MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000046640
Querying Taster for transcript #2: ENST00000381870
Querying Taster for transcript #3: ENST00000441220
Querying Taster for transcript #4: ENST00000414524
MT speed 0 s - this script 4.494357 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CTNS	polymorphism_automatic	0.929603697851878	simple_aae				T260I	single base exchange	rs161400		show file
CTNS	polymorphism_automatic	0.929603697851878	simple_aae				T260I	single base exchange	rs161400		show file
CTNS	polymorphism_automatic	0.929603697851878	simple_aae				T113I	single base exchange	rs161400		show file
CTNS	polymorphism_automatic	0.956386510002696	simple_aae				T152I	single base exchange	rs161400		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0703963021481221 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3561396C>TN/A show variant in all transcripts IGV

HGNC symbol

CTNS

Ensembl transcript ID

ENST00000381870

Genbank transcript ID

NM_001031681

UniProt peptide

O60931

alteration type

single base exchange

alteration region

CDS

DNA changes

c.779C>T
cDNA.1238C>T
g.21635C>T

AA changes

T260I Score: 89 explain score(s)

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

260

frameshift

known variant

Reference ID: rs161400

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1769	560	2329
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.977	0.99
	2.394	1
(flanking)	3.715	1

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

260

mutated

not conserved

260

Ptroglodytes

all identical

ENSPTRG00000008572

235

Mmulatta

all identical

ENSMMUG00000023389

260

Fcatus

all identical

ENSFCAG00000007923

260

Mmusculus

all identical

ENSMUSG00000005949

260

Ggallus

not conserved

ENSGALG00000004628

271

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000008890

265

Dmelanogaster

not conserved

FBgn0039045

265

Celegans

not conserved

C41C4.7

262

Xtropicalis

not conserved

ENSXETG00000005795

270

protein features

start (aa)	end (aa)	feature	details
259	261	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1203 / 1203

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

401 / 401

position of stopcodon in wt / mu cDNA

1662 / 1662

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

460 / 460

chromosome

strand

last intron/exon boundary

1545

theoretical NMD boundary in CDS

1035

length of CDS

1203

coding sequence (CDS) position

779

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

1238

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

21635

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

3561396

original gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

original cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

wildtype AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGLQAARTGS GSRLRQDWAP SLQPKALPQT TSVSASSLKG *

mutated AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVI TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGLQAARTGS GSRLRQDWAP SLQPKALPQT TSVSASSLKG *

speed

0.73 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: 0.0703963021481221 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3561396C>TN/A show variant in all transcripts IGV

HGNC symbol

CTNS

Ensembl transcript ID

ENST00000046640

Genbank transcript ID

NM_004937

UniProt peptide

O60931

alteration type

single base exchange

alteration region

CDS

DNA changes

c.779C>T
cDNA.1372C>T
g.21635C>T

AA changes

T260I Score: 89 explain score(s)

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

260

frameshift

known variant

Reference ID: rs161400

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1769	560	2329
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.977	0.99
	2.394	1
(flanking)	3.715	1

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

260

mutated

not conserved

260

Ptroglodytes

all identical

ENSPTRG00000008572

235

Mmulatta

all identical

ENSMMUG00000023389

260

Fcatus

all identical

ENSFCAG00000007923

260

Mmusculus

all identical

ENSMUSG00000005949

260

Ggallus

not conserved

ENSGALG00000004628

271

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000008890

265

Dmelanogaster

not conserved

FBgn0039045

265

Celegans

not conserved

C41C4.7

262

Xtropicalis

not conserved

ENSXETG00000005795

270

protein features

start (aa)	end (aa)	feature	details
259	261	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1104 / 1104

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

368 / 368

position of stopcodon in wt / mu cDNA

1697 / 1697

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

594 / 594

chromosome

strand

last intron/exon boundary

1564

theoretical NMD boundary in CDS

920

length of CDS

1104

coding sequence (CDS) position

779

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

1372

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

21635

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

3561396

original gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

original cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

wildtype AA sequence

mutated AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVI TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGYDQLN*

speed

0.75 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0703963021481221 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3561396C>TN/A show variant in all transcripts IGV

HGNC symbol

CTNS

Ensembl transcript ID

ENST00000414524

Genbank transcript ID

N/A

UniProt peptide

O60931

alteration type

single base exchange

alteration region

CDS

DNA changes

c.338C>T
cDNA.864C>T
g.21635C>T

AA changes

T113I Score: 89 explain score(s)

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

113

frameshift

known variant

Reference ID: rs161400

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1769	560	2329
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.977	0.99
	2.394	1
(flanking)	3.715	1

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

113

mutated

not conserved

113

Ptroglodytes

all identical

ENSPTRG00000008572

254

Mmulatta

all identical

ENSMMUG00000023389

260

Fcatus

all identical

ENSFCAG00000007923

260

Mmusculus

all identical

ENSMUSG00000005949

260

Ggallus

not conserved

ENSGALG00000004628

271

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000008890

265

Dmelanogaster

not conserved

FBgn0039045

265

Celegans

not conserved

C41C4.7

262

Xtropicalis

not conserved

ENSXETG00000005795

270

protein features

start (aa)	end (aa)	feature	details
1	121	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

663 / 663

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

221 / 221

position of stopcodon in wt / mu cDNA

1189 / 1189

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

527 / 527

chromosome

strand

last intron/exon boundary

1056

theoretical NMD boundary in CDS

479

length of CDS

663

coding sequence (CDS) position

338

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

864

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

21635

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

3561396

original gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

original cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

wildtype AA sequence

MNWRRKSVIG LSFDFVALNL TGFVAYSVFN IGLLWVPYIK EQFLLKYPNG VNPVNSNDVF
FSLHAVVLTL IIIVQCCLYE RGGQRVSWPA IGFLVLAWLF AFVTMIVAAV GVTTWLQFLF
CFSYIKLAVT LVKYFPQAYM NFYYKSTEGW SIGNVLLDFT GGSFSLLQMF LQSYNNDQWT
LIFGDPTKFG LGVFSIVFDV VFFIQHFCLY RKRPGYDQLN *

mutated AA sequence

MNWRRKSVIG LSFDFVALNL TGFVAYSVFN IGLLWVPYIK EQFLLKYPNG VNPVNSNDVF
FSLHAVVLTL IIIVQCCLYE RGGQRVSWPA IGFLVLAWLF AFVTMIVAAV GVITWLQFLF
CFSYIKLAVT LVKYFPQAYM NFYYKSTEGW SIGNVLLDFT GGSFSLLQMF LQSYNNDQWT
LIFGDPTKFG LGVFSIVFDV VFFIQHFCLY RKRPGYDQLN *

speed

1.11 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0436134899973044 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3561396C>TN/A show variant in all transcripts IGV

HGNC symbol

CTNS

Ensembl transcript ID

ENST00000441220

Genbank transcript ID

N/A

UniProt peptide

O60931

alteration type

single base exchange

alteration region

CDS

DNA changes

c.455C>T
cDNA.843C>T
g.21635C>T

AA changes

T152I Score: 89 explain score(s)

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

152

frameshift

known variant

Reference ID: rs161400

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1769	560	2329
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.977	0.99
	2.394	1
(flanking)	3.715	1

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

152

mutated

not conserved

152

Ptroglodytes

all identical

ENSPTRG00000008572

235

Mmulatta

all identical

ENSMMUG00000023389

260

Fcatus

all identical

ENSFCAG00000007923

260

Mmusculus

all identical

ENSMUSG00000005949

260

Ggallus

not conserved

ENSGALG00000004628

271

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000008890

265

Dmelanogaster

not conserved

FBgn0039045

265

Celegans

not conserved

C41C4.7

262

Xtropicalis

not conserved

ENSXETG00000005795

270

protein features

start (aa)	end (aa)	feature	details
123	189	DOMAIN	PQ-loop 1.	lost
143	161	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

879 / 879

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

293 / 293

position of stopcodon in wt / mu cDNA

1267 / 1267

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

389 / 389

chromosome

strand

last intron/exon boundary

1150

theoretical NMD boundary in CDS

711

length of CDS

879

coding sequence (CDS) position

455

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

843

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

21635

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

3561396

original gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

original cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

wildtype AA sequence

MCPRIRFLVI RSSAISIINQ VIGWIYFVAW SISFYPQVIM NWRRKSVIGL SFDFVALNLT
GFVAYSVFNI GLLWVPYIKE QFLLKYPNGV NPVNSNDVFF SLHAVVLTLI IIVQCCLYER
GGQRVSWPAI GFLVLAWLFA FVTMIVAAVG VTTWLQFLFC FSYIKLAVTL VKYFPQAYMN
FYYKSTEGWS IGNVLLDFTG GSFSLLQMFL QSYNNDQWTL IFGDPTKFGL GVFSIVFDVV
FFIQHFCLYR KRPGLQAART GSGSRLRQDW APSLQPKALP QTTSVSASSL KG*

mutated AA sequence

MCPRIRFLVI RSSAISIINQ VIGWIYFVAW SISFYPQVIM NWRRKSVIGL SFDFVALNLT
GFVAYSVFNI GLLWVPYIKE QFLLKYPNGV NPVNSNDVFF SLHAVVLTLI IIVQCCLYER
GGQRVSWPAI GFLVLAWLFA FVTMIVAAVG VITWLQFLFC FSYIKLAVTL VKYFPQAYMN
FYYKSTEGWS IGNVLLDFTG GSFSLLQMFL QSYNNDQWTL IFGDPTKFGL GVFSIVFDVV
FFIQHFCLYR KRPGLQAART GSGSRLRQDW APSLQPKALP QTTSVSASSL KG*

speed

0.59 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