MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000378979
Querying Taster for transcript #2: ENST00000303142
MT speed 0.54 s - this script 2.521275 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SHLD1	polymorphism_automatic	3.18967074974807e-13	simple_aae		affected		A23V	single base exchange	rs237422		show file
SHLD1	polymorphism_automatic	3.18967074974807e-13	simple_aae		affected		A23V	single base exchange	rs237422		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999681 (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)

chr20:5753579C>TN/A show variant in all transcripts IGV

HGNC symbol

SHLD1

Ensembl transcript ID

ENST00000378979

Genbank transcript ID

N/A

UniProt peptide

Q8IYI0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.68C>T
cDNA.159C>T
g.22541C>T

AA changes

A23V Score: 64 explain score(s)

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

frameshift

known variant

Reference ID: rs237422

database	homozygous (T/T)	heterozygous	allele carriers
1000G	137	898	1035
ExAC	3901	22494	26395

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.109	0
	0.124	0
(flanking)	-1.34	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
Acc gained	22539	0.31	mu: AGTGCTTTGGACCTGCCATCAGTGTGTGACATAAGAGATTA	atca\|GTGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000013229

Mmulatta

not conserved

ENSMMUG00000022345

Fcatus

no alignment

ENSFCAG00000003101

n/a

Mmusculus

not conserved

ENSMUSG00000044991

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

189 / 189

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

63 / 63

position of stopcodon in wt / mu cDNA

280 / 280

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

92 / 92

chromosome

strand

last intron/exon boundary

270

theoretical NMD boundary in CDS

128

length of CDS

189

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)

22541

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

5753579

original gDNA sequence snippet

TGCTTTGGACCTGCCATCAGCGTGTGACATAAGAGATTACG

altered gDNA sequence snippet

TGCTTTGGACCTGCCATCAGTGTGTGACATAAGAGATTACG

original cDNA sequence snippet

TGCTTTGGACCTGCCATCAGCGTGTGACATAAGAGATTACG

altered cDNA sequence snippet

TGCTTTGGACCTGCCATCAGTGTGTGACATAAGAGATTACG

wildtype AA sequence

MAARDATSGS LSEESSALDL PSACDIRDYV LQGPSQEANS EAFSSLEFHS FPYSSDVDPA
DL*

mutated AA sequence

MAARDATSGS LSEESSALDL PSVCDIRDYV LQGPSQEANS EAFSSLEFHS FPYSSDVDPA
DL*

speed

0.27 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: 0.999999999999681 (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)

chr20:5753579C>TN/A show variant in all transcripts IGV

HGNC symbol

SHLD1

Ensembl transcript ID

ENST00000303142

Genbank transcript ID

NM_152504

UniProt peptide

Q8IYI0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.68C>T
cDNA.155C>T
g.22541C>T

AA changes

A23V Score: 64 explain score(s)

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

frameshift

known variant

Reference ID: rs237422

database	homozygous (T/T)	heterozygous	allele carriers
1000G	137	898	1035
ExAC	3901	22494	26395

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.109	0
	0.124	0
(flanking)	-1.34	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
Acc gained	22539	0.31	mu: AGTGCTTTGGACCTGCCATCAGTGTGTGACATAAGAGATTA	atca\|GTGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000013229

Mmulatta

not conserved

ENSMMUG00000022345

Fcatus

no alignment

ENSFCAG00000003101

n/a

Mmusculus

not conserved

ENSMUSG00000044991

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

618 / 618

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

206 / 206

position of stopcodon in wt / mu cDNA

705 / 705

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

88 / 88

chromosome

strand

last intron/exon boundary

266

theoretical NMD boundary in CDS

128

length of CDS

618

coding sequence (CDS) position

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

155

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

22541

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

5753579

original gDNA sequence snippet

TGCTTTGGACCTGCCATCAGCGTGTGACATAAGAGATTACG

altered gDNA sequence snippet

TGCTTTGGACCTGCCATCAGTGTGTGACATAAGAGATTACG

original cDNA sequence snippet

TGCTTTGGACCTGCCATCAGCGTGTGACATAAGAGATTACG

altered cDNA sequence snippet

TGCTTTGGACCTGCCATCAGTGTGTGACATAAGAGATTACG

wildtype AA sequence

MAARDATSGS LSEESSALDL PSACDIRDYV LQGPSQEANS EAFSSLEFHS FPYSSDVDPD
TSNLNIEQNN SWTAENFWLD PAVKGQSEKE EDDGLRKSLD RFYEMFGHPQ PGSANSLSAS
VCKCLSQKIT QLRGQESQKY ALRSFQMARV IFNRDGCSVL QRHSRDTHFY PLEEGSTSLD
DEKPNPGLSK DITHFLLQQN VMKDL*

mutated AA sequence

MAARDATSGS LSEESSALDL PSVCDIRDYV LQGPSQEANS EAFSSLEFHS FPYSSDVDPD
TSNLNIEQNN SWTAENFWLD PAVKGQSEKE EDDGLRKSLD RFYEMFGHPQ PGSANSLSAS
VCKCLSQKIT QLRGQESQKY ALRSFQMARV IFNRDGCSVL QRHSRDTHFY PLEEGSTSLD
DEKPNPGLSK DITHFLLQQN VMKDL*

speed

0.27 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems