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: ENST00000359520
Querying Taster for transcript #2: ENST00000558678
MT speed 1.8 s - this script 3.836203 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TECPR2	polymorphism_automatic	3.44668550390503e-05	simple_aae		affected		V320I	single base exchange	rs1309353		show file
TECPR2	polymorphism_automatic	3.44668550390503e-05	simple_aae		affected		V320I	single base exchange	rs1309353		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999965533144961 (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)

chr14:102894593G>AN/A show variant in all transcripts IGV

HGNC symbol

TECPR2

Ensembl transcript ID

ENST00000359520

Genbank transcript ID

NM_014844

UniProt peptide

O15040

alteration type

single base exchange

alteration region

CDS

DNA changes

c.958G>A
cDNA.1184G>A
g.65294G>A

AA changes

V320I Score: 29 explain score(s)

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

320

frameshift

known variant

Reference ID: rs1309353

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1923	463	2386
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.34	0.864
	0.416	0.906
(flanking)	4.363	1

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
Acc marginally decreased	65287	wt: 0.9978 / mu: 0.9975 (marginal change - not scored)	wt: TTTTTTTTTTTTTTTTGACAGGCCACAGTTGCTGGTTTGGA mu: TTTTTTTTTTTTTTTTGACAGGCCACAATTGCTGGTTTGGA	acag\|GCCA
Acc marginally increased	65285	wt: 0.8018 / mu: 0.8126 (marginal change - not scored)	wt: TTTTTTTTTTTTTTTTTTGACAGGCCACAGTTGCTGGTTTG mu: TTTTTTTTTTTTTTTTTTGACAGGCCACAATTGCTGGTTTG	tgac\|AGGC
Acc marginally increased	65294	wt: 0.2204 / mu: 0.2412 (marginal change - not scored)	wt: TTTTTTTTTGACAGGCCACAGTTGCTGGTTTGGAAGGATCC mu: TTTTTTTTTGACAGGCCACAATTGCTGGTTTGGAAGGATCC	acag\|TTGC
Donor gained	65289	0.61	mu: ACAGGCCACAATTGC	AGGC\|caca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

320

mutated

all conserved

320

Ptroglodytes

all conserved

ENSPTRG00000024401

214

Mmulatta

no alignment

ENSMMUG00000029189

n/a

Fcatus

all conserved

ENSFCAG00000004651

317

Mmusculus

all identical

ENSMUSG00000021275

320

Ggallus

all conserved

ENSGALG00000011373

328

Trubripes

all conserved

ENSTRUG00000005024

321

Drerio

all conserved

ENSDARG00000060835

318

Dmelanogaster

not conserved

FBgn0033177

337

DGHDSLLV

LYVLNLDRLKVE

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
448	448	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
449	449	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
462	471	COMPBIAS	Poly-Lys.	might get lost (downstream of altered splice site)
945	976	REPEAT	TECPR 1.	might get lost (downstream of altered splice site)
994	1027	REPEAT	TECPR 2.	might get lost (downstream of altered splice site)
1179	1209	REPEAT	TECPR 3.	might get lost (downstream of altered splice site)
1226	1259	REPEAT	TECPR 4.	might get lost (downstream of altered splice site)
1279	1310	REPEAT	TECPR 5.	might get lost (downstream of altered splice site)
1322	1353	REPEAT	TECPR 6.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4236 / 4236

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

1412 / 1412

position of stopcodon in wt / mu cDNA

4462 / 4462

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

227 / 227

chromosome

strand

last intron/exon boundary

4308

theoretical NMD boundary in CDS

4031

length of CDS

4236

coding sequence (CDS) position

958

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

1184

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

65294

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

102894593

original gDNA sequence snippet

TTTTTTTTTGACAGGCCACAGTTGCTGGTTTGGAAGGATCC

altered gDNA sequence snippet

TTTTTTTTTGACAGGCCACAATTGCTGGTTTGGAAGGATCC

original cDNA sequence snippet

ACACAGTCAACCAGGCCACAGTTGCTGGTTTGGAAGGATCC

altered cDNA sequence snippet

ACACAGTCAACCAGGCCACAATTGCTGGTTTGGAAGGATCC

wildtype AA sequence

MASISEPVTF REFCPLYYLL NAIPTKIQKG FRSIVVYLTA LDTNGDYIAV GSSIGMLYLY
CRHLNQMRKY NFEGKTESIT VVKLLSCFDD LVAAGTASGR VAVFQLVSSL PGRNKQLRRF
DVTGIHKNSI TALAWSPNGM KLFSGDDKGK IVYSSLDLDQ GLCNSQLVLE EPSSIVQLDY
SQKVLLVSTL QRSLLFYTEE KSVRQIGTQP RKSTGKFGAC FIPGLCKQSD LTLYASRPGL
RLWKADVHGT VQATFILKDA FAGGVKPFEL HPRLESPNSG SCSLPERHLG LVSCFFQEGW
VLSWNEYSIY LLDTVNQATV AGLEGSGDIV SVSCTENEIF FLKGDRNIIR ISSRPEGLTS
TVRDGLEMSG CSERVHVQQA EKLPGATVSE TRLRGSSMAS SVASEPRSRS SSLNSTDSGS
GLLPPGLQAT PELGKGSQPL SQRFNAISSE DFDQELVVKP IKVKRKKKKK KTEGGSRSTC
HSSLESTPCS EFPGDSPQSL NTDLLSMTSS VLGSSVDQLS AESPDQESSF NGEVNGVPQE
NTDPETFNVL EVSGSMPDSL AEEDDIRTEM PHCHHAHGRE LLNGAREDVG GSDVTGLGDE
PCPADDGPNS TQLPFQEQDS SPGAHDGEDI QPIGPQSTFC EVPLLNSLTV PSSLSWAPSA
EQWLPGTRAD EGSPVEPSQE QDILTSMEAS GHLSTNLWHA VTDDDTGQKE IPISERVLGS
VGGQLTPVSA LAASTHKPWL EQPPRDQTLT SSDEEDIYAH GLPSSSSETS VTELGPSCSQ
QDLSRLGAED AGLLKPDQFA ESWMGYSGPG YGILSLVVSE KYIWCLDYKG GLFCSALPGA
GLRWQKFEDA VQQVAVSPSG ALLWKIEQKS NRAFACGKVT IKGKRHWYEA LPQAVFVALS
DDTAWIIRTS GDLYLQTGLS VDRPCARAVK VDCPYPLSQI TARNNVVWAL TEQRALLYRE
GVSSFCPEGE QWKCDIVSER QALEPVCITL GDQQTLWALD IHGNLWFRTG IISKKPQGDD
DHWWQVSITD YVVFDQCSLF QTIIHATHSV ATAAQAPVEK VADKLRMAFW SQQLQCQPSL
LGVNNSGVWI SSGKNEFHVA KGSLIGTYWN HVVPRGTASA TKWAFVLASA APTKEGSFLW
LCQSSKDLCS VSAQSAQSRP STVQLPPEAE MRAYAACQDA LWALDSLGQV FIRTLSKSCP
TGMHWTRLDL SQLGAVKLTS LACGNQHIWA CDSRGGVYFR VGTQPLNPSL MLPAWIMIEP
PVQPAGVSLV SVHSSPNDQM LWVLDSRWNV HVRTGITEEM PVGTAWEHVP GLQACQLALS
TRTVWARCPN GDLARRYGVT DKNPAGDYWK KIPGSVSCFT VTASDELWAV GPPGYLLQRL
TKTFSHSHGT QKSSQAAMPH PEDLEDEWEV I*

mutated AA sequence

MASISEPVTF REFCPLYYLL NAIPTKIQKG FRSIVVYLTA LDTNGDYIAV GSSIGMLYLY
CRHLNQMRKY NFEGKTESIT VVKLLSCFDD LVAAGTASGR VAVFQLVSSL PGRNKQLRRF
DVTGIHKNSI TALAWSPNGM KLFSGDDKGK IVYSSLDLDQ GLCNSQLVLE EPSSIVQLDY
SQKVLLVSTL QRSLLFYTEE KSVRQIGTQP RKSTGKFGAC FIPGLCKQSD LTLYASRPGL
RLWKADVHGT VQATFILKDA FAGGVKPFEL HPRLESPNSG SCSLPERHLG LVSCFFQEGW
VLSWNEYSIY LLDTVNQATI AGLEGSGDIV SVSCTENEIF FLKGDRNIIR ISSRPEGLTS
TVRDGLEMSG CSERVHVQQA EKLPGATVSE TRLRGSSMAS SVASEPRSRS SSLNSTDSGS
GLLPPGLQAT PELGKGSQPL SQRFNAISSE DFDQELVVKP IKVKRKKKKK KTEGGSRSTC
HSSLESTPCS EFPGDSPQSL NTDLLSMTSS VLGSSVDQLS AESPDQESSF NGEVNGVPQE
NTDPETFNVL EVSGSMPDSL AEEDDIRTEM PHCHHAHGRE LLNGAREDVG GSDVTGLGDE
PCPADDGPNS TQLPFQEQDS SPGAHDGEDI QPIGPQSTFC EVPLLNSLTV PSSLSWAPSA
EQWLPGTRAD EGSPVEPSQE QDILTSMEAS GHLSTNLWHA VTDDDTGQKE IPISERVLGS
VGGQLTPVSA LAASTHKPWL EQPPRDQTLT SSDEEDIYAH GLPSSSSETS VTELGPSCSQ
QDLSRLGAED AGLLKPDQFA ESWMGYSGPG YGILSLVVSE KYIWCLDYKG GLFCSALPGA
GLRWQKFEDA VQQVAVSPSG ALLWKIEQKS NRAFACGKVT IKGKRHWYEA LPQAVFVALS
DDTAWIIRTS GDLYLQTGLS VDRPCARAVK VDCPYPLSQI TARNNVVWAL TEQRALLYRE
GVSSFCPEGE QWKCDIVSER QALEPVCITL GDQQTLWALD IHGNLWFRTG IISKKPQGDD
DHWWQVSITD YVVFDQCSLF QTIIHATHSV ATAAQAPVEK VADKLRMAFW SQQLQCQPSL
LGVNNSGVWI SSGKNEFHVA KGSLIGTYWN HVVPRGTASA TKWAFVLASA APTKEGSFLW
LCQSSKDLCS VSAQSAQSRP STVQLPPEAE MRAYAACQDA LWALDSLGQV FIRTLSKSCP
TGMHWTRLDL SQLGAVKLTS LACGNQHIWA CDSRGGVYFR VGTQPLNPSL MLPAWIMIEP
PVQPAGVSLV SVHSSPNDQM LWVLDSRWNV HVRTGITEEM PVGTAWEHVP GLQACQLALS
TRTVWARCPN GDLARRYGVT DKNPAGDYWK KIPGSVSCFT VTASDELWAV GPPGYLLQRL
TKTFSHSHGT QKSSQAAMPH PEDLEDEWEV I*

speed

0.92 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: 0.999965533144961 (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)

chr14:102894593G>AN/A show variant in all transcripts IGV

HGNC symbol

TECPR2

Ensembl transcript ID

ENST00000558678

Genbank transcript ID

NM_001172631

UniProt peptide

O15040

alteration type

single base exchange

alteration region

CDS

DNA changes

c.958G>A
cDNA.1068G>A
g.65294G>A

AA changes

V320I Score: 29 explain score(s)

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

320

frameshift

known variant

Reference ID: rs1309353

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1923	463	2386
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.34	0.864
	0.416	0.906
(flanking)	4.363	1

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
Acc marginally decreased	65287	wt: 0.9978 / mu: 0.9975 (marginal change - not scored)	wt: TTTTTTTTTTTTTTTTGACAGGCCACAGTTGCTGGTTTGGA mu: TTTTTTTTTTTTTTTTGACAGGCCACAATTGCTGGTTTGGA	acag\|GCCA
Acc marginally increased	65285	wt: 0.8018 / mu: 0.8126 (marginal change - not scored)	wt: TTTTTTTTTTTTTTTTTTGACAGGCCACAGTTGCTGGTTTG mu: TTTTTTTTTTTTTTTTTTGACAGGCCACAATTGCTGGTTTG	tgac\|AGGC
Acc marginally increased	65294	wt: 0.2204 / mu: 0.2412 (marginal change - not scored)	wt: TTTTTTTTTGACAGGCCACAGTTGCTGGTTTGGAAGGATCC mu: TTTTTTTTTGACAGGCCACAATTGCTGGTTTGGAAGGATCC	acag\|TTGC
Donor gained	65289	0.61	mu: ACAGGCCACAATTGC	AGGC\|caca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

320

mutated

all conserved

320

Ptroglodytes

all conserved

ENSPTRG00000024401

214

Mmulatta

no alignment

ENSMMUG00000029189

n/a

Fcatus

all conserved

ENSFCAG00000004651

317

Mmusculus

all identical

ENSMUSG00000021275

320

Ggallus

all conserved

ENSGALG00000011373

328

Trubripes

all conserved

ENSTRUG00000005024

321

Drerio

all conserved

ENSDARG00000060835

318

Dmelanogaster

not conserved

FBgn0033177

337

DGHDSLLV

LYVLNLDRLKVE

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
448	448	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
449	449	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
462	471	COMPBIAS	Poly-Lys.	might get lost (downstream of altered splice site)
945	976	REPEAT	TECPR 1.	might get lost (downstream of altered splice site)
994	1027	REPEAT	TECPR 2.	might get lost (downstream of altered splice site)
1179	1209	REPEAT	TECPR 3.	might get lost (downstream of altered splice site)
1226	1259	REPEAT	TECPR 4.	might get lost (downstream of altered splice site)
1279	1310	REPEAT	TECPR 5.	might get lost (downstream of altered splice site)
1322	1353	REPEAT	TECPR 6.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3804 / 3804

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

1268 / 1268

position of stopcodon in wt / mu cDNA

3914 / 3914

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

111 / 111

chromosome

strand

last intron/exon boundary

3751

theoretical NMD boundary in CDS

3590

length of CDS

3804

coding sequence (CDS) position

958

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

1068

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

65294

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

102894593

original gDNA sequence snippet

TTTTTTTTTGACAGGCCACAGTTGCTGGTTTGGAAGGATCC

altered gDNA sequence snippet

TTTTTTTTTGACAGGCCACAATTGCTGGTTTGGAAGGATCC

original cDNA sequence snippet

ACACAGTCAACCAGGCCACAGTTGCTGGTTTGGAAGGATCC

altered cDNA sequence snippet

ACACAGTCAACCAGGCCACAATTGCTGGTTTGGAAGGATCC

wildtype AA sequence

mutated AA sequence

MASISEPVTF REFCPLYYLL NAIPTKIQKG FRSIVVYLTA LDTNGDYIAV GSSIGMLYLY
CRHLNQMRKY NFEGKTESIT VVKLLSCFDD LVAAGTASGR VAVFQLVSSL PGRNKQLRRF
DVTGIHKNSI TALAWSPNGM KLFSGDDKGK IVYSSLDLDQ GLCNSQLVLE EPSSIVQLDY
SQKVLLVSTL QRSLLFYTEE KSVRQIGTQP RKSTGKFGAC FIPGLCKQSD LTLYASRPGL
RLWKADVHGT VQATFILKDA FAGGVKPFEL HPRLESPNSG SCSLPERHLG LVSCFFQEGW
VLSWNEYSIY LLDTVNQATI AGLEGSGDIV SVSCTENEIF FLKGDRNIIR ISSRPEGLTS
TVRDGLEMSG CSERVHVQQA EKLPGATVSE TRLRGSSMAS SVASEPRSRS SSLNSTDSGS
GLLPPGLQAT PELGKGSQPL SQRFNAISSE DFDQELVVKP IKVKRKKKKK KTEGGSRSTC
HSSLESTPCS EFPGDSPQSL NTDLLSMTSS VLGSSVDQLS AESPDQESSF NGEVNGVPQE
NTDPETFNVL EVSGSMPDSL AEEDDIRTEM PHCHHAHGRE LLNGAREDVG GSDVTGLGDE
PCPADDGPNS TQLPFQEQDS SPGAHDGEDI QPIGPQSTFC EVPLLNSLTV PSSLSWAPSA
EQWLPGTRAD EGSPVEPSQE QDILTSMEAS GHLSTNLWHA VTDDDTGQKE IPISERVLGS
VGGQLTPVSA LAASTHKPWL EQPPRDQTLT SSDEEDIYAH GLPSSSSETS VTELGPSCSQ
QDLSRLGAED AGLLKPDQFA ESWMGYSGPG YGILSLVVSE KYIWCLDYKG GLFCSALPGA
GLRWQKFEDA VQQVAVSPSG ALLWKIEQKS NRAFACGKVT IKGKRHWYEA LPQAVFVALS
DDTAWIIRTS GDLYLQTGLS VDRPCARAVK VDCPYPLSQI TARNNVVWAL TEQRALLYRE
GVSSFCPEGE QWKCDIVSER QALEPVCITL GDQQTLWALD IHGNLWFRTG IISKKPQGDD
DHWWQVSITD YVVFDQCSLF QTIIHATHSV ATAAQAPVEK VADKLRMAFW SQQLQCQPSL
LGVNNSGVWI SSGKNEFHVA KGSLIGTYWN HVVPRGTASA TKWAFVLASA APTKEGSFLW
LCQSSKDLCS VSAQSAQSRP STVQLPPEAE MRAYAACQDA LWALDSLGQV FIRTLSKSCP
TGMHWTRLDL SQLGAVKLTS LACGNQHIWA CDSRGGVYFR VGTQPLNPSL MLPAWIMIEP
PVQVSRS*

speed

0.88 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems