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: ENST00000360507
Querying Taster for transcript #2: ENST00000409789
MT speed 0 s - this script 3.683643 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CNPPD1	polymorphism_automatic	1.67976743625786e-13	simple_aae				I262T	single base exchange	rs1043160		show file
CNPPD1	polymorphism_automatic	1.67976743625786e-13	simple_aae				I262T	single base exchange	rs1043160		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999832 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:220037756A>GN/A show variant in all transcripts IGV

HGNC symbol

CNPPD1

Ensembl transcript ID

ENST00000360507

Genbank transcript ID

NM_015680

UniProt peptide

Q9BV87

alteration type

single base exchange

alteration region

CDS

DNA changes

c.785T>C
cDNA.923T>C
g.5073T>C

AA changes

I262T Score: 89 explain score(s)

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

262

frameshift

known variant

Reference ID: rs1043160

database	homozygous (G/G)	heterozygous	allele carriers
1000G	498	1059	1557
ExAC	18605	-4443	14162

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.009	0.005
	0.044	0.004
(flanking)	0.648	0.016

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 increased	5073	wt: 0.2358 / mu: 0.2386 (marginal change - not scored)	wt: GTCTTTGGGGCTGTCCTGCATCCCTACACCTGGGCCGCCTG mu: GTCTTTGGGGCTGTCCTGCACCCCTACACCTGGGCCGCCTG	gcat\|CCCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

262

mutated

not conserved

262

Ptroglodytes

not conserved

ENSPTRG00000012941

262

Mmulatta

not conserved

ENSMMUG00000000791

262

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000033159

262

Ggallus

all identical

ENSGALG00000011337

256

VCT

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000027078

258

QLG

Dmelanogaster

no alignment

FBgn0058191

n/a

Celegans

all conserved

F09G2.2

235

Xtropicalis

all conserved

ENSXETG00000013889

270

TWEMN

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1233 / 1233

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

411 / 411

position of stopcodon in wt / mu cDNA

1371 / 1371

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

139 / 139

chromosome

strand

-1

last intron/exon boundary

829

theoretical NMD boundary in CDS

640

length of CDS

1233

coding sequence (CDS) position

785

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

923

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

5073

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

220037756

original gDNA sequence snippet

GTCTTTGGGGCTGTCCTGCATCCCTACACCTGGGCCGCCTG

altered gDNA sequence snippet

GTCTTTGGGGCTGTCCTGCACCCCTACACCTGGGCCGCCTG

original cDNA sequence snippet

GTCTTTGGGGCTGTCCTGCATCCCTACACCTGGGCCGCCTG

altered cDNA sequence snippet

GTCTTTGGGGCTGTCCTGCACCCCTACACCTGGGCCGCCTG

wildtype AA sequence

MDLTGLLLDE EGTFSLAGFQ DFTFLPGHQK LSARIRRRLY YGWDWEADCS LEELSSPVAD
IAVELLQKAA PSPIRRLQKK YVAHVSREAC ISPCAMMLAL VYIERLRHRN PDYLQHVSSS
DLFLISMMVA SKYLYDEGEE EEVFNDEWGA AGGVAVPTLN ALERGFLSAM DWHLYTDPRE
IFEVLSWLES CVAEQQGRWR GWYTYTDLCV LLEQPTWQLA LGSLCQRLVK LSCLLAVAYV
SSVALAVASV AVIHQSLGLS CIPTPGPPDL GLTSRCLLEP CIPSVPQCLP SLANVSSCLE
GSMGLRSLWG SLLASLTPPP LPPPDPPAPP TLLHNCHLCQ KLQRDSPTCH ACLHPNRTVP
TALSSPWYHT YGLAPPWPWS PVLLSLPQPQ QCSLFSVMEL ARLKSFVFPG *

mutated AA sequence

MDLTGLLLDE EGTFSLAGFQ DFTFLPGHQK LSARIRRRLY YGWDWEADCS LEELSSPVAD
IAVELLQKAA PSPIRRLQKK YVAHVSREAC ISPCAMMLAL VYIERLRHRN PDYLQHVSSS
DLFLISMMVA SKYLYDEGEE EEVFNDEWGA AGGVAVPTLN ALERGFLSAM DWHLYTDPRE
IFEVLSWLES CVAEQQGRWR GWYTYTDLCV LLEQPTWQLA LGSLCQRLVK LSCLLAVAYV
SSVALAVASV AVIHQSLGLS CTPTPGPPDL GLTSRCLLEP CIPSVPQCLP SLANVSSCLE
GSMGLRSLWG SLLASLTPPP LPPPDPPAPP TLLHNCHLCQ KLQRDSPTCH ACLHPNRTVP
TALSSPWYHT YGLAPPWPWS PVLLSLPQPQ QCSLFSVMEL ARLKSFVFPG *

speed

0.97 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: 0.999999999999832 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:220037756A>GN/A show variant in all transcripts IGV

HGNC symbol

CNPPD1

Ensembl transcript ID

ENST00000409789

Genbank transcript ID

N/A

UniProt peptide

Q9BV87

alteration type

single base exchange

alteration region

CDS

DNA changes

c.785T>C
cDNA.1213T>C
g.5073T>C

AA changes

I262T Score: 89 explain score(s)

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

262

frameshift

known variant

Reference ID: rs1043160

database	homozygous (G/G)	heterozygous	allele carriers
1000G	498	1059	1557
ExAC	18605	-4443	14162

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.009	0.005
	0.044	0.004
(flanking)	0.648	0.016

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 increased	5073	wt: 0.2358 / mu: 0.2386 (marginal change - not scored)	wt: GTCTTTGGGGCTGTCCTGCATCCCTACACCTGGGCCGCCTG mu: GTCTTTGGGGCTGTCCTGCACCCCTACACCTGGGCCGCCTG	gcat\|CCCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

262

mutated

not conserved

262

Ptroglodytes

not conserved

ENSPTRG00000012941

262

Mmulatta

not conserved

ENSMMUG00000000791

262

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000033159

262

Ggallus

all identical

ENSGALG00000011337

256

VCT

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000027078

258

QLG

Dmelanogaster

no alignment

FBgn0058191

n/a

Celegans

all conserved

F09G2.2

235

Xtropicalis

all conserved

ENSXETG00000013889

270

TWEMN

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1233 / 1233

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

411 / 411

position of stopcodon in wt / mu cDNA

1661 / 1661

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

429 / 429

chromosome

strand

-1

last intron/exon boundary

1119

theoretical NMD boundary in CDS

640

length of CDS

1233

coding sequence (CDS) position

785

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

1213

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

5073

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

220037756

original gDNA sequence snippet

GTCTTTGGGGCTGTCCTGCATCCCTACACCTGGGCCGCCTG

altered gDNA sequence snippet

GTCTTTGGGGCTGTCCTGCACCCCTACACCTGGGCCGCCTG

original cDNA sequence snippet

GTCTTTGGGGCTGTCCTGCATCCCTACACCTGGGCCGCCTG

altered cDNA sequence snippet

GTCTTTGGGGCTGTCCTGCACCCCTACACCTGGGCCGCCTG

wildtype AA sequence

mutated AA sequence

MDLTGLLLDE EGTFSLAGFQ DFTFLPGHQK LSARIRRRLY YGWDWEADCS LEELSSPVAD
IAVELLQKAA PSPIRRLQKK YVAHVSREAC ISPCAMMLAL VYIERLRHRN PDYLQHVSSS
DLFLISMMVA SKYLYDEGEE EEVFNDEWGA AGGVAVPTLN ALERGFLSAM DWHLYTDPRE
IFEVLSWLES CVAEQQGRWR GWYTYTDLCV LLEQPTWQLA LGSLCQRLVK LSCLLAVAYV
SSVALAVASV AVIHQSLGLS CTPTPGPPDL GLTSRCLLEP CIPSVPQCLP SLANVSSCLE
GSMGLRSLWG SLLASLTPPP LPPPDPPAPP TLLHNCHLCQ KLQRDSPTCH ACLHPNRTVP
TALSSPWYHT YGLAPPWPWS PVLLSLPQPQ QCSLFSVMEL ARLKSFVFPG *

speed

0.76 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems