MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000253262
Querying Taster for transcript #2: ENST00000335456
Querying Taster for transcript #3: ENST00000341207
MT speed 0 s - this script 2.785152 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NUTM2F	polymorphism_automatic	1.48991929904696e-13	simple_aae				R176G	single base exchange	rs190275133		show file
NUTM2F	polymorphism_automatic	1.48991929904696e-13	simple_aae				R176G	single base exchange	rs190275133		show file
NUTM2F	polymorphism_automatic	1.48991929904696e-13	simple_aae				R176G	single base exchange	rs190275133		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999851 (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)

chr9:97087707T>CN/A show variant in all transcripts IGV

HGNC symbol

NUTM2F

Ensembl transcript ID

ENST00000335456

Genbank transcript ID

N/A

UniProt peptide

A1L443

alteration type

single base exchange

alteration region

CDS

DNA changes

c.526A>G
cDNA.547A>G
g.3220A>G

AA changes

R176G Score: 125 explain score(s)

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

176

frameshift

known variant

Reference ID: rs190275133

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1923	223	2146
ExAC	114	63	177

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.173	0.003
	-0.631	0
(flanking)	-0.323	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
Acc marginally increased	3210	wt: 0.8014 / mu: 0.8190 (marginal change - not scored)	wt: GTGGCCCCCATCGTGTCCCCAGGGAACGCTAGGCCATGGCC mu: GTGGCCCCCATCGTGTCCCCAGGGAACGCTGGGCCATGGCC	ccca\|GGGA

distance from splice site

188

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

176

mutated

not conserved

176

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000020164

Fcatus

not conserved

ENSFCAG00000010760

Mmusculus

not conserved

ENSMUSG00000071909

191

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

1479 / 1479

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

493 / 493

position of stopcodon in wt / mu cDNA

1500 / 1500

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

22 / 22

chromosome

strand

-1

last intron/exon boundary

1462

theoretical NMD boundary in CDS

1390

length of CDS

1479

coding sequence (CDS) position

526

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

547

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

3220

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

97087707

original gDNA sequence snippet

TCGTGTCCCCAGGGAACGCTAGGCCATGGCCACAAGGGGCT

altered gDNA sequence snippet

TCGTGTCCCCAGGGAACGCTGGGCCATGGCCACAAGGGGCT

original cDNA sequence snippet

TCGTGTCCCCAGGGAACGCTAGGCCATGGCCACAAGGGGCT

altered cDNA sequence snippet

TCGTGTCCCCAGGGAACGCTGGGCCATGGCCACAAGGGGCT

wildtype AA sequence

mutated AA sequence

speed

0.35 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: 0.999999999999851 (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)

chr9:97087707T>CN/A show variant in all transcripts IGV

HGNC symbol

NUTM2F

Ensembl transcript ID

ENST00000253262

Genbank transcript ID

NM_017561

UniProt peptide

A1L443

alteration type

single base exchange

alteration region

CDS

DNA changes

c.526A>G
cDNA.547A>G
g.3220A>G

AA changes

R176G Score: 125 explain score(s)

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

176

frameshift

known variant

Reference ID: rs190275133

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1923	223	2146
ExAC	114	63	177

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.173	0.003
	-0.631	0
(flanking)	-0.323	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
Acc marginally increased	3210	wt: 0.8014 / mu: 0.8190 (marginal change - not scored)	wt: GTGGCCCCCATCGTGTCCCCAGGGAACGCTAGGCCATGGCC mu: GTGGCCCCCATCGTGTCCCCAGGGAACGCTGGGCCATGGCC	ccca\|GGGA

distance from splice site

188

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

176

mutated

not conserved

176

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000020164

Fcatus

not conserved

ENSFCAG00000010760

Mmusculus

not conserved

ENSMUSG00000071909

191

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

2271 / 2271

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

757 / 757

position of stopcodon in wt / mu cDNA

2292 / 2292

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

22 / 22

chromosome

strand

-1

last intron/exon boundary

1507

theoretical NMD boundary in CDS

1435

length of CDS

2271

coding sequence (CDS) position

526

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

547

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

3220

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

97087707

original gDNA sequence snippet

TCGTGTCCCCAGGGAACGCTAGGCCATGGCCACAAGGGGCT

altered gDNA sequence snippet

TCGTGTCCCCAGGGAACGCTGGGCCATGGCCACAAGGGGCT

original cDNA sequence snippet

TCGTGTCCCCAGGGAACGCTAGGCCATGGCCACAAGGGGCT

altered cDNA sequence snippet

TCGTGTCCCCAGGGAACGCTGGGCCATGGCCACAAGGGGCT

wildtype AA sequence

MASNGAYPVL GPGVTVNPGT SLSVFTALPF ATPAPGPAHR PPLVTAVVPP AGPLVLSAFP
STPLVAGQDG RGPSGAGASN VFVQMRTEVG PVKPPQAQTL ILTQAPLVWQ APGTLCGGVM
CPPPLLLAAA PGVPVTSAQV VGGTQACEGG WSHGLPLPPP PPAAQVAPIV SPGNARPWPQ
GAHGEGSLAP SQAKARPDDS CKPKSVYENF RLWQHYKPLA RRHLPQSPDT EALSCFLIPV
LRSLARRKPT MTLEEGLWQA MREWQHTSNF DRMIFYEMAE KFLEFEAEEE MQIQKSQWMK
GPQSLPPPAP PRLEPRGPPA PEVVKQPVYL PSKDGPKAPT ACLPPPRPQR PAETKAHLPP
PRPQRPAETN AHLPPPRPQR PAETKVPEEI PPEVVQEYVD IMEELLGSHP GDTGEPEGQR
EKGKVEQPQE EDGITSDPGL LSYIDKLCSQ EDFVTKVEAV IHPRFLEELL SPDPQMDFLA
LSQELEQEEG LTLAQLVEKR LLSLKEKGCG RAAPRHGTAR LDSSPSEFAA GQEAAREVPD
PQQRVSVETS PPQTAAQDPQ GQGRVRTGMA RSEDPAVLLG CQDSPRLKAV RPTSPPQDHR
PTCPGLGTKD ALGLPGESPV KESHGLAKGS SEETELPGMV YVVGSHHRLR PWRLSQSPVP
SSGLLSPGGR GPQGALQSPS AQKRGLSPSP SPASKSKKRP LFGSPSPAEK TPHPGPGLRV
SGEQSLAWGL GGPSQSQKRK GDPLASRRKK KRHCSQ*

mutated AA sequence

MASNGAYPVL GPGVTVNPGT SLSVFTALPF ATPAPGPAHR PPLVTAVVPP AGPLVLSAFP
STPLVAGQDG RGPSGAGASN VFVQMRTEVG PVKPPQAQTL ILTQAPLVWQ APGTLCGGVM
CPPPLLLAAA PGVPVTSAQV VGGTQACEGG WSHGLPLPPP PPAAQVAPIV SPGNAGPWPQ
GAHGEGSLAP SQAKARPDDS CKPKSVYENF RLWQHYKPLA RRHLPQSPDT EALSCFLIPV
LRSLARRKPT MTLEEGLWQA MREWQHTSNF DRMIFYEMAE KFLEFEAEEE MQIQKSQWMK
GPQSLPPPAP PRLEPRGPPA PEVVKQPVYL PSKDGPKAPT ACLPPPRPQR PAETKAHLPP
PRPQRPAETN AHLPPPRPQR PAETKVPEEI PPEVVQEYVD IMEELLGSHP GDTGEPEGQR
EKGKVEQPQE EDGITSDPGL LSYIDKLCSQ EDFVTKVEAV IHPRFLEELL SPDPQMDFLA
LSQELEQEEG LTLAQLVEKR LLSLKEKGCG RAAPRHGTAR LDSSPSEFAA GQEAAREVPD
PQQRVSVETS PPQTAAQDPQ GQGRVRTGMA RSEDPAVLLG CQDSPRLKAV RPTSPPQDHR
PTCPGLGTKD ALGLPGESPV KESHGLAKGS SEETELPGMV YVVGSHHRLR PWRLSQSPVP
SSGLLSPGGR GPQGALQSPS AQKRGLSPSP SPASKSKKRP LFGSPSPAEK TPHPGPGLRV
SGEQSLAWGL GGPSQSQKRK GDPLASRRKK KRHCSQ*

speed

0.36 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999851 (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)

chr9:97087707T>CN/A show variant in all transcripts IGV

HGNC symbol

NUTM2F

Ensembl transcript ID

ENST00000341207

Genbank transcript ID

N/A

UniProt peptide

A1L443

alteration type

single base exchange

alteration region

CDS

DNA changes

c.526A>G
cDNA.547A>G
g.3220A>G

AA changes

R176G Score: 125 explain score(s)

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

176

frameshift

known variant

Reference ID: rs190275133

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1923	223	2146
ExAC	114	63	177

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.173	0.003
	-0.631	0
(flanking)	-0.323	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
Acc marginally increased	3210	wt: 0.8014 / mu: 0.8190 (marginal change - not scored)	wt: GTGGCCCCCATCGTGTCCCCAGGGAACGCTAGGCCATGGCC mu: GTGGCCCCCATCGTGTCCCCAGGGAACGCTGGGCCATGGCC	ccca\|GGGA

distance from splice site

188

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

176

mutated

not conserved

176

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000020164

Fcatus

not conserved

ENSFCAG00000010760

Mmusculus

not conserved

ENSMUSG00000071909

191

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

2226 / 2226

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

742 / 742

position of stopcodon in wt / mu cDNA

2247 / 2247

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

22 / 22

chromosome

strand

-1

last intron/exon boundary

1462

theoretical NMD boundary in CDS

1390

length of CDS

2226

coding sequence (CDS) position

526

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

547

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

3220

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

97087707

original gDNA sequence snippet

TCGTGTCCCCAGGGAACGCTAGGCCATGGCCACAAGGGGCT

altered gDNA sequence snippet

TCGTGTCCCCAGGGAACGCTGGGCCATGGCCACAAGGGGCT

original cDNA sequence snippet

TCGTGTCCCCAGGGAACGCTAGGCCATGGCCACAAGGGGCT

altered cDNA sequence snippet

TCGTGTCCCCAGGGAACGCTGGGCCATGGCCACAAGGGGCT

wildtype AA sequence

MASNGAYPVL GPGVTVNPGT SLSVFTALPF ATPAPGPAHR PPLVTAVVPP AGPLVLSAFP
STPLVAGQDG RGPSGAGASN VFVQMRTEVG PVKPPQAQTL ILTQAPLVWQ APGTLCGGVM
CPPPLLLAAA PGVPVTSAQV VGGTQACEGG WSHGLPLPPP PPAAQVAPIV SPGNARPWPQ
GAHGEGSLAP SQAKARPDDS CKPKSVYENF RLWQHYKPLA RRHLPQSPDT EALSCFLIPV
LRSLARRKPT MTLEEGLWQA MREWQHTSNF DRMIFYEMAE KFLEFEAEEE MQIQKSQWMK
GPQSLPPPAP PRLEPRGPPA PEVVKQPVYL PSKDGPKAPT ACLPPPRPQR PAETKAHLPP
PRPQRPAETK VPEEIPPEVV QEYVDIMEEL LGSHPGDTGE PEGQREKGKV EQPQEEDGIT
SDPGLLSYID KLCSQEDFVT KVEAVIHPRF LEELLSPDPQ MDFLALSQEL EQEEGLTLAQ
LVEKRLLSLK EKGCGRAAPR HGTARLDSSP SEFAAGQEAA REVPDPQQRV SVETSPPQTA
AQDPQGQGRV RTGMARSEDP AVLLGCQDSP RLKAVRPTSP PQDHRPTCPG LGTKDALGLP
GESPVKESHG LAKGSSEETE LPGMVYVVGS HHRLRPWRLS QSPVPSSGLL SPGGRGPQGA
LQSPSAQKRG LSPSPSPASK SKKRPLFGSP SPAEKTPHPG PGLRVSGEQS LAWGLGGPSQ
SQKRKGDPLA SRRKKKRHCS Q*

mutated AA sequence

MASNGAYPVL GPGVTVNPGT SLSVFTALPF ATPAPGPAHR PPLVTAVVPP AGPLVLSAFP
STPLVAGQDG RGPSGAGASN VFVQMRTEVG PVKPPQAQTL ILTQAPLVWQ APGTLCGGVM
CPPPLLLAAA PGVPVTSAQV VGGTQACEGG WSHGLPLPPP PPAAQVAPIV SPGNAGPWPQ
GAHGEGSLAP SQAKARPDDS CKPKSVYENF RLWQHYKPLA RRHLPQSPDT EALSCFLIPV
LRSLARRKPT MTLEEGLWQA MREWQHTSNF DRMIFYEMAE KFLEFEAEEE MQIQKSQWMK
GPQSLPPPAP PRLEPRGPPA PEVVKQPVYL PSKDGPKAPT ACLPPPRPQR PAETKAHLPP
PRPQRPAETK VPEEIPPEVV QEYVDIMEEL LGSHPGDTGE PEGQREKGKV EQPQEEDGIT
SDPGLLSYID KLCSQEDFVT KVEAVIHPRF LEELLSPDPQ MDFLALSQEL EQEEGLTLAQ
LVEKRLLSLK EKGCGRAAPR HGTARLDSSP SEFAAGQEAA REVPDPQQRV SVETSPPQTA
AQDPQGQGRV RTGMARSEDP AVLLGCQDSP RLKAVRPTSP PQDHRPTCPG LGTKDALGLP
GESPVKESHG LAKGSSEETE LPGMVYVVGS HHRLRPWRLS QSPVPSSGLL SPGGRGPQGA
LQSPSAQKRG LSPSPSPASK SKKRPLFGSP SPAEKTPHPG PGLRVSGEQS LAWGLGGPSQ
SQKRKGDPLA SRRKKKRHCS Q*

speed

0.42 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