MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000401642
Querying Taster for transcript #2: ENST00000388940
MT speed 0 s - this script 4.091168 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SCFD2	polymorphism_automatic	0.958973691453902	simple_aae		affected		L512S	single base exchange	rs7675987		show file
SCFD2	polymorphism_automatic	0.958973691453902	simple_aae		affected		L512S	single base exchange	rs7675987		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0410263085460984 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:54011526A>GN/A show variant in all transcripts IGV

HGNC symbol

SCFD2

Ensembl transcript ID

ENST00000401642

Genbank transcript ID

NM_152540

UniProt peptide

Q8WU76

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1535T>C
cDNA.1669T>C
g.220717T>C

AA changes

L512S Score: 145 explain score(s)

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

512

frameshift

known variant

Reference ID: rs7675987

database	homozygous (G/G)	heterozygous	allele carriers
1000G	183	900	1083
ExAC	5929	20909	26838

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.036	0.989
	1.916	0.952
(flanking)	-0.239	0.309

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	220717	wt: 0.21 / mu: 0.52	wt: TGGATTGTCACCTTT mu: TGGATCGTCACCTTT	GATT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

512

mutated

not conserved

512

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017393

512

Fcatus

no alignment

ENSFCAG00000007895

n/a

Mmusculus

all identical

ENSMUSG00000062110

512

Ggallus

no alignment

ENSGALG00000013946

n/a

Trubripes

all identical

ENSTRUG00000014970

513

Drerio

all identical

ENSDARG00000040005

504

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

2055 / 2055

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

685 / 685

position of stopcodon in wt / mu cDNA

2189 / 2189

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

135 / 135

chromosome

strand

-1

last intron/exon boundary

2097

theoretical NMD boundary in CDS

1912

length of CDS

2055

coding sequence (CDS) position

1535

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

1669

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

220717

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

54011526

original gDNA sequence snippet

CTTCTGTGAGGAATCTGGATTGTCACCTTTGCTGCAAAAAA

altered gDNA sequence snippet

CTTCTGTGAGGAATCTGGATCGTCACCTTTGCTGCAAAAAA

original cDNA sequence snippet

CTTCTGTGAGGAATCTGGATTGTCACCTTTGCTGCAAAAAA

altered cDNA sequence snippet

CTTCTGTGAGGAATCTGGATCGTCACCTTTGCTGCAAAAAA

wildtype AA sequence

MSASGVLSFT QQGWEQVLAK VKRAVVYLDA ACAESLHWGC GSTRLLEAVG GPDCHLREFE
PDAIGGGAKQ PKAVFVLSCL LKGRTVEILR DIICRSHFQY CVVVTTVSHA VHLTANHVPA
AAAAEMEGQQ PVFEQLEEKL CEWMGNMNYT AEVFHVPLLL APVAPHFALT PAFASLFPLL
PQDVHLLNSA RPDKRKLGSL GDVDSTTLTP ELLLQIRCLV SGLSSLCEHL GVREECFAVG
SLSQVIAADL ANYAPAKNRK KTAAGRASVV FVDRTLDLTG AVGHHGDNLV EKIISALPQL
PGHTNDVMVN MIALTALHTE EENYNVVAPG CLSQSSDTTA KALWEALLNT KHKEAVMEVR
RHLVEAASRE NLPIKMSMGR VTPGQLMSYI QLFKNNLKAL MNHCGLLQLG LATAQTLKHP
QTAKWDNFLA FERLLLQSIG ESAMSVVLNQ LLPMIKPVTQ RTNEDYSPEE LLILLIYIYS
VTGELTVDKD LCEAEEKVKK ALAQVFCEES GLSPLLQKIT DWDSSINLTF HKSKIAVDEL
FTSLRDIAGA RSLLKQFKSV YVPGNHTHQA SYKPLLKQVV EEIFHPERPD SVDIEHMSSG
LTDLLKTGFS MFMKVSRPHP SDYPLLILFV VGGVTVSEVK MVKDLVASLK PGTQVIVLST
RLLKPLNIPE LLFATDRLHP DLGF*

mutated AA sequence

MSASGVLSFT QQGWEQVLAK VKRAVVYLDA ACAESLHWGC GSTRLLEAVG GPDCHLREFE
PDAIGGGAKQ PKAVFVLSCL LKGRTVEILR DIICRSHFQY CVVVTTVSHA VHLTANHVPA
AAAAEMEGQQ PVFEQLEEKL CEWMGNMNYT AEVFHVPLLL APVAPHFALT PAFASLFPLL
PQDVHLLNSA RPDKRKLGSL GDVDSTTLTP ELLLQIRCLV SGLSSLCEHL GVREECFAVG
SLSQVIAADL ANYAPAKNRK KTAAGRASVV FVDRTLDLTG AVGHHGDNLV EKIISALPQL
PGHTNDVMVN MIALTALHTE EENYNVVAPG CLSQSSDTTA KALWEALLNT KHKEAVMEVR
RHLVEAASRE NLPIKMSMGR VTPGQLMSYI QLFKNNLKAL MNHCGLLQLG LATAQTLKHP
QTAKWDNFLA FERLLLQSIG ESAMSVVLNQ LLPMIKPVTQ RTNEDYSPEE LLILLIYIYS
VTGELTVDKD LCEAEEKVKK ALAQVFCEES GSSPLLQKIT DWDSSINLTF HKSKIAVDEL
FTSLRDIAGA RSLLKQFKSV YVPGNHTHQA SYKPLLKQVV EEIFHPERPD SVDIEHMSSG
LTDLLKTGFS MFMKVSRPHP SDYPLLILFV VGGVTVSEVK MVKDLVASLK PGTQVIVLST
RLLKPLNIPE LLFATDRLHP DLGF*

speed

1.07 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: 0.0410263085460984 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:54011526A>GN/A show variant in all transcripts IGV

HGNC symbol

SCFD2

Ensembl transcript ID

ENST00000388940

Genbank transcript ID

N/A

UniProt peptide

Q8WU76

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1535T>C
cDNA.1655T>C
g.220717T>C

AA changes

L512S Score: 145 explain score(s)

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

512

frameshift

known variant

Reference ID: rs7675987

database	homozygous (G/G)	heterozygous	allele carriers
1000G	183	900	1083
ExAC	5929	20909	26838

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.036	0.989
	1.916	0.952
(flanking)	-0.239	0.309

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	220717	wt: 0.21 / mu: 0.52	wt: TGGATTGTCACCTTT mu: TGGATCGTCACCTTT	GATT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

512

mutated

not conserved

512

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017393

512

Fcatus

no alignment

ENSFCAG00000007895

n/a

Mmusculus

all identical

ENSMUSG00000062110

512

Ggallus

no alignment

ENSGALG00000013946

n/a

Trubripes

all identical

ENSTRUG00000014970

513

Drerio

all identical

ENSDARG00000040005

504

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

1920 / 1920

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

640 / 640

position of stopcodon in wt / mu cDNA

2040 / 2040

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

121 / 121

chromosome

strand

-1

last intron/exon boundary

1948

theoretical NMD boundary in CDS

1777

length of CDS

1920

coding sequence (CDS) position

1535

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

1655

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

220717

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

54011526

original gDNA sequence snippet

CTTCTGTGAGGAATCTGGATTGTCACCTTTGCTGCAAAAAA

altered gDNA sequence snippet

CTTCTGTGAGGAATCTGGATCGTCACCTTTGCTGCAAAAAA

original cDNA sequence snippet

CTTCTGTGAGGAATCTGGATTGTCACCTTTGCTGCAAAAAA

altered cDNA sequence snippet

CTTCTGTGAGGAATCTGGATCGTCACCTTTGCTGCAAAAAA

wildtype AA sequence

MSASGVLSFT QQGWEQVLAK VKRAVVYLDA ACAESLHWGC GSTRLLEAVG GPDCHLREFE
PDAIGGGAKQ PKAVFVLSCL LKGRTVEILR DIICRSHFQY CVVVTTVSHA VHLTANHVPA
AAAAEMEGQQ PVFEQLEEKL CEWMGNMNYT AEVFHVPLLL APVAPHFALT PAFASLFPLL
PQDVHLLNSA RPDKRKLGSL GDVDSTTLTP ELLLQIRCLV SGLSSLCEHL GVREECFAVG
SLSQVIAADL ANYAPAKNRK KTAAGRASVV FVDRTLDLTG AVGHHGDNLV EKIISALPQL
PGHTNDVMVN MIALTALHTE EENYNVVAPG CLSQSSDTTA KALWEALLNT KHKEAVMEVR
RHLVEAASRE NLPIKMSMGR VTPGQLMSYI QLFKNNLKAL MNHCGLLQLG LATAQTLKHP
QTAKWDNFLA FERLLLQSIG ESAMSVVLNQ LLPMIKPVTQ RTNEDYSPEE LLILLIYIYS
VTGELTVDKD LCEAEEKVKK ALAQVFCEES GLSPLLQKIT DWDSSINLTF HKSKIAVDEL
FTSLRDIAGA RSLLKQFKSV YVPGNHTHQV SRPHPSDYPL LILFVVGGVT VSEVKMVKDL
VASLKPGTQV IVLSTRLLKP LNIPELLFAT DRLHPDLGF*

mutated AA sequence

MSASGVLSFT QQGWEQVLAK VKRAVVYLDA ACAESLHWGC GSTRLLEAVG GPDCHLREFE
PDAIGGGAKQ PKAVFVLSCL LKGRTVEILR DIICRSHFQY CVVVTTVSHA VHLTANHVPA
AAAAEMEGQQ PVFEQLEEKL CEWMGNMNYT AEVFHVPLLL APVAPHFALT PAFASLFPLL
PQDVHLLNSA RPDKRKLGSL GDVDSTTLTP ELLLQIRCLV SGLSSLCEHL GVREECFAVG
SLSQVIAADL ANYAPAKNRK KTAAGRASVV FVDRTLDLTG AVGHHGDNLV EKIISALPQL
PGHTNDVMVN MIALTALHTE EENYNVVAPG CLSQSSDTTA KALWEALLNT KHKEAVMEVR
RHLVEAASRE NLPIKMSMGR VTPGQLMSYI QLFKNNLKAL MNHCGLLQLG LATAQTLKHP
QTAKWDNFLA FERLLLQSIG ESAMSVVLNQ LLPMIKPVTQ RTNEDYSPEE LLILLIYIYS
VTGELTVDKD LCEAEEKVKK ALAQVFCEES GSSPLLQKIT DWDSSINLTF HKSKIAVDEL
FTSLRDIAGA RSLLKQFKSV YVPGNHTHQV SRPHPSDYPL LILFVVGGVT VSEVKMVKDL
VASLKPGTQV IVLSTRLLKP LNIPELLFAT DRLHPDLGF*

speed

1.07 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems