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: ENST00000381920
Querying Taster for transcript #2: ENST00000561758
MT speed 0 s - this script 3.408983 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
METTL22	polymorphism_automatic	0.015674069464644	simple_aae				A219T	single base exchange	rs2302607		show file
METTL22	polymorphism_automatic	0.015674069464644	simple_aae				A163T	single base exchange	rs2302607		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.984325930535356 (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)

chr16:8729124G>AN/A show variant in all transcripts IGV

HGNC symbol

METTL22

Ensembl transcript ID

ENST00000381920

Genbank transcript ID

NM_024109

UniProt peptide

Q9BUU2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.655G>A
cDNA.913G>A
g.13585G>A

AA changes

A219T Score: 58 explain score(s)

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

219

frameshift

known variant

Reference ID: rs2302607

database	homozygous (A/A)	heterozygous	allele carriers
1000G	125	688	813
ExAC	3455	19929	23384

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.916	0.001
	0.231	0.152
(flanking)	3.63	0.997

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

219

mutated

not conserved

219

Ptroglodytes

all identical

ENSPTRG00000007745

219

Mmulatta

all identical

ENSMMUG00000006900

219

Fcatus

all identical

ENSFCAG00000001434

209

Mmusculus

all identical

ENSMUSG00000039345

208

Ggallus

all identical

ENSGALG00000000305

208

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000077863

171

Dmelanogaster

not conserved

FBgn0037045

107

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000008690

196

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1215 / 1215

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

405 / 405

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

259 / 259

chromosome

strand

last intron/exon boundary

1438

theoretical NMD boundary in CDS

1129

length of CDS

1215

coding sequence (CDS) position

655

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

913

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

13585

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

8729124

original gDNA sequence snippet

TCGGGGCCGGCACGGGGCTCGCTAGCATCATCGCAGCCACC

altered gDNA sequence snippet

TCGGGGCCGGCACGGGGCTCACTAGCATCATCGCAGCCACC

original cDNA sequence snippet

TCGGGGCCGGCACGGGGCTCGCTAGCATCATCGCAGCCACC

altered cDNA sequence snippet

TCGGGGCCGGCACGGGGCTCACTAGCATCATCGCAGCCACC

wildtype AA sequence

MVQLAPAAAM DEVTFRSDTV LSDVHLYTPN HRHLMVRLNS VGQPVFLSQF KLLWSQDSWT
DSGAKGGSHR DVHTKEPPSA ETGSTGSPPG SGHGNEGFSL QAGTDTTGQE VAEAQLDEDG
DLDVVRRPRA ASDSNPAGPL RDKVHPMILA QEEDDVLGEE AQGSPHDIIR IEHTMATPLE
DVGKQVWRGA LLLADYILFR QDLFRGCTAL ELGAGTGLAS IIAATMARTV YCTDVGADLL
SMCQRNIALN SHLAATGGGI VRVKELDWLK DDLCTDPKVP FSWSQEEISD LYDHTTILFA
AEVFYDDDLT DAVFKTLSRL AHRLKNACTA ILSVEKRLNF TLRHLDVTCE AYDHFRSCLH
ALEQLADGKL RFVVEPVEAS FPQLLVYERL QQLELWKIIA EPVT*

mutated AA sequence

MVQLAPAAAM DEVTFRSDTV LSDVHLYTPN HRHLMVRLNS VGQPVFLSQF KLLWSQDSWT
DSGAKGGSHR DVHTKEPPSA ETGSTGSPPG SGHGNEGFSL QAGTDTTGQE VAEAQLDEDG
DLDVVRRPRA ASDSNPAGPL RDKVHPMILA QEEDDVLGEE AQGSPHDIIR IEHTMATPLE
DVGKQVWRGA LLLADYILFR QDLFRGCTAL ELGAGTGLTS IIAATMARTV YCTDVGADLL
SMCQRNIALN SHLAATGGGI VRVKELDWLK DDLCTDPKVP FSWSQEEISD LYDHTTILFA
AEVFYDDDLT DAVFKTLSRL AHRLKNACTA ILSVEKRLNF TLRHLDVTCE AYDHFRSCLH
ALEQLADGKL RFVVEPVEAS FPQLLVYERL QQLELWKIIA EPVT*

speed

0.76 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: 0.984325930535356 (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)

chr16:8729124G>AN/A show variant in all transcripts IGV

HGNC symbol

METTL22

Ensembl transcript ID

ENST00000561758

Genbank transcript ID

N/A

UniProt peptide

Q9BUU2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.487G>A
cDNA.704G>A
g.13585G>A

AA changes

A163T Score: 58 explain score(s)

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

163

frameshift

known variant

Reference ID: rs2302607

database	homozygous (A/A)	heterozygous	allele carriers
1000G	125	688	813
ExAC	3455	19929	23384

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.916	0.001
	0.231	0.152
(flanking)	3.63	0.997

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

163

mutated

not conserved

163

Ptroglodytes

all identical

ENSPTRG00000007745

219

Mmulatta

all identical

ENSMMUG00000006900

219

Fcatus

all identical

ENSFCAG00000001434

209

Mmusculus

all identical

ENSMUSG00000039345

208

Ggallus

all identical

ENSGALG00000000305

208

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000077863

171

Dmelanogaster

not conserved

FBgn0037045

107

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000008690

196

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1047 / 1047

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

349 / 349

position of stopcodon in wt / mu cDNA

1264 / 1264

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

218 / 218

chromosome

strand

last intron/exon boundary

1229

theoretical NMD boundary in CDS

961

length of CDS

1047

coding sequence (CDS) position

487

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

704

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

13585

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

8729124

original gDNA sequence snippet

TCGGGGCCGGCACGGGGCTCGCTAGCATCATCGCAGCCACC

altered gDNA sequence snippet

TCGGGGCCGGCACGGGGCTCACTAGCATCATCGCAGCCACC

original cDNA sequence snippet

TCGGGGCCGGCACGGGGCTCGCTAGCATCATCGCAGCCACC

altered cDNA sequence snippet

TCGGGGCCGGCACGGGGCTCACTAGCATCATCGCAGCCACC

wildtype AA sequence

MVQLAPAAAM DEVTFRSDTV LSDVHLYTPN HRHLMVRLNS VGQPVFLSQF KLLWSQDSWT
DSGAKGGSHR DVHTKEPPSA ETGSTGSPPG SGHAQEEDDV LGEEAQGSPH DIIRIEHTMA
TPLEDVGKQV WRGALLLADY ILFRQDLFRG CTALELGAGT GLASIIAATM ARTVYCTDVG
ADLLSMCQRN IALNSHLAAT GGGIVRVKEL DWLKDDLCTD PKVPFSWSQE EISDLYDHTT
ILFAAEVFYD DDLTDAVFKT LSRLAHRLKN ACTAILSVEK RLNFTLRHLD VTCEAYDHFR
SCLHALEQLA DGKLRFVVEP VEASFPQLLV YERLQQLELW KIIAEPVT*

mutated AA sequence

MVQLAPAAAM DEVTFRSDTV LSDVHLYTPN HRHLMVRLNS VGQPVFLSQF KLLWSQDSWT
DSGAKGGSHR DVHTKEPPSA ETGSTGSPPG SGHAQEEDDV LGEEAQGSPH DIIRIEHTMA
TPLEDVGKQV WRGALLLADY ILFRQDLFRG CTALELGAGT GLTSIIAATM ARTVYCTDVG
ADLLSMCQRN IALNSHLAAT GGGIVRVKEL DWLKDDLCTD PKVPFSWSQE EISDLYDHTT
ILFAAEVFYD DDLTDAVFKT LSRLAHRLKN ACTAILSVEK RLNFTLRHLD VTCEAYDHFR
SCLHALEQLA DGKLRFVVEP VEASFPQLLV YERLQQLELW KIIAEPVT*

speed

0.71 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems