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: ENST00000285599
Querying Taster for transcript #2: ENST00000504248
MT speed 2.36 s - this script 4.728828 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MAN2B2	polymorphism_automatic	0.02996166170884	simple_aae				V320M	single base exchange	rs2301795		show file
MAN2B2	polymorphism_automatic	0.02996166170884	simple_aae				V269M	single base exchange	rs2301795		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.97003833829116 (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)

chr4:6596360G>AN/A show variant in all transcripts IGV

HGNC symbol

MAN2B2

Ensembl transcript ID

ENST00000285599

Genbank transcript ID

NM_015274

UniProt peptide

Q9Y2E5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.958G>A
cDNA.994G>A
g.19459G>A

AA changes

V320M Score: 21 explain score(s)

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

320

frameshift

known variant

Reference ID: rs2301795

database	homozygous (A/A)	heterozygous	allele carriers
1000G	521	1239	1760
ExAC	14930	2907	17837

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.496	0.063
	1.945	0.533
(flanking)	1.438	0.549

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

splice sites

no abrogation of potential splice sites

distance from splice site

100

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

320

mutated

all conserved

320

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000005298

320

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029119

320

Ggallus

all identical

ENSGALG00000015537

319

Trubripes

no homologue

Drerio

all identical

ENSDARG00000079463

316

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000011609

318

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3030 / 3030

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

1010 / 1010

position of stopcodon in wt / mu cDNA

3066 / 3066

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

37 / 37

chromosome

strand

last intron/exon boundary

2969

theoretical NMD boundary in CDS

2882

length of CDS

3030

coding sequence (CDS) position

958

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

994

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

19459

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

6596360

original gDNA sequence snippet

CTGCCGAGCTCGGTGTCTCGGTGCAGTATGCCACGCTGGGC

altered gDNA sequence snippet

CTGCCGAGCTCGGTGTCTCGATGCAGTATGCCACGCTGGGC

original cDNA sequence snippet

CTGCCGAGCTCGGTGTCTCGGTGCAGTATGCCACGCTGGGC

altered cDNA sequence snippet

CTGCCGAGCTCGGTGTCTCGATGCAGTATGCCACGCTGGGC

wildtype AA sequence

MGQLCWLPLL APLLLLRPPG VQSAGPIRAF VVPHSHMDVG WVYTVQESMR AYAANVYTSV
VEELARGQQR RFIAVEQEFF RLWWDGVASD QQKYQVRQLL EEGRLEFVIG GQVMHDEAVT
HLDDQILQLT EGHGFLYETF GIRPQFSWHV DPFGASATTP TLFALAGFNA HLGSRIDYDL
KAAMQEARGL QFVWRGSPSL SERQEIFTHI MDQYSYCTPS HIPFSNRSGF YWNGVAVFPK
PPQDGVYPNM SEPVTPANIN LYAEALVANV KQRAAWFRTP HVLWPWGCDK QFFNASVQFA
NMDPLLDHIN SHAAELGVSV QYATLGDYFR ALHALNVTWR VRDHHDFLPY STEPFQAWTG
FYTSRSSLKG LARRASALLY AGESMFTRYL WPAPRGHLDP TWALQQLQQL RWAVSEVQHH
DAITGTESPK VRDMYATHLA SGMLGMRKLM ASIVLDELQP QAPMAASSDA GPAGHFASVY
NPLAWTVTTI VTLTVGFPGV RVTDEAGHPV PSQIQNSTET PSAYDLLILT TIPGLSYRHY
NIRPTAGAQE GTQEPAATVA STLQFGRRLR RRTSHAGRYL VPVANDCYIV LLDQDTNLMH
SIWERQSNRT VRVTQEFLEY HVNGDVKQGP ISDNYLFTPG KAAVPAWEAV EMEIVAGQLV
TEIRQYFYRN MTAQNYTYAI RSRLTHVPQG HDGELLCHRI EQEYQAGPLE LNREAVLRTS
TNLNSQQVIY SDNNGYQMQR RPYVSYVNNS IARNYYPMVQ SAFMEDGKSR LVLLSERAHG
ISSQGNGQVE VMLHRRLWNN FDWDLGYNLT LNDTSVVHPV LWLLLGSWSL TTALRQRSAL
ALQHRPVVLF GDLAGTAPKL PGPQQQEAVT LPPNLHLQIL SIPGWRYSSN HTEHSQNLRK
GHRGEAQADL RRVLLRLYHL YEVGEDPVLS QPVTVNLEAV LQALGSVVAV EERSLTGTWD
LSMLHRWSWR TGPGRHRGDT TSPSRPPGGP IITVHPKEIR TFFIHFQQQ*

mutated AA sequence

MGQLCWLPLL APLLLLRPPG VQSAGPIRAF VVPHSHMDVG WVYTVQESMR AYAANVYTSV
VEELARGQQR RFIAVEQEFF RLWWDGVASD QQKYQVRQLL EEGRLEFVIG GQVMHDEAVT
HLDDQILQLT EGHGFLYETF GIRPQFSWHV DPFGASATTP TLFALAGFNA HLGSRIDYDL
KAAMQEARGL QFVWRGSPSL SERQEIFTHI MDQYSYCTPS HIPFSNRSGF YWNGVAVFPK
PPQDGVYPNM SEPVTPANIN LYAEALVANV KQRAAWFRTP HVLWPWGCDK QFFNASVQFA
NMDPLLDHIN SHAAELGVSM QYATLGDYFR ALHALNVTWR VRDHHDFLPY STEPFQAWTG
FYTSRSSLKG LARRASALLY AGESMFTRYL WPAPRGHLDP TWALQQLQQL RWAVSEVQHH
DAITGTESPK VRDMYATHLA SGMLGMRKLM ASIVLDELQP QAPMAASSDA GPAGHFASVY
NPLAWTVTTI VTLTVGFPGV RVTDEAGHPV PSQIQNSTET PSAYDLLILT TIPGLSYRHY
NIRPTAGAQE GTQEPAATVA STLQFGRRLR RRTSHAGRYL VPVANDCYIV LLDQDTNLMH
SIWERQSNRT VRVTQEFLEY HVNGDVKQGP ISDNYLFTPG KAAVPAWEAV EMEIVAGQLV
TEIRQYFYRN MTAQNYTYAI RSRLTHVPQG HDGELLCHRI EQEYQAGPLE LNREAVLRTS
TNLNSQQVIY SDNNGYQMQR RPYVSYVNNS IARNYYPMVQ SAFMEDGKSR LVLLSERAHG
ISSQGNGQVE VMLHRRLWNN FDWDLGYNLT LNDTSVVHPV LWLLLGSWSL TTALRQRSAL
ALQHRPVVLF GDLAGTAPKL PGPQQQEAVT LPPNLHLQIL SIPGWRYSSN HTEHSQNLRK
GHRGEAQADL RRVLLRLYHL YEVGEDPVLS QPVTVNLEAV LQALGSVVAV EERSLTGTWD
LSMLHRWSWR TGPGRHRGDT TSPSRPPGGP IITVHPKEIR TFFIHFQQQ*

speed

1.16 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: 0.97003833829116 (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)

chr4:6596360G>AN/A show variant in all transcripts IGV

HGNC symbol

MAN2B2

Ensembl transcript ID

ENST00000504248

Genbank transcript ID

N/A

UniProt peptide

Q9Y2E5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.805G>A
cDNA.827G>A
g.19459G>A

AA changes

V269M Score: 21 explain score(s)

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

269

frameshift

known variant

Reference ID: rs2301795

database	homozygous (A/A)	heterozygous	allele carriers
1000G	521	1239	1760
ExAC	14930	2907	17837

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.496	0.063
	1.945	0.533
(flanking)	1.438	0.549

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

269

mutated

all conserved

269

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000005298

301

NWEPQALGSLP

DPGRGCLCSP

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029119

305

NMDPLLDYINQRTAQ

Ggallus

all identical

ENSGALG00000015537

312

YINKHSD

Trubripes

no homologue

Drerio

all identical

ENSDARG00000079463

307

YINTHSDQY

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000011609

306

LLLDYINKHTE

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2877 / 2877

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

959 / 959

position of stopcodon in wt / mu cDNA

2899 / 2899

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

23 / 23

chromosome

strand

last intron/exon boundary

2802

theoretical NMD boundary in CDS

2729

length of CDS

2877

coding sequence (CDS) position

805

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

827

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

19459

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

6596360

original gDNA sequence snippet

CTGCCGAGCTCGGTGTCTCGGTGCAGTATGCCACGCTGGGC

altered gDNA sequence snippet

CTGCCGAGCTCGGTGTCTCGATGCAGTATGCCACGCTGGGC

original cDNA sequence snippet

ATGCCGAGCTCGGTGTCTCGGTGCAGTATGCCACGCTGGGC

altered cDNA sequence snippet

ATGCCGAGCTCGGTGTCTCGATGCAGTATGCCACGCTGGGC

wildtype AA sequence

MGQLCWLPLL APLLLLRPPG VQSAGPIRAF VVPHSHMDVG WVYTVQESMR AYAANVYTSV
VEELARGQQR RFIAVEQEFF RLWWDGVASD QQKYQVRQLL EEGRLEFVIG GQVMHDEAVT
HLDDQILQLT EGHGFLYETF GIRPQFSWHV DPFGASATTP TLFALAGFNA HLGSRIDYDL
KAAMQEARGL QFVWRGSPSL SERQEIFTHI MDQYSYCTPS HIPFSNRSGF YWNGVAVFPK
PPQDGVYPNM SEPVTPANIN LYAELGVSVQ YATLGDYFRA LHALNVTWRV RDHHDFLPYS
TEPFQAWTGF YTSRSSLKGL ARRASALLYA GESMFTRYLW PAPRGHLDPT WALQQLQQLR
WAVSEVQHHD AITGTESPKV RDMYATHLAS GMLGMRKLMA SIVLDELQPQ APMAASSDAG
PAGHFASVYN PLAWTVTTIV TLTVGFPGVR VTDEAGHPVP SQIQNSTETP SAYDLLILTT
IPGLSYRHYN IRPTAGAQEG TQEPAATVAS TLQFGRRLRR RTSHAGRYLV PVANDCYIVL
LDQDTNLMHS IWERQSNRTV RVTQEFLEYH VNGDVKQGPI SDNYLFTPGK AAVPAWEAVE
MEIVAGQLVT EIRQYFYRNM TAQNYTYAIR SRLTHVPQGH DGELLCHRIE QEYQAGPLEL
NREAVLRTST NLNSQQVIYS DNNGYQMQRR PYVSYVNNSI ARNYYPMVQS AFMEDGKSRL
VLLSERAHGI SSQGNGQVEV MLHRRLWNNF DWDLGYNLTL NDTSVVHPVL WLLLGSWSLT
TALRQRSALA LQHRPVVLFG DLAGTAPKLP GPQQQEAVTL PPNLHLQILS IPGWRYSSNH
TEHSQNLRKG HRGEAQADLR RVLLRLYHLY EVGEDPVLSQ PVTVNLEAVL QALGSVVAVE
ERSLTGTWDL SMLHRWSWRT GPGRHRGDTT SPSRPPGGPI ITVHPKEIRT FFIHFQQQ*

mutated AA sequence

MGQLCWLPLL APLLLLRPPG VQSAGPIRAF VVPHSHMDVG WVYTVQESMR AYAANVYTSV
VEELARGQQR RFIAVEQEFF RLWWDGVASD QQKYQVRQLL EEGRLEFVIG GQVMHDEAVT
HLDDQILQLT EGHGFLYETF GIRPQFSWHV DPFGASATTP TLFALAGFNA HLGSRIDYDL
KAAMQEARGL QFVWRGSPSL SERQEIFTHI MDQYSYCTPS HIPFSNRSGF YWNGVAVFPK
PPQDGVYPNM SEPVTPANIN LYAELGVSMQ YATLGDYFRA LHALNVTWRV RDHHDFLPYS
TEPFQAWTGF YTSRSSLKGL ARRASALLYA GESMFTRYLW PAPRGHLDPT WALQQLQQLR
WAVSEVQHHD AITGTESPKV RDMYATHLAS GMLGMRKLMA SIVLDELQPQ APMAASSDAG
PAGHFASVYN PLAWTVTTIV TLTVGFPGVR VTDEAGHPVP SQIQNSTETP SAYDLLILTT
IPGLSYRHYN IRPTAGAQEG TQEPAATVAS TLQFGRRLRR RTSHAGRYLV PVANDCYIVL
LDQDTNLMHS IWERQSNRTV RVTQEFLEYH VNGDVKQGPI SDNYLFTPGK AAVPAWEAVE
MEIVAGQLVT EIRQYFYRNM TAQNYTYAIR SRLTHVPQGH DGELLCHRIE QEYQAGPLEL
NREAVLRTST NLNSQQVIYS DNNGYQMQRR PYVSYVNNSI ARNYYPMVQS AFMEDGKSRL
VLLSERAHGI SSQGNGQVEV MLHRRLWNNF DWDLGYNLTL NDTSVVHPVL WLLLGSWSLT
TALRQRSALA LQHRPVVLFG DLAGTAPKLP GPQQQEAVTL PPNLHLQILS IPGWRYSSNH
TEHSQNLRKG HRGEAQADLR RVLLRLYHLY EVGEDPVLSQ PVTVNLEAVL QALGSVVAVE
ERSLTGTWDL SMLHRWSWRT GPGRHRGDTT SPSRPPGGPI ITVHPKEIRT FFIHFQQQ*

speed

1.20 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems