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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000447419
Querying Taster for transcript #2: ENST00000440447
Querying Taster for transcript #3: ENST00000293922
MT speed 0 s - this script 3.694274 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PTX4	polymorphism_automatic	2.59792187762287e-14	simple_aae		affected		R281K	single base exchange	rs2745098		show file
PTX4	polymorphism_automatic	2.59792187762287e-14	simple_aae		affected		R276K	single base exchange	rs2745098		show file
PTX4	polymorphism_automatic	1.48694601076471e-09	simple_aae		affected		G133R	single base exchange	rs2745098		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999974 (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)

chr16:1536535C>TN/A show variant in all transcripts IGV

HGNC symbol

PTX4

Ensembl transcript ID

ENST00000447419

Genbank transcript ID

N/A

UniProt peptide

Q96A99

alteration type

single base exchange

alteration region

CDS

DNA changes

c.842G>A
cDNA.868G>A
g.2448G>A

AA changes

R281K Score: 26 explain score(s)

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

281

frameshift

known variant

Reference ID: rs2745098

database	homozygous (T/T)	heterozygous	allele carriers
1000G	708	1070	1778
ExAC	10176	12415	22591

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.102	0.215
	0.858	0.156
(flanking)	0.006	0.007

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 gained	2443	0.89	mu: GCCTCCACCAAGAAC	CTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

281

mutated

all conserved

281

Ptroglodytes

all conserved

ENSPTRG00000007595

281

Mmulatta

all conserved

ENSMMUG00000007049

281

Fcatus

all conserved

ENSFCAG00000010651

239

Mmusculus

not conserved

ENSMUSG00000044172

291

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000038072

334

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000009128

283

protein features

start (aa)	end (aa)	feature	details
271	469	DOMAIN	Pentaxin.	lost
300	300	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
407	407	METAL	Calcium 1; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1437 / 1437

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

479 / 479

position of stopcodon in wt / mu cDNA

1463 / 1463

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

27 / 27

chromosome

strand

-1

last intron/exon boundary

823

theoretical NMD boundary in CDS

746

length of CDS

1437

coding sequence (CDS) position

842

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

868

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

2448

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

1536535

original gDNA sequence snippet

TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC

altered gDNA sequence snippet

TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC

original cDNA sequence snippet

TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC

altered cDNA sequence snippet

TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC

wildtype AA sequence

MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKVDT
RLRALDLTLG ERSQQRARER KAHKAQRDAL QDSLARLEGL VHSQGARLAA LEGRLPVAHP
GTAALGPALV PTPTQPEELG PTSLKLQRDR QELRAASEHR GPPQDSSAPL QGRREPPASG
SHRVLSGTAP KDPRQQAWSP QVPGEICGVG PTLVFPNAST RNVVFLSPGF VTALRALSFC
SWVRTASGRL GTLLSYATED NDNKLVLHGR DSLLPGSIHF VIGDPAFREL PLQLLLDGQW
HHICVIWTST QGRYWLHVDR RLVATGSRFR EGYEIPPGGS LVLGQEQDSV GGGFDSSEAF
VGSMSGLAIW DRALVPGEVA NLAIGKEFPT GAILTLANAA LAGGFVQGAN CTCLERCP*

mutated AA sequence

MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKVDT
RLRALDLTLG ERSQQRARER KAHKAQRDAL QDSLARLEGL VHSQGARLAA LEGRLPVAHP
GTAALGPALV PTPTQPEELG PTSLKLQRDR QELRAASEHR GPPQDSSAPL QGRREPPASG
SHRVLSGTAP KDPRQQAWSP QVPGEICGVG PTLVFPNAST KNVVFLSPGF VTALRALSFC
SWVRTASGRL GTLLSYATED NDNKLVLHGR DSLLPGSIHF VIGDPAFREL PLQLLLDGQW
HHICVIWTST QGRYWLHVDR RLVATGSRFR EGYEIPPGGS LVLGQEQDSV GGGFDSSEAF
VGSMSGLAIW DRALVPGEVA NLAIGKEFPT GAILTLANAA LAGGFVQGAN CTCLERCP*

speed

0.71 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: 0.999999999999974 (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)

chr16:1536535C>TN/A show variant in all transcripts IGV

HGNC symbol

PTX4

Ensembl transcript ID

ENST00000293922

Genbank transcript ID

NM_001013658

UniProt peptide

Q96A99

alteration type

single base exchange

alteration region

CDS

DNA changes

c.827G>A
cDNA.827G>A
g.2448G>A

AA changes

R276K Score: 26 explain score(s)

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

276

frameshift

known variant

Reference ID: rs2745098

database	homozygous (T/T)	heterozygous	allele carriers
1000G	708	1070	1778
ExAC	10176	12415	22591

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.102	0.215
	0.858	0.156
(flanking)	0.006	0.007

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 gained	2443	0.89	mu: GCCTCCACCAAGAAC	CTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

276

mutated

all conserved

276

Ptroglodytes

all conserved

ENSPTRG00000007595

281

Mmulatta

all conserved

ENSMMUG00000007049

281

Fcatus

all conserved

ENSFCAG00000010651

239

Mmusculus

not conserved

ENSMUSG00000044172

281

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000038072

329

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000009128

271

protein features

start (aa)	end (aa)	feature	details
271	469	DOMAIN	Pentaxin.	lost
300	300	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
407	407	METAL	Calcium 1; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1422 / 1422

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

474 / 474

position of stopcodon in wt / mu cDNA

1422 / 1422

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

782

theoretical NMD boundary in CDS

731

length of CDS

1422

coding sequence (CDS) position

827

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

827

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

2448

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

1536535

original gDNA sequence snippet

TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC

altered gDNA sequence snippet

TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC

original cDNA sequence snippet

TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC

altered cDNA sequence snippet

TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC

wildtype AA sequence

MGSGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTRNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*

mutated AA sequence

MGSGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTKNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*

speed

0.93 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999998513054 (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)

chr16:1536535C>TN/A show variant in all transcripts IGV

HGNC symbol

PTX4

Ensembl transcript ID

ENST00000440447

Genbank transcript ID

N/A

UniProt peptide

Q96A99

alteration type

single base exchange

alteration region

CDS

DNA changes

c.397G>A
cDNA.469G>A
g.2448G>A

AA changes

G133R Score: 125 explain score(s)

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

133

frameshift

known variant

Reference ID: rs2745098

database	homozygous (T/T)	heterozygous	allele carriers
1000G	708	1070	1778
ExAC	10176	12415	22591

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.102	0.215
	0.858	0.156
(flanking)	0.006	0.007

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 gained	2443	0.89	mu: GCCTCCACCAAGAAC	CTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

133

mutated

not conserved

133

Ptroglodytes

no alignment

ENSPTRG00000007595

n/a

Mmulatta

no alignment

ENSMMUG00000007049

n/a

Fcatus

no alignment

ENSFCAG00000010651

n/a

Mmusculus

no alignment

ENSMUSG00000044172

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000038072

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000009128

n/a

protein features

start (aa)	end (aa)	feature	details
271	469	DOMAIN	Pentaxin.	might get lost (downstream of altered splice site)
300	300	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
407	407	METAL	Calcium 1; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

579 / 579

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

193 / 193

position of stopcodon in wt / mu cDNA

651 / 651

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

73 / 73

chromosome

strand

-1

last intron/exon boundary

424

theoretical NMD boundary in CDS

301

length of CDS

579

coding sequence (CDS) position

397

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

469

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

2448

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

1536535

original gDNA sequence snippet

TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC

altered gDNA sequence snippet

TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC

original cDNA sequence snippet

TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC

altered cDNA sequence snippet

TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC

wildtype AA sequence

MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKFAA
WAPPSFSQTP PPGTWSSSAL VSSLPCEPCP SAAGSARPPA AWAPSCPTPP RTMTTSWCCT
AETPCCPDPS TS*

mutated AA sequence

MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKFAA
WAPPSFSQTP PPRTWSSSAL VSSLPCEPCP SAAGSARPPA AWAPSCPTPP RTMTTSWCCT
AETPCCPDPS TS*

speed

0.72 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