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: ENST00000493231
Querying Taster for transcript #2: ENST00000465414
MT speed 0 s - this script 3.290529 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CLEC19A	polymorphism_automatic	3.55390161743685e-11	simple_aae		affected		S16A	single base exchange	rs179196		show file
CLEC19A	polymorphism_automatic	3.55390161743685e-11	simple_aae		affected		S16A	single base exchange	rs179196		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999964461 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:19297219T>GN/A show variant in all transcripts IGV

HGNC symbol

CLEC19A

Ensembl transcript ID

ENST00000493231

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.46T>G
cDNA.159T>G
g.159T>G

AA changes

S16A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs179196

database	homozygous (G/G)	heterozygous	allele carriers
1000G	207	644	851
ExAC	309	2133	2442

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.127	0.004
	2.455	0.009
(flanking)	0.049	0.003

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	156	wt: 0.5836 / mu: 0.5963 (marginal change - not scored)	wt: CTGCAGCCTTCCTGACCCTCCACTCTGCACAGGCCTTTCCA mu: CTGCAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCA	ctcc\|ACTC
Acc gained	158	0.70	mu: GCAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCACA	ccac\|GCTG
Donor gained	153	0.57	mu: TGACCCTCCACGCTG	ACCC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000014758

Fcatus

all identical

ENSFCAG00000013855

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000020911

n/a

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037978

Dmelanogaster

no homologue

Celegans

no alignment

K02F3.5

n/a

Xtropicalis

no homologue

protein features

N/A

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

261 / 261

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

87 / 87

position of stopcodon in wt / mu cDNA

374 / 374

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

114 / 114

chromosome

strand

last intron/exon boundary

368

theoretical NMD boundary in CDS

204

length of CDS

261

coding sequence (CDS) position

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

159

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

159

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

19297219

original gDNA sequence snippet

CAGCCTTCCTGACCCTCCACTCTGCACAGGCCTTTCCACAA

altered gDNA sequence snippet

CAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCACAA

original cDNA sequence snippet

CAGCCTTCCTGACCCTCCACTCTGCACAGGCCTTTCCACAA

altered cDNA sequence snippet

CAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCACAA

wildtype AA sequence

MQRWTLWAAA FLTLHSAQAF PQTDISISPA LPELPLPSLC PLFWMEFKGH CYRFFPLNKT
WAEADLYCSE FSVGRKSAKL ASIHSL*

mutated AA sequence

MQRWTLWAAA FLTLHAAQAF PQTDISISPA LPELPLPSLC PLFWMEFKGH CYRFFPLNKT
WAEADLYCSE FSVGRKSAKL ASIHSL*

speed

0.11 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: 0.999999999964461 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:19297219T>GN/A show variant in all transcripts IGV

HGNC symbol

CLEC19A

Ensembl transcript ID

ENST00000465414

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.46T>G
cDNA.119T>G
g.159T>G

AA changes

S16A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs179196

database	homozygous (G/G)	heterozygous	allele carriers
1000G	207	644	851
ExAC	309	2133	2442

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.127	0.004
	2.455	0.009
(flanking)	0.049	0.003

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	156	wt: 0.5836 / mu: 0.5963 (marginal change - not scored)	wt: CTGCAGCCTTCCTGACCCTCCACTCTGCACAGGCCTTTCCA mu: CTGCAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCA	ctcc\|ACTC
Acc gained	158	0.70	mu: GCAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCACA	ccac\|GCTG
Donor gained	153	0.57	mu: TGACCCTCCACGCTG	ACCC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000014758

Fcatus

all identical

ENSFCAG00000013855

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000020911

n/a

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037978

Dmelanogaster

no homologue

Celegans

no alignment

K02F3.5

n/a

Xtropicalis

no homologue

protein features

N/A

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

411 / 411

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

137 / 137

position of stopcodon in wt / mu cDNA

484 / 484

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

74 / 74

chromosome

strand

last intron/exon boundary

328

theoretical NMD boundary in CDS

204

length of CDS

411

coding sequence (CDS) position

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

119

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

159

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

19297219

original gDNA sequence snippet

CAGCCTTCCTGACCCTCCACTCTGCACAGGCCTTTCCACAA

altered gDNA sequence snippet

CAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCACAA

original cDNA sequence snippet

CAGCCTTCCTGACCCTCCACTCTGCACAGGCCTTTCCACAA

altered cDNA sequence snippet

CAGCCTTCCTGACCCTCCACGCTGCACAGGCCTTTCCACAA

wildtype AA sequence

MQRWTLWAAA FLTLHSAQAF PQTDISISPA LPELPLPSLC PLFWMEFKGH CYRFFPLNKT
WAEADLYCSE FSVGRKSAKL ASIHSWEENV FVYDLVNSCV PGIPADVWTG LHDHRQVRKQ
WPLGPLGSSS QDSILI*

mutated AA sequence

MQRWTLWAAA FLTLHAAQAF PQTDISISPA LPELPLPSLC PLFWMEFKGH CYRFFPLNKT
WAEADLYCSE FSVGRKSAKL ASIHSWEENV FVYDLVNSCV PGIPADVWTG LHDHRQVRKQ
WPLGPLGSSS QDSILI*

speed

1.24 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems