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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000282881
Querying Taster for transcript #2: ENST00000539744
Querying Taster for transcript #3: ENST00000458174
Querying Taster for transcript #4: ENST00000445693
Querying Taster for transcript #5: ENST00000413632
MT speed 0 s - this script 6.077693 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LMNTD1	polymorphism_automatic	1.99840144432528e-15	simple_aae		affected		T269S	single base exchange	rs1479500		show file
LMNTD1	polymorphism_automatic	1.99840144432528e-15	simple_aae		affected		T387S	single base exchange	rs1479500		show file
LMNTD1	polymorphism_automatic	1.99840144432528e-15	simple_aae		affected		T366S	single base exchange	rs1479500		show file
LMNTD1	polymorphism_automatic	1.99840144432528e-15	simple_aae		affected		T303S	single base exchange	rs1479500		show file
LMNTD1	polymorphism_automatic	1.99840144432528e-15	simple_aae		affected		T347S	single base exchange	rs1479500		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:25671759T>AN/A show variant in all transcripts IGV

HGNC symbol

LMNTD1

Ensembl transcript ID

ENST00000539744

Genbank transcript ID

NM_001256266

UniProt peptide

Q8N9Z9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.805A>T
cDNA.1285A>T
g.129755A>T

AA changes

T269S Score: 58 explain score(s)

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

269

frameshift

known variant

Reference ID: rs1479500

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1324	932	2256
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.404	0.001
	-0.995	0
(flanking)	0.102	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 gained	129748	0.92	mu: AGACAGCCCAGGTCT	ACAG\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

269

mutated

all conserved

269

Ptroglodytes

all conserved

ENSPTRG00000004776

387

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054966

395

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
381	381	CONFLICT	K -> E (in Ref. 1; BAG59389).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

876 / 876

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

292 / 292

position of stopcodon in wt / mu cDNA

1356 / 1356

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

481 / 481

chromosome

strand

-1

last intron/exon boundary

1379

theoretical NMD boundary in CDS

848

length of CDS

876

coding sequence (CDS) position

805

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

1285

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

129755

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

25671759

original gDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered gDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

original cDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered cDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

wildtype AA sequence

MIGDGEDYFL SLFGDSKKLT AHSNYTQKTL KYFSMILEEV GQFTSSSLGD VEIAEVNVKG
LFVKLINSSL DKEMAIGDHI LQQNVNGQTI SLYRFLPNIV MQANSTVTVW AAASEAKHQP
PSDFLWKEQD KFRASPDCIT ILCKPNGQAI AWYTPIHWKQ AWEKLDADVE FNRCSVVSPT
FRKRVFQWTA STATITKEKQ DQPKKDISNY QVEQAQVLLK REKEIPPTVF PNRSPWCQNP
YVSAHPYCPL IEPHNTSTAG GRLDRQPRTR STRPNRASGS KKKKTSESQK Q*

mutated AA sequence

speed

1.07 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: 0.999999999999998 (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)

chr12:25671759T>AN/A show variant in all transcripts IGV

HGNC symbol

LMNTD1

Ensembl transcript ID

ENST00000458174

Genbank transcript ID

NM_001145728

UniProt peptide

Q8N9Z9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1159A>T
cDNA.1404A>T
g.129755A>T

AA changes

T387S Score: 58 explain score(s)

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

387

frameshift

known variant

Reference ID: rs1479500

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1324	932	2256
ExAC	-	-	-

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.404	0.001
	-0.995	0
(flanking)	0.102	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 gained	129748	0.92	mu: AGACAGCCCAGGTCT	ACAG\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

387

mutated

all conserved

387

Ptroglodytes

all conserved

ENSPTRG00000004776

387

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054966

395

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

1230 / 1230

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

410 / 410

position of stopcodon in wt / mu cDNA

1475 / 1475

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

246 / 246

chromosome

strand

-1

last intron/exon boundary

1498

theoretical NMD boundary in CDS

1202

length of CDS

1230

coding sequence (CDS) position

1159

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

1404

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

129755

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

25671759

original gDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered gDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

original cDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered cDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

wildtype AA sequence

MKDTQDIQEA SKAMQNKVHE QEDKNEKQKQ REDKLGVYSL VHFSPKMLGS VATTLPLSSS
NSSGMPLGYY LSSPQISRVT ISTTGQLTSK ATVGSCSRVE NSLDASPFSV PKKQDESPMI
GDGEDYFLSL FGDSKKLTAH SNYTQKTLKY FSMILEEVGQ FTSSSLGDVE IAEVNVKGLF
VKLINSSLDK EMAIGDHILQ QNVNGQTISL YRFLPNIVMQ ANSTVTVWAA ASEAKHQPPS
DFLWKEQDKF RASPDCITIL CKPNGQAIAW YTPIHWKQAW EKLDADVEFN RCSVVSPTFR
KRVFQWTAST ATITKEKQDQ PKKDISNYQV EQAQVLLKRE KEIPPTVFPN RSPWCQNPYV
SAHPYCPLIE PHNTSTAGGR LDRQPRTRST RPNRASGSKK KKTSESQKQ*

mutated AA sequence

speed

1.09 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:25671759T>AN/A show variant in all transcripts IGV

HGNC symbol

LMNTD1

Ensembl transcript ID

ENST00000282881

Genbank transcript ID

NM_152590

UniProt peptide

Q8N9Z9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1096A>T
cDNA.1246A>T
g.129755A>T

AA changes

T366S Score: 58 explain score(s)

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

366

frameshift

known variant

Reference ID: rs1479500

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1324	932	2256
ExAC	-	-	-

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.404	0.001
	-0.995	0
(flanking)	0.102	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 gained	129748	0.92	mu: AGACAGCCCAGGTCT	ACAG\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

366

mutated

all conserved

366

Ptroglodytes

all conserved

ENSPTRG00000004776

387

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054966

395

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
381	381	CONFLICT	K -> E (in Ref. 1; BAG59389).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1167 / 1167

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

389 / 389

position of stopcodon in wt / mu cDNA

1317 / 1317

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

151 / 151

chromosome

strand

-1

last intron/exon boundary

1340

theoretical NMD boundary in CDS

1139

length of CDS

1167

coding sequence (CDS) position

1096

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

1246

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

129755

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

25671759

original gDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered gDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

original cDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered cDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

wildtype AA sequence

MLEGSWINRR EDKLGVYSLV HFSPKMLGSV ATTLPLSSSN SSGMPLGYYL SSPQISRVTI
STTGQLTSKA TVGSCSRVEN SLDASPFSVP KKQDESPMIG DGEDYFLSLF GDSKKLTAHS
NYTQKTLKYF SMILEEVGQF TSSSLGDVEI AEVNVKGLFV KLINSSLDKE MAIGDHILQQ
NVNGQTISLY RFLPNIVMQA NSTVTVWAAA SEAKHQPPSD FLWKEQDKFR ASPDCITILC
KPNGQAIAWY TPIHWKQAWE KLDADVEFNR CSVVSPTFRK RVFQWTASTA TITKEKQDQP
KKDISNYQVE QAQVLLKREK EIPPTVFPNR SPWCQNPYVS AHPYCPLIEP HNTSTAGGRL
DRQPRTRSTR PNRASGSKKK KTSESQKQ*

mutated AA sequence

speed

1.20 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:25671759T>AN/A show variant in all transcripts IGV

HGNC symbol

LMNTD1

Ensembl transcript ID

ENST00000445693

Genbank transcript ID

NM_001145727

UniProt peptide

Q8N9Z9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.907A>T
cDNA.910A>T
g.129755A>T

AA changes

T303S Score: 58 explain score(s)

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

303

frameshift

known variant

Reference ID: rs1479500

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1324	932	2256
ExAC	-	-	-

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.404	0.001
	-0.995	0
(flanking)	0.102	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 gained	129748	0.92	mu: AGACAGCCCAGGTCT	ACAG\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

303

mutated

all conserved

303

Ptroglodytes

all conserved

ENSPTRG00000004776

387

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054966

395

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
381	381	CONFLICT	K -> E (in Ref. 1; BAG59389).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

978 / 978

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

326 / 326

position of stopcodon in wt / mu cDNA

981 / 981

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

4 / 4

chromosome

strand

-1

last intron/exon boundary

1004

theoretical NMD boundary in CDS

950

length of CDS

978

coding sequence (CDS) position

907

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

910

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

129755

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

25671759

original gDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered gDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

original cDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered cDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

wildtype AA sequence

MQQPVRAGDI GVSRVQTHHN ASPFSVPKKQ DESPMIGDGE DYFLSLFGDS KKLTAHSNYT
QKTLKYFSMI LEEVGQFTSS SLGDVEIAEV NVKGLFVKLI NSSLDKEMAI GDHILQQNVN
GQTISLYRFL PNIVMQANST VTVWAAASEA KHQPPSDFLW KEQDKFRASP DCITILCKPN
GQAIAWYTPI HWKQAWEKLD ADVEFNRCSV VSPTFRKRVF QWTASTATIT KEKQDQPKKD
ISNYQVEQAQ VLLKREKEIP PTVFPNRSPW CQNPYVSAHP YCPLIEPHNT STAGGRLDRQ
PRTRSTRPNR ASGSKKKKTS ESQKQ*

mutated AA sequence

speed

1.08 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:25671759T>AN/A show variant in all transcripts IGV

HGNC symbol

LMNTD1

Ensembl transcript ID

ENST00000413632

Genbank transcript ID

NM_001145729

UniProt peptide

Q8N9Z9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1039A>T
cDNA.1282A>T
g.129755A>T

AA changes

T347S Score: 58 explain score(s)

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

347

frameshift

known variant

Reference ID: rs1479500

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1324	932	2256
ExAC	-	-	-

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.404	0.001
	-0.995	0
(flanking)	0.102	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 gained	129748	0.92	mu: AGACAGCCCAGGTCT	ACAG\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

347

mutated

all conserved

347

Ptroglodytes

all conserved

ENSPTRG00000004776

387

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054966

395

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
381	381	CONFLICT	K -> E (in Ref. 1; BAG59389).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1110 / 1110

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

370 / 370

position of stopcodon in wt / mu cDNA

1353 / 1353

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

244 / 244

chromosome

strand

-1

last intron/exon boundary

1376

theoretical NMD boundary in CDS

1082

length of CDS

1110

coding sequence (CDS) position

1039

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

1282

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

129755

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

25671759

original gDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered gDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

original cDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered cDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

wildtype AA sequence

MKDTQDIQEA SKAMQNKVHE QEDKNEKQKQ REDKLGVYSL VHFSPKMLGS VATTLPLSSS
NSSGMPLGYY LSSPQISRVT ISTTGQLTSK ATVGSCSRVE NSLDASPFSV PKKQDESPMI
GDGEDYFLSL FGDSKKLTAH SNYTQKTLKY FSMILEEVGQ FTSSSLGDVE IAEVNVKGLF
VKLINSSLDK EMAIGDHILQ QNVNGQTISL YRFLPNIVMQ ANSTVTAIAW YTPIHWKQAW
EKLDADVEFN RCSVVSPTFR KRVFQWTAST ATITKEKQDQ PKKDISNYQV EQAQVLLKRE
KEIPPTVFPN RSPWCQNPYV SAHPYCPLIE PHNTSTAGGR LDRQPRTRST RPNRASGSKK
KKTSESQKQ*

mutated AA sequence

MKDTQDIQEA SKAMQNKVHE QEDKNEKQKQ REDKLGVYSL VHFSPKMLGS VATTLPLSSS
NSSGMPLGYY LSSPQISRVT ISTTGQLTSK ATVGSCSRVE NSLDASPFSV PKKQDESPMI
GDGEDYFLSL FGDSKKLTAH SNYTQKTLKY FSMILEEVGQ FTSSSLGDVE IAEVNVKGLF
VKLINSSLDK EMAIGDHILQ QNVNGQTISL YRFLPNIVMQ ANSTVTAIAW YTPIHWKQAW
EKLDADVEFN RCSVVSPTFR KRVFQWTAST ATITKEKQDQ PKKDISNYQV EQAQVLLKRE
KEIPPTVFPN RSPWCQNPYV SAHPYCPLIE PHNTSTAGGR LDRQPRSRST RPNRASGSKK
KKTSESQKQ*

speed

0.65 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems