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: ENST00000340758
Querying Taster for transcript #2: ENST00000270218
MT speed 0 s - this script 3.393621 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
IL19	polymorphism_automatic	6.29496454962464e-14	simple_aae				F213S	single base exchange	rs2243191		show file
IL19	polymorphism_automatic	6.29496454962464e-14	simple_aae				F175S	single base exchange	rs2243191		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999937 (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)

chr1:207015957T>CN/A show variant in all transcripts IGV

HGNC symbol

IL19

Ensembl transcript ID

ENST00000340758

Genbank transcript ID

NM_153758

UniProt peptide

Q9UHD0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.638T>C
cDNA.663T>C
g.43743T>C

AA changes

F213S Score: 155 explain score(s)

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

213

frameshift

known variant

Reference ID: rs2243191

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1235	900	2135
ExAC	12303	8161	20464

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.168	0
	1.253	0.003
(flanking)	-1.947	0

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 marginally increased	43735	wt: 0.9986 / mu: 0.9991 (marginal change - not scored)	wt: CATGAAGTAATGTTC mu: CATGAAGTAATGTCC	TGAA\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

213

mutated

not conserved

213

Ptroglodytes

not conserved

ENSPTRG00000001917

213

Mmulatta

not conserved

ENSMMUG00000023570

175

Fcatus

no alignment

ENSFCAG00000006476

n/a

Mmusculus

no alignment

ENSMUSG00000016524

n/a

Ggallus

no alignment

ENSGALG00000000911

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000090344

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

648 / 648

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

216 / 216

position of stopcodon in wt / mu cDNA

673 / 673

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

26 / 26

chromosome

strand

last intron/exon boundary

578

theoretical NMD boundary in CDS

502

length of CDS

648

coding sequence (CDS) position

638

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

663

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

43743

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

207015957

original gDNA sequence snippet

TAAGAATCATGAAGTAATGTTCTCAGCTTGATGACAAGGAA

altered gDNA sequence snippet

TAAGAATCATGAAGTAATGTCCTCAGCTTGATGACAAGGAA

original cDNA sequence snippet

TAAGAATCATGAAGTAATGTTCTCAGCTTGATGACAAGGAA

altered cDNA sequence snippet

TAAGAATCATGAAGTAATGTCCTCAGCTTGATGACAAGGAA

wildtype AA sequence

MCTEGAFPHR SACSLPLTHV HTHIHVCVPV LWGSVPRGMK LQCVSLWLLG TILILCSVDN
HGLRRCLIST DMHHIEESFQ EIKRAIQAKD TFPNVTILST LETLQIIKPL DVCCVTKNLL
AFYVDRVFKD HQEPNPKILR KISSIANSFL YMQKTLRQCQ EQRQCHCRQE ATNATRVIHD
NYDQLEVHAA AIKSLGELDV FLAWINKNHE VMFSA*

mutated AA sequence

speed

0.81 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: 0.999999999999937 (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)

chr1:207015957T>CN/A show variant in all transcripts IGV

HGNC symbol

IL19

Ensembl transcript ID

ENST00000270218

Genbank transcript ID

NM_013371

UniProt peptide

Q9UHD0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.524T>C
cDNA.1463T>C
g.43743T>C

AA changes

F175S Score: 155 explain score(s)

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

175

frameshift

known variant

Reference ID: rs2243191

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1235	900	2135
ExAC	12303	8161	20464

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.168	0
	1.253	0.003
(flanking)	-1.947	0

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 marginally increased	43735	wt: 0.9986 / mu: 0.9991 (marginal change - not scored)	wt: CATGAAGTAATGTTC mu: CATGAAGTAATGTCC	TGAA\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

175

mutated

not conserved

175

Ptroglodytes

not conserved

ENSPTRG00000001917

213

Mmulatta

not conserved

ENSMMUG00000023570

175

Fcatus

no alignment

ENSFCAG00000006476

n/a

Mmusculus

no alignment

ENSMUSG00000016524

n/a

Ggallus

no alignment

ENSGALG00000000911

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000090344

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

534 / 534

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

178 / 178

position of stopcodon in wt / mu cDNA

1473 / 1473

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

940 / 940

chromosome

strand

last intron/exon boundary

1378

theoretical NMD boundary in CDS

388

length of CDS

534

coding sequence (CDS) position

524

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

1463

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

43743

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

207015957

original gDNA sequence snippet

TAAGAATCATGAAGTAATGTTCTCAGCTTGATGACAAGGAA

altered gDNA sequence snippet

TAAGAATCATGAAGTAATGTCCTCAGCTTGATGACAAGGAA

original cDNA sequence snippet

TAAGAATCATGAAGTAATGTTCTCAGCTTGA

altered cDNA sequence snippet

TAAGAATCATGAAGTAATGTCCTCAGCTTGA

wildtype AA sequence

MKLQCVSLWL LGTILILCSV DNHGLRRCLI STDMHHIEES FQEIKRAIQA KDTFPNVTIL
STLETLQIIK PLDVCCVTKN LLAFYVDRVF KDHQEPNPKI LRKISSIANS FLYMQKTLRQ
CQEQRQCHCR QEATNATRVI HDNYDQLEVH AAAIKSLGEL DVFLAWINKN HEVMFSA*

mutated AA sequence

MKLQCVSLWL LGTILILCSV DNHGLRRCLI STDMHHIEES FQEIKRAIQA KDTFPNVTIL
STLETLQIIK PLDVCCVTKN LLAFYVDRVF KDHQEPNPKI LRKISSIANS FLYMQKTLRQ
CQEQRQCHCR QEATNATRVI HDNYDQLEVH AAAIKSLGEL DVFLAWINKN HEVMSSA*

speed

0.63 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems