QAEEDTLPSA ETALILHRKG
FDCGLEAKNL GFNCTTSQGK VALGSLFHGL DVVFLQPTSL TLLYPLASPS NSTDVYLEPM
EIATFRLRLG *

speed

0.83 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 2.97068054545935e-13 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr15:91452595A>GN/A show variant in all transcripts IGV

HGNC symbol

MAN2A2

Ensembl transcript ID

ENST00000431652

Genbank transcript ID

N/A

UniProt peptide

P49641

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.147A>G
g.7148A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2106673

database	homozygous (G/G)	heterozygous	allele carriers
1000G	816	930	1746
ExAC	12566	7635	20201

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.769	1
	0.96	1
(flanking)	2.769	1

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

splice sites

splice site change before start ATG (at aa -14) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	7142	0.36	mu: GAAGAAGTCCCGGCT	AGAA\|gtcc

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	5	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
6	26	TRANSMEM	Helical; Signal-anchor for type II membrane protein; (Potential).	might get lost (downstream of altered splice site)
27	796	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
95	95	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
175	175	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
177	177	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
289	289	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
289	289	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
569	569	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
1093	1093	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1131	1131	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

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

186 / 186

chromosome

strand

last intron/exon boundary

2010

theoretical NMD boundary in CDS

1774

length of CDS

1977

coding sequence (CDS) position

N/A

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

147

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

7148

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

91452595

original gDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered gDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

original cDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered cDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

wildtype AA sequence

MTSDMTSPRS GMPSSSTTNG SLTSSTAGLT SMCRGAEVLY SLAAAHARRS GLAGRYPLSD
FTLLTEARRT LGLFQHHDAI TGTAKEAVVV DYGVRLLRSL VNLKQVIIHA AHYLVLGDKE
TYHFDPEAPF LQVDDTRLSH DALPERTVIQ LDSSPRFVVL FNPLEQERFS MVSLLVNSPR
VRVLSEEGQP LAVQISAHWS SATEAVPDVY QVSVPVRLPA LGLGVLQLQL GLDGHRTLPS
SVRIYLHGRQ LSVSRHEAFP LRVIDSGTSD FALSNRYMQV WFSGLTGLLK SIRRVDEEHE
QQVDMQVLVY GTRTSKDKSG AYLFLPDGEA KPYVPKEPPV LRVTEGPFFS EVVAYYEHIH
QAVRLYNLPG VEGLSLDISS LVDIRDYVNK ELALHIHTDI DSQGIFFTDL NGFQVQPRRY
LKKLPLQANF YPMPVMAYIQ DAQKRLTLHT AQALGVSSLK DGQLEVILDR RLMQDDNRGL
GQGLKDNKRT CNRFRLLLER RTVGSEVQDS HSTSYPSLLS HLTSMYLNAP ALALPVARMQ
LPGPGLRSFH PLASSLPCDF HLLNLRTLQA EEDTLPSAET ALILHRKGFD CGLEAKNLGF
NCTTSQGKVA LGSLFHGLDV VFLQPTSLTL LYPLASPSNS TDVYLEPMEI ATFRLRLG*

mutated AA sequence

N/A

speed

0.90 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems