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: ENST00000447399
Querying Taster for transcript #2: ENST00000318950
MT speed 0 s - this script 2.771505 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SWAP70	polymorphism_automatic	0.978334383404614	simple_aae		affected		Q447E	single base exchange	rs415895		show file
SWAP70	polymorphism_automatic	0.978334383404614	simple_aae		affected		Q505E	single base exchange	rs415895		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0216656165953863 (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)

chr11:9769562C>GN/A show variant in all transcripts IGV

HGNC symbol

SWAP70

Ensembl transcript ID

ENST00000447399

Genbank transcript ID

N/A

UniProt peptide

Q9UH65

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1339C>G
cDNA.1442C>G
g.83939C>G

AA changes

Q447E Score: 29 explain score(s)

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

447

frameshift

known variant

Reference ID: rs415895

database	homozygous (G/G)	heterozygous	allele carriers
1000G	713	1180	1893
ExAC	23973	-15179	8794

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.105	0.439
	3.772	0.994
(flanking)	0.794	0.995

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	83935	wt: 0.21 / mu: 0.95	wt: CAGCTGGAGCAGCTT mu: CAGCTGGAGGAGCTT	GCTG\|gagc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

447

mutated

all conserved

447

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009204

505

Fcatus

all identical

ENSFCAG00000003774

505

Mmusculus

all identical

ENSMUSG00000031015

505

Ggallus

all identical

ENSGALG00000005750

436

Trubripes

not conserved

ENSTRUG00000009866

514

Drerio

all identical

ENSDARG00000057286

504

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
316	539	COILED	Potential.	lost
526	585	MUTAGEN	Missing: Affects targeting to loose actin filament arrays.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1584 / 1584

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

528 / 528

position of stopcodon in wt / mu cDNA

1687 / 1687

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

104 / 104

chromosome

strand

last intron/exon boundary

1581

theoretical NMD boundary in CDS

1427

length of CDS

1584

coding sequence (CDS) position

1339

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

1442

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

83939

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

9769562

original gDNA sequence snippet

AGGCCATGGAGCAGCTGGAGCAGCTTGAGTTAGAACGGAAG

altered gDNA sequence snippet

AGGCCATGGAGCAGCTGGAGGAGCTTGAGTTAGAACGGAAG

original cDNA sequence snippet

AGGCCATGGAGCAGCTGGAGCAGCTTGAGTTAGAACGGAAG

altered cDNA sequence snippet

AGGCCATGGAGCAGCTGGAGGAGCTTGAGTTAGAACGGAAG

wildtype AA sequence

MGSLKEELLK AIWHAFTALD QDHSGKVSKS QLKVLSHNLC TVLKVPHDPV ALEEHFRDDD
EGPVSNQGYM PYLNRFILEK IEYLLKKLTE AMGGGWQQEQ FEHYKINFDD SKNGLSAWEL
IELIGNGQFS KGMDRQTVSM AINEVFNELI LDVLKQGYMM KKGHRRKNWT ERWFVLKPNI
ISYYVSEDLK DKKGDILLDE NCCVESLPDK DGKKCLFLVK CFDKTFEISA SDKKKKQEWI
QAIHSTIHLL KLGSPPPHKE ARQRRKELRK KQLAEQEELE RQMKELQAAN ESKQQELEAV
RKKLEEAASR AAEEEKKRLQ TQVELQARFS TELEREKLIR QQMEEQVAQK SSELEQYLQR
VRELEDMYLK LQEALEDERQ ARQDEETVRK LQARLLEEES SKRAELEKWH LEQQQAIQTT
EAEKQELENQ RVLKEQALQE AMEQLEQLEL ERKQALEQYE EVKKKLEMAT NKTKSWKDKV
AHHEGLIRLI EPGSKNPHLI TNWGPAAFTE AELEEREKNW KEKKTTE*

mutated AA sequence

MGSLKEELLK AIWHAFTALD QDHSGKVSKS QLKVLSHNLC TVLKVPHDPV ALEEHFRDDD
EGPVSNQGYM PYLNRFILEK IEYLLKKLTE AMGGGWQQEQ FEHYKINFDD SKNGLSAWEL
IELIGNGQFS KGMDRQTVSM AINEVFNELI LDVLKQGYMM KKGHRRKNWT ERWFVLKPNI
ISYYVSEDLK DKKGDILLDE NCCVESLPDK DGKKCLFLVK CFDKTFEISA SDKKKKQEWI
QAIHSTIHLL KLGSPPPHKE ARQRRKELRK KQLAEQEELE RQMKELQAAN ESKQQELEAV
RKKLEEAASR AAEEEKKRLQ TQVELQARFS TELEREKLIR QQMEEQVAQK SSELEQYLQR
VRELEDMYLK LQEALEDERQ ARQDEETVRK LQARLLEEES SKRAELEKWH LEQQQAIQTT
EAEKQELENQ RVLKEQALQE AMEQLEELEL ERKQALEQYE EVKKKLEMAT NKTKSWKDKV
AHHEGLIRLI EPGSKNPHLI TNWGPAAFTE AELEEREKNW KEKKTTE*

speed

0.68 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: 0.0216656165953863 (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)

chr11:9769562C>GN/A show variant in all transcripts IGV

HGNC symbol

SWAP70

Ensembl transcript ID

ENST00000318950

Genbank transcript ID

NM_015055

UniProt peptide

Q9UH65

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1513C>G
cDNA.1616C>G
g.83939C>G

AA changes

Q505E Score: 29 explain score(s)

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

505

frameshift

known variant

Reference ID: rs415895

database	homozygous (G/G)	heterozygous	allele carriers
1000G	713	1180	1893
ExAC	23973	-15179	8794

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.105	0.439
	3.772	0.994
(flanking)	0.794	0.995

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	83935	wt: 0.21 / mu: 0.95	wt: CAGCTGGAGCAGCTT mu: CAGCTGGAGGAGCTT	GCTG\|gagc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

505

mutated

all conserved

505

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009204

505

Fcatus

all identical

ENSFCAG00000003774

505

Mmusculus

all identical

ENSMUSG00000031015

505

Ggallus

all identical

ENSGALG00000005750

436

Trubripes

not conserved

ENSTRUG00000009866

514

Drerio

all identical

ENSDARG00000057286

504

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
316	539	COILED	Potential.	lost
526	585	MUTAGEN	Missing: Affects targeting to loose actin filament arrays.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1758 / 1758

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

586 / 586

position of stopcodon in wt / mu cDNA

1861 / 1861

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

104 / 104

chromosome

strand

last intron/exon boundary

1755

theoretical NMD boundary in CDS

1601

length of CDS

1758

coding sequence (CDS) position

1513

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

1616

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

83939

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

9769562

original gDNA sequence snippet

AGGCCATGGAGCAGCTGGAGCAGCTTGAGTTAGAACGGAAG

altered gDNA sequence snippet

AGGCCATGGAGCAGCTGGAGGAGCTTGAGTTAGAACGGAAG

original cDNA sequence snippet

AGGCCATGGAGCAGCTGGAGCAGCTTGAGTTAGAACGGAAG

altered cDNA sequence snippet

AGGCCATGGAGCAGCTGGAGGAGCTTGAGTTAGAACGGAAG

wildtype AA sequence

MGSLKEELLK AIWHAFTALD QDHSGKVSKS QLKVLSHNLC TVLKVPHDPV ALEEHFRDDD
EGPVSNQGYM PYLNRFILEK VQDNFDKIEF NRMCWTLCVK KNLTKNPLLI TEEDAFKIWV
IFNFLSEDKY PLIIVSEEIE YLLKKLTEAM GGGWQQEQFE HYKINFDDSK NGLSAWELIE
LIGNGQFSKG MDRQTVSMAI NEVFNELILD VLKQGYMMKK GHRRKNWTER WFVLKPNIIS
YYVSEDLKDK KGDILLDENC CVESLPDKDG KKCLFLVKCF DKTFEISASD KKKKQEWIQA
IHSTIHLLKL GSPPPHKEAR QRRKELRKKQ LAEQEELERQ MKELQAANES KQQELEAVRK
KLEEAASRAA EEEKKRLQTQ VELQARFSTE LEREKLIRQQ MEEQVAQKSS ELEQYLQRVR
ELEDMYLKLQ EALEDERQAR QDEETVRKLQ ARLLEEESSK RAELEKWHLE QQQAIQTTEA
EKQELENQRV LKEQALQEAM EQLEQLELER KQALEQYEEV KKKLEMATNK TKSWKDKVAH
HEGLIRLIEP GSKNPHLITN WGPAAFTEAE LEEREKNWKE KKTTE*

mutated AA sequence

MGSLKEELLK AIWHAFTALD QDHSGKVSKS QLKVLSHNLC TVLKVPHDPV ALEEHFRDDD
EGPVSNQGYM PYLNRFILEK VQDNFDKIEF NRMCWTLCVK KNLTKNPLLI TEEDAFKIWV
IFNFLSEDKY PLIIVSEEIE YLLKKLTEAM GGGWQQEQFE HYKINFDDSK NGLSAWELIE
LIGNGQFSKG MDRQTVSMAI NEVFNELILD VLKQGYMMKK GHRRKNWTER WFVLKPNIIS
YYVSEDLKDK KGDILLDENC CVESLPDKDG KKCLFLVKCF DKTFEISASD KKKKQEWIQA
IHSTIHLLKL GSPPPHKEAR QRRKELRKKQ LAEQEELERQ MKELQAANES KQQELEAVRK
KLEEAASRAA EEEKKRLQTQ VELQARFSTE LEREKLIRQQ MEEQVAQKSS ELEQYLQRVR
ELEDMYLKLQ EALEDERQAR QDEETVRKLQ ARLLEEESSK RAELEKWHLE QQQAIQTTEA
EKQELENQRV LKEQALQEAM EQLEELELER KQALEQYEEV KKKLEMATNK TKSWKDKVAH
HEGLIRLIEP GSKNPHLITN WGPAAFTEAE LEEREKNWKE KKTTE*

speed

0.69 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems