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: ENST00000367341
Querying Taster for transcript #2: ENST00000286380
MT speed 0 s - this script 3.227019 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RAET1L	polymorphism_automatic	4.9960036108132e-15	simple_aae				T147I	single base exchange	rs61730071		show file
RAET1L	polymorphism_automatic	4.9960036108132e-15	simple_aae				T147I	single base exchange	rs61730071		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (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)

chr6:150342232G>AN/A show variant in all transcripts IGV

HGNC symbol

RAET1L

Ensembl transcript ID

ENST00000367341

Genbank transcript ID

N/A

UniProt peptide

Q5VY80

alteration type

single base exchange

alteration region

CDS

DNA changes

c.440C>T
cDNA.440C>T
g.4437C>T

AA changes

T147I Score: 89 explain score(s)

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

147

frameshift

known variant

Reference ID: rs61730071

database	homozygous (A/A)	heterozygous	allele carriers
1000G	297	1054	1351
ExAC	9302	14163	23465

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.65	0
	-0.562	0
(flanking)	-0.589	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 marginally increased	4447	wt: 0.7128 / mu: 0.7278 (marginal change - not scored)	wt: GATGGACAGACCTTCCTACTCTTTGACTCAGAGAAGAGAAT mu: GATGGACAGATCTTCCTACTCTTTGACTCAGAGAAGAGAAT	actc\|TTTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

147

mutated

not conserved

147

Ptroglodytes

not conserved

ENSPTRG00000033979

147

Mmulatta

not conserved

ENSMMUG00000029466

147

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000079685

145

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
118	210	REGION	MHC class I alpha-2 like (By similarity).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

741 / 741

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

247 / 247

position of stopcodon in wt / mu cDNA

741 / 741

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

764

theoretical NMD boundary in CDS

713

length of CDS

741

coding sequence (CDS) position

440

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

440

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

4437

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

150342232

original gDNA sequence snippet

GTTCAGTATCGATGGACAGACCTTCCTACTCTTTGACTCAG

altered gDNA sequence snippet

GTTCAGTATCGATGGACAGATCTTCCTACTCTTTGACTCAG

original cDNA sequence snippet

GTTCAGTATCGATGGACAGACCTTCCTACTCTTTGACTCAG

altered cDNA sequence snippet

GTTCAGTATCGATGGACAGATCTTCCTACTCTTTGACTCAG

wildtype AA sequence

MAAAAIPALL LCLPLLFLLF GWSRARRDDP HSLCYDITVI PKFRPGPRWC AVQGQVDEKT
FLHYDCGNKT VTPVSPLGKK LNVTMAWKAQ NPVLREVVDI LTEQLLDIQL ENYTPKEPLT
LQARMSCEQK AEGHSSGSWQ FSIDGQTFLL FDSEKRMWTT VHPGARKMKE KWENDKDVAM
SFHYISMGDC IGWLEDFLMG MDSTLEPSAG APLAMSSGTT QLRATATTLI LCCLLIILPC
FILPGI*

mutated AA sequence

MAAAAIPALL LCLPLLFLLF GWSRARRDDP HSLCYDITVI PKFRPGPRWC AVQGQVDEKT
FLHYDCGNKT VTPVSPLGKK LNVTMAWKAQ NPVLREVVDI LTEQLLDIQL ENYTPKEPLT
LQARMSCEQK AEGHSSGSWQ FSIDGQIFLL FDSEKRMWTT VHPGARKMKE KWENDKDVAM
SFHYISMGDC IGWLEDFLMG MDSTLEPSAG APLAMSSGTT QLRATATTLI LCCLLIILPC
FILPGI*

speed

0.39 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: 0.999999999999995 (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)

chr6:150342232G>AN/A show variant in all transcripts IGV

HGNC symbol

RAET1L

Ensembl transcript ID

ENST00000286380

Genbank transcript ID

NM_130900

UniProt peptide

Q5VY80

alteration type

single base exchange

alteration region

CDS

DNA changes

c.440C>T
cDNA.501C>T
g.4437C>T

AA changes

T147I Score: 89 explain score(s)

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

147

frameshift

known variant

Reference ID: rs61730071

database	homozygous (A/A)	heterozygous	allele carriers
1000G	297	1054	1351
ExAC	9302	14163	23465

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.65	0
	-0.562	0
(flanking)	-0.589	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 marginally increased	4447	wt: 0.7128 / mu: 0.7278 (marginal change - not scored)	wt: GATGGACAGACCTTCCTACTCTTTGACTCAGAGAAGAGAAT mu: GATGGACAGATCTTCCTACTCTTTGACTCAGAGAAGAGAAT	actc\|TTTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

147

mutated

not conserved

147

Ptroglodytes

not conserved

ENSPTRG00000033979

147

Mmulatta

not conserved

ENSMMUG00000029466

147

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000079685

145

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
118	210	REGION	MHC class I alpha-2 like (By similarity).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

741 / 741

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

247 / 247

position of stopcodon in wt / mu cDNA

802 / 802

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

62 / 62

chromosome

strand

-1

last intron/exon boundary

693

theoretical NMD boundary in CDS

581

length of CDS

741

coding sequence (CDS) position

440

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

501

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

4437

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

150342232

original gDNA sequence snippet

GTTCAGTATCGATGGACAGACCTTCCTACTCTTTGACTCAG

altered gDNA sequence snippet

GTTCAGTATCGATGGACAGATCTTCCTACTCTTTGACTCAG

original cDNA sequence snippet

GTTCAGTATCGATGGACAGACCTTCCTACTCTTTGACTCAG

altered cDNA sequence snippet

GTTCAGTATCGATGGACAGATCTTCCTACTCTTTGACTCAG

wildtype AA sequence

mutated AA sequence

speed

0.60 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems