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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000328913
Querying Taster for transcript #2: ENST00000473233
Querying Taster for transcript #3: ENST00000447025
Querying Taster for transcript #4: ENST00000414362
MT speed 0 s - this script 5.459854 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MCF2L2	polymorphism_automatic	0.000205651843986021	simple_aae				I359L	single base exchange	rs7639705		show file
MCF2L2	polymorphism_automatic	0.000205651843986021	simple_aae				I359L	single base exchange	rs7639705		show file
MCF2L2	polymorphism_automatic	0.000205651843986021	simple_aae				I359L	single base exchange	rs7639705		show file
MCF2L2	polymorphism_automatic	0.000205651843986021	simple_aae				I359L	single base exchange	rs7639705		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999794348156014 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM105035)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183027542T>GN/A show variant in all transcripts IGV

HGNC symbol

MCF2L2

Ensembl transcript ID

ENST00000328913

Genbank transcript ID

NM_015078

UniProt peptide

Q86YR7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1075A>C
cDNA.1373A>C
g.119025A>C

AA changes

I359L Score: 5 explain score(s)

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

359

frameshift

known variant

Reference ID: rs7639705

database	homozygous (G/G)	heterozygous	allele carriers
1000G	314	1047	1361
ExAC	4380	22360	26740

known disease mutation at this position, please check HGMD for details (HGMD ID CM105035)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.375	0.965
	2.756	0.966
(flanking)	-0.656	0.753

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

359

mutated

all conserved

359

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000001456

276

Fcatus

all conserved

ENSFCAG00000014298

358

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003813

358

Drerio

all conserved

ENSDARG00000079742

361

Dmelanogaster

no alignment

FBgn0050440

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
323	428	REPEAT	Spectrin.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3345 / 3345

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

1115 / 1115

position of stopcodon in wt / mu cDNA

3643 / 3643

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

299 / 299

chromosome

strand

-1

last intron/exon boundary

3520

theoretical NMD boundary in CDS

3171

length of CDS

3345

coding sequence (CDS) position

1075

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

1373

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

119025

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

183027542

original gDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered gDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

original cDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered cDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

wildtype AA sequence

MLSCLKEEMP PQELTRRLAT VITHVDEIMQ QEVRPLMAVE IIEQLHRQFA ILSGGRGEDG
APIITFPEFS GFKHIPDEDF LNVMTYLTSI PSVEAASIGF IVVIDRRRDK WSSVKASLTR
IAVAFPGNLQ LIFILRPSRF IQRTFTDIGI KYYRNEFKTK VPIIMVNSVS DLHGYIDKSQ
LTRELGGTLE YRHGQWVNHR TAIENFALTL KTTAQMLQTF GSCLATAELP RSMLSTEDLL
MSHTRQRDKL QDELKLLGKQ GTTLLSCIQE PATKCPNSKL NLNQLENVTT MERLLVQLDE
TEKAFSHFWS EHHLKLNQCL QLQHFEHDFC KAKLALDNLL EEQAEFTGIG DSVMHVEQIL
KEHKKLEEKS QEPLEKAQLL ALVGDQLIQS HHYAADAIRP RCVELRHLCD DFINGNKKKW
DILGKSLEFH RQLDKVSQWC EAGIYLLASQ AVDKCQSREG VDIALNDIAT FLGTVKEYPL
LSPKEFYNEF ELLLTLDAKA KAQKVLQRLD DVQEIFHKRQ VSLMKLAAKQ TRPVQPVAPH
PESSPKWVSS KTSQPSTSVP LARPLRTSEE PYTETELNSR GKEDDETKFE VKSEEIFESH
HERGNPELEQ QARLGDLSPR RRIIRDLLET EEIYIKEIKS IIDGYITPMD FIWLKHLIPD
VLQNNKDFLF GNIRELYEFH NRTFLKELEK CAENPELLAH CFLKRKEDLQ IYFKYHKNLP
RARAIWQECQ DCAYFGVCQR QLDHNLPLFK YLKGPSQRLI KYQMLLKGLL DFESPEDMEI
DPGELGGSAK DGPKRTKDSA FSTELQQALA VIEDLIKSCE LAVDLAAVTE CPDDIGKLGK
LLLHGPFSVW TIHKDRYKMK DLIRFKPSQR QIYLFERGIV FCKIRMEPGD QGLSPHYSFK
KTMKLMTLSI RQLGRGSHRK FEIASRNGLE KYILQAASKE IRDCWFSEIS KLLMEQQNNI
KDQGNPQFEM STSKGSGAGS GPWIKNMERA TTSKEDPASS TGGIKGCSSR EFSSMDTFED
CEGAEDMEKE SSALSLAGLF QSDDSHETCS SKSAFLERGE SSQGEKEERD EEETATRSTE
EERAGASTGR LAPAGATAGF QARALRPRTS AQES*

mutated AA sequence

MLSCLKEEMP PQELTRRLAT VITHVDEIMQ QEVRPLMAVE IIEQLHRQFA ILSGGRGEDG
APIITFPEFS GFKHIPDEDF LNVMTYLTSI PSVEAASIGF IVVIDRRRDK WSSVKASLTR
IAVAFPGNLQ LIFILRPSRF IQRTFTDIGI KYYRNEFKTK VPIIMVNSVS DLHGYIDKSQ
LTRELGGTLE YRHGQWVNHR TAIENFALTL KTTAQMLQTF GSCLATAELP RSMLSTEDLL
MSHTRQRDKL QDELKLLGKQ GTTLLSCIQE PATKCPNSKL NLNQLENVTT MERLLVQLDE
TEKAFSHFWS EHHLKLNQCL QLQHFEHDFC KAKLALDNLL EEQAEFTGIG DSVMHVEQLL
KEHKKLEEKS QEPLEKAQLL ALVGDQLIQS HHYAADAIRP RCVELRHLCD DFINGNKKKW
DILGKSLEFH RQLDKVSQWC EAGIYLLASQ AVDKCQSREG VDIALNDIAT FLGTVKEYPL
LSPKEFYNEF ELLLTLDAKA KAQKVLQRLD DVQEIFHKRQ VSLMKLAAKQ TRPVQPVAPH
PESSPKWVSS KTSQPSTSVP LARPLRTSEE PYTETELNSR GKEDDETKFE VKSEEIFESH
HERGNPELEQ QARLGDLSPR RRIIRDLLET EEIYIKEIKS IIDGYITPMD FIWLKHLIPD
VLQNNKDFLF GNIRELYEFH NRTFLKELEK CAENPELLAH CFLKRKEDLQ IYFKYHKNLP
RARAIWQECQ DCAYFGVCQR QLDHNLPLFK YLKGPSQRLI KYQMLLKGLL DFESPEDMEI
DPGELGGSAK DGPKRTKDSA FSTELQQALA VIEDLIKSCE LAVDLAAVTE CPDDIGKLGK
LLLHGPFSVW TIHKDRYKMK DLIRFKPSQR QIYLFERGIV FCKIRMEPGD QGLSPHYSFK
KTMKLMTLSI RQLGRGSHRK FEIASRNGLE KYILQAASKE IRDCWFSEIS KLLMEQQNNI
KDQGNPQFEM STSKGSGAGS GPWIKNMERA TTSKEDPASS TGGIKGCSSR EFSSMDTFED
CEGAEDMEKE SSALSLAGLF QSDDSHETCS SKSAFLERGE SSQGEKEERD EEETATRSTE
EERAGASTGR LAPAGATAGF QARALRPRTS AQES*

speed

0.80 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: 0.999794348156014 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM105035)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183027542T>GN/A show variant in all transcripts IGV

HGNC symbol

MCF2L2

Ensembl transcript ID

ENST00000473233

Genbank transcript ID

N/A

UniProt peptide

Q86YR7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1075A>C
cDNA.1075A>C
g.119025A>C

AA changes

I359L Score: 5 explain score(s)

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

359

frameshift

known variant

Reference ID: rs7639705

database	homozygous (G/G)	heterozygous	allele carriers
1000G	314	1047	1361
ExAC	4380	22360	26740

known disease mutation at this position, please check HGMD for details (HGMD ID CM105035)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.375	0.965
	2.756	0.966
(flanking)	-0.656	0.753

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

359

mutated

all conserved

359

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000001456

276

Fcatus

all conserved

ENSFCAG00000014298

358

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003813

358

Drerio

all conserved

ENSDARG00000079742

361

Dmelanogaster

no alignment

FBgn0050440

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
323	428	REPEAT	Spectrin.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3225 / 3225

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

1075 / 1075

position of stopcodon in wt / mu cDNA

3225 / 3225

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

3106

theoretical NMD boundary in CDS

3055

length of CDS

3225

coding sequence (CDS) position

1075

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

1075

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

119025

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

183027542

original gDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered gDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

original cDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered cDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

wildtype AA sequence

mutated AA sequence

MLSCLKEEMP PQELTRRLAT VITHVDEIMQ QEVRPLMAVE IIEQLHRQFA ILSGGRGEDG
APIITFPEFS GFKHIPDEDF LNVMTYLTSI PSVEAASIGF IVVIDRRRDK WSSVKASLTR
IAVAFPGNLQ LIFILRPSRF IQRTFTDIGI KYYRNEFKTK VPIIMVNSVS DLHGYIDKSQ
LTRELGGTLE YRHGQWVNHR TAIENFALTL KTTAQMLQTF GSCLATAELP RSMLSTEDLL
MSHTRQRDKL QDELKLLGKQ GTTLLSCIQE PATKCPNSKL NLNQLENVTT MERLLVQLDE
TEKAFSHFWS EHHLKLNQCL QLQHFEHDFC KAKLALDNLL EEQAEFTGIG DSVMHVEQLL
KEHKKLEEKS QEPLEKAQLL ALVGDQLIQS HHYAADAIRP RCVELRHLCD DFINGNKKKW
DILGKSLEFH RQLDKVSQWC EAGIYLLASQ AVDKCQSREG VDIALNDIAT FLGTVKEYPL
LSPKEFYNEF ELLLTLDAKA KAQKVLQRLD DVQEIFHKRQ VSLMKLAAKQ TRPVQPVAPH
PESSPKWVSS KTSQPSTSVP LARPLRTSEE PYTETELNSR GKEDDETKFE VKSEEIFESH
HERGNPELEQ QARLGDLSPR RRIIRDLLET EEIYIKEIKS IIDGYITPMD FIWLKHLIPD
VLQNNKDFLF GNIRELYEFH NRTFLKELEK CAENPELLAH CFLKRKEDLQ IYFKYHKNLP
RARAIWQECQ DCAYFGVCQR QLDHNLPLFK YLKGPSQRLI KYQMLLKGLL DFESPEDMEI
DPGELGGSAK DGPKRTKDSA FSTELQQALA VIEDLIKSCE LAVDLAAVTE CPDDIGKLGK
LLLHGPFSVW TIHKDRYKMK DLIRFKPSQR QIYLFERGIV FCKIRMEPGD QGLSPHYSFK
KTMKLMTLSI RQLGRGSHRK FEIASRNGLE KYILQAASKE IRDCWFSEIS KLLMEQQNNI
KDQGNPQFEM STSKGSGAGS GPWIKNMERA TTSKEDPASS TGGIKGCSSR EFSSMDTFED
CEGAEDMEKE SSALSLAGLF QSDDSHETCS SKSAFLERGE SSQGEKEERD EEET*

speed

1.16 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999794348156014 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM105035)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183027542T>GN/A show variant in all transcripts IGV

HGNC symbol

MCF2L2

Ensembl transcript ID

ENST00000447025

Genbank transcript ID

N/A

UniProt peptide

Q86YR7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1075A>C
cDNA.1183A>C
g.119025A>C

AA changes

I359L Score: 5 explain score(s)

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

359

frameshift

known variant

Reference ID: rs7639705

database	homozygous (G/G)	heterozygous	allele carriers
1000G	314	1047	1361
ExAC	4380	22360	26740

known disease mutation at this position, please check HGMD for details (HGMD ID CM105035)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.375	0.965
	2.756	0.966
(flanking)	-0.656	0.753

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

359

mutated

all conserved

359

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000001456

276

Fcatus

all conserved

ENSFCAG00000014298

358

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003813

358

Drerio

all conserved

ENSDARG00000079742

361

Dmelanogaster

no alignment

FBgn0050440

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
323	428	REPEAT	Spectrin.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2136 / 2136

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

712 / 712

position of stopcodon in wt / mu cDNA

2244 / 2244

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

109 / 109

chromosome

strand

-1

last intron/exon boundary

2154

theoretical NMD boundary in CDS

1995

length of CDS

2136

coding sequence (CDS) position

1075

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

1183

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

119025

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

183027542

original gDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered gDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

original cDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered cDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

wildtype AA sequence

mutated AA sequence

speed

1.09 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999794348156014 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM105035)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183027542T>GN/A show variant in all transcripts IGV

HGNC symbol

MCF2L2

Ensembl transcript ID

ENST00000414362

Genbank transcript ID

N/A

UniProt peptide

Q86YR7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1075A>C
cDNA.1199A>C
g.119025A>C

AA changes

I359L Score: 5 explain score(s)

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

359

frameshift

known variant

Reference ID: rs7639705

database	homozygous (G/G)	heterozygous	allele carriers
1000G	314	1047	1361
ExAC	4380	22360	26740

known disease mutation at this position, please check HGMD for details (HGMD ID CM105035)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.375	0.965
	2.756	0.966
(flanking)	-0.656	0.753

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

359

mutated

all conserved

359

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000001456

276

Fcatus

all conserved

ENSFCAG00000014298

358

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003813

358

Drerio

all conserved

ENSDARG00000079742

361

Dmelanogaster

no alignment

FBgn0050440

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
323	428	REPEAT	Spectrin.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1887 / 1887

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

629 / 629

position of stopcodon in wt / mu cDNA

2011 / 2011

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

125 / 125

chromosome

strand

-1

last intron/exon boundary

1987

theoretical NMD boundary in CDS

1812

length of CDS

1887

coding sequence (CDS) position

1075

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

1199

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

119025

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

183027542

original gDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered gDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

original cDNA sequence snippet

GCGTGATGCACGTGGAGCAGATTCTTAAGGAACACAAAAAA

altered cDNA sequence snippet

GCGTGATGCACGTGGAGCAGCTTCTTAAGGAACACAAAAAA

wildtype AA sequence

mutated AA sequence

speed

1.14 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems