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: ENST00000521271
Querying Taster for transcript #2: ENST00000198765
MT speed 0 s - this script 3.366006 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CPNE3	polymorphism_automatic	0.995341939953042	simple_aae				T412M	single base exchange	rs2304789		show file
CPNE3	polymorphism_automatic	0.995341939953042	simple_aae				T412M	single base exchange	rs2304789		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00465806004695762 (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)

chr8:87567193C>TN/A show variant in all transcripts IGV

HGNC symbol

CPNE3

Ensembl transcript ID

ENST00000521271

Genbank transcript ID

NM_003909

UniProt peptide

O75131

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1235C>T
cDNA.1397C>T
g.70135C>T

AA changes

T412M Score: 81 explain score(s)

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

412

frameshift

known variant

Reference ID: rs2304789

database	homozygous (T/T)	heterozygous	allele carriers
1000G	160	746	906
ExAC	4960	22436	27396

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.069	0.997
	3.219	0.996
(flanking)	-0.849	0.705

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

412

mutated

not conserved

412

Ptroglodytes

all identical

ENSPTRG00000020397

412

Mmulatta

all identical

ENSMMUG00000006308

412

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028228

412

Ggallus

all identical

ENSGALG00000015881

412

Trubripes

not conserved

ENSTRUG00000009713

512

Drerio

not conserved

ENSDARG00000013175

411

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000013714

398

protein features

start (aa)	end (aa)	feature	details
291	513	DOMAIN	VWFA.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1614 / 1614

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

538 / 538

position of stopcodon in wt / mu cDNA

1776 / 1776

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

163 / 163

chromosome

strand

last intron/exon boundary

1654

theoretical NMD boundary in CDS

1441

length of CDS

1614

coding sequence (CDS) position

1235

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

1397

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

70135

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

87567193

original gDNA sequence snippet

CAGGTTTGCTGCTGCAGCCACGCAACAGCAGACAGCTTCTG

altered gDNA sequence snippet

CAGGTTTGCTGCTGCAGCCATGCAACAGCAGACAGCTTCTG

original cDNA sequence snippet

CAGGTTTGCTGCTGCAGCCACGCAACAGCAGACAGCTTCTC

altered cDNA sequence snippet

CAGGTTTGCTGCTGCAGCCATGCAACAGCAGACAGCTTCTC

wildtype AA sequence

MAAQCVTKVA LNVSCANLLD KDIGSKSDPL CVLFLNTSGQ QWYEVERTER IKNCLNPQFS
KTFIIDYYFE VVQKLKFGVY DIDNKTIELS DDDFLGECEC TLGQIVSSKK LTRPLVMKTG
RPAGKGSITI SAEEIKDNRV VLFEMEARKL DNKDLFGKSD PYLEFHKQTS DGNWLMVHRT
EVVKNNLNPV WRPFKISLNS LCYGDMDKTI KVECYDYDND GSHDLIGTFQ TTMTKLKEAS
RSSPVEFECI NEKKRQKKKS YKNSGVISVK QCEITVECTF LDYIMGGCQL NFTVGVDFTG
SNGDPRSPDS LHYISPNGVN EYLTALWSVG LVIQDYDADK MFPAFGFGAQ IPPQWQVSHE
FPMNFNPSNP YCNGIQGIVE AYRSCLPQIK LYGPTNFSPI INHVARFAAA ATQQQTASQY
FVLLIITDGV ITDLDETRQA IVNASRLPMS IIIVGVGGAD FSAMEFLDGD GGSLRSPLGE
VAIRDIVQFV PFRQFQNAPK EALAQCVLAE IPQQVVGYFN TYKLLPPKNP ATKQQKQ*

mutated AA sequence

MAAQCVTKVA LNVSCANLLD KDIGSKSDPL CVLFLNTSGQ QWYEVERTER IKNCLNPQFS
KTFIIDYYFE VVQKLKFGVY DIDNKTIELS DDDFLGECEC TLGQIVSSKK LTRPLVMKTG
RPAGKGSITI SAEEIKDNRV VLFEMEARKL DNKDLFGKSD PYLEFHKQTS DGNWLMVHRT
EVVKNNLNPV WRPFKISLNS LCYGDMDKTI KVECYDYDND GSHDLIGTFQ TTMTKLKEAS
RSSPVEFECI NEKKRQKKKS YKNSGVISVK QCEITVECTF LDYIMGGCQL NFTVGVDFTG
SNGDPRSPDS LHYISPNGVN EYLTALWSVG LVIQDYDADK MFPAFGFGAQ IPPQWQVSHE
FPMNFNPSNP YCNGIQGIVE AYRSCLPQIK LYGPTNFSPI INHVARFAAA AMQQQTASQY
FVLLIITDGV ITDLDETRQA IVNASRLPMS IIIVGVGGAD FSAMEFLDGD GGSLRSPLGE
VAIRDIVQFV PFRQFQNAPK EALAQCVLAE IPQQVVGYFN TYKLLPPKNP ATKQQKQ*

speed

0.82 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: 0.00465806004695762 (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)

chr8:87567193C>TN/A show variant in all transcripts IGV

HGNC symbol

CPNE3

Ensembl transcript ID

ENST00000198765

Genbank transcript ID

N/A

UniProt peptide

O75131

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1235C>T
cDNA.1293C>T
g.70135C>T

AA changes

T412M Score: 81 explain score(s)

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

412

frameshift

known variant

Reference ID: rs2304789

database	homozygous (T/T)	heterozygous	allele carriers
1000G	160	746	906
ExAC	4960	22436	27396

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.069	0.997
	3.219	0.996
(flanking)	-0.849	0.705

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

412

mutated

not conserved

412

Ptroglodytes

all identical

ENSPTRG00000020397

412

Mmulatta

all identical

ENSMMUG00000006308

412

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028228

412

Ggallus

all identical

ENSGALG00000015881

412

Trubripes

not conserved

ENSTRUG00000009713

512

Drerio

not conserved

ENSDARG00000013175

411

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000013714

398

protein features

start (aa)	end (aa)	feature	details
291	513	DOMAIN	VWFA.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1614 / 1614

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

538 / 538

position of stopcodon in wt / mu cDNA

1672 / 1672

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

59 / 59

chromosome

strand

last intron/exon boundary

1550

theoretical NMD boundary in CDS

1441

length of CDS

1614

coding sequence (CDS) position

1235

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

1293

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

70135

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

87567193

original gDNA sequence snippet

CAGGTTTGCTGCTGCAGCCACGCAACAGCAGACAGCTTCTG

altered gDNA sequence snippet

CAGGTTTGCTGCTGCAGCCATGCAACAGCAGACAGCTTCTG

original cDNA sequence snippet

CAGGTTTGCTGCTGCAGCCACGCAACAGCAGACAGCTTCTC

altered cDNA sequence snippet

CAGGTTTGCTGCTGCAGCCATGCAACAGCAGACAGCTTCTC

wildtype AA sequence

mutated AA sequence

MAAQCVTKVA LNVSCANLLD KDIGSKSDPL CVLFLNTSGQ QWYEVERTER IKNCLNPQFS
KTFIIDYYFE VVQKLKFGVY DIDNKTIELS DDDFLGECEC TLGQIVSSKK LTRPLVMKTG
RPAGKGSITI SAEEIKDNRV VLFEMEARKL DNKDLFGKSD PYLEFHKQTS DGNWLMVHRT
EVVKNNLNPV WRPFKISLNS LCYGDMDKTI KVECYDYDND GSHDLIGTFQ TTMTKLKEAS
RSSPVEFECI NEKKRQKKKS YKNSGVISVK QCEITVECTF LDYIMGGCQL NFTVGVDFTG
SNGDPRSPDS LHYISPNGVN EYLTALWSVG LVIQDYDADK MFPAFGFGAQ IPPQWQVSHE
FPMNFNPSNP YCNGIQGIVE AYRSCLPQIK LYGPTNFSPI INHVARFAAA AMQQQTASQY
FVLLIITDGV ITDLDETRQA IVNASRLPMS IIIVGVGGAD FSAMEFLDGD GGSLRSPLGE
VAIRDIVQFV PFRQFQNAPK EALAQCVLAE IPQQVVGYFN TYKLLPPKNP ATKQQKQ*

speed

0.60 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems