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: ENST00000265598
Querying Taster for transcript #2: ENST00000466939
MT speed 1.81 s - this script 4.154289 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LAMP3	polymorphism_automatic	2.15094608790878e-12	simple_aae		affected		I318V	single base exchange	rs482912		show file
LAMP3	polymorphism_automatic	2.15094608790878e-12	simple_aae		affected		I294V	single base exchange	rs482912		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997849 (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)

chr3:182853670T>CN/A show variant in all transcripts IGV

HGNC symbol

LAMP3

Ensembl transcript ID

ENST00000265598

Genbank transcript ID

NM_014398

UniProt peptide

Q9UQV4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.952A>G
cDNA.1208A>G
g.27958A>G

AA changes

I318V Score: 29 explain score(s)

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

318

frameshift

known variant

Reference ID: rs482912

database	homozygous (C/C)	heterozygous	allele carriers
1000G	714	1058	1772
ExAC	26741	-20715	6026

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.065	0
	-0.06	0
(flanking)	-0.275	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	27949	wt: 0.6039 / mu: 0.6178 (marginal change - not scored)	wt: TGCATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGA mu: TGCATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGA	tttt\|CAGA
Acc marginally increased	27952	wt: 0.9303 / mu: 0.9399 (marginal change - not scored)	wt: ATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAATC mu: ATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAATC	tcag\|AGAC
Acc marginally increased	27951	wt: 0.9780 / mu: 0.9855 (marginal change - not scored)	wt: CATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAAT mu: CATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAAT	ttca\|GAGA
Acc marginally increased	27953	wt: 0.5976 / mu: 0.6246 (marginal change - not scored)	wt: TCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAATCA mu: TCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAATCA	caga\|GACA
Acc increased	27950	wt: 0.68 / mu: 0.77	wt: GCATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAA mu: GCATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAA	tttc\|AGAG
Donor marginally increased	27951	wt: 0.9015 / mu: 0.9024 (marginal change - not scored)	wt: TTTTCAGAGACAATT mu: TTTTCAGAGACAGTT	TTCA\|gaga
Donor gained	27957	0.31	mu: GAGACAGTTTACCAA	GACA\|gttt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

318

mutated

all conserved

318

Ptroglodytes

all identical

ENSPTRG00000015663

247

Mmulatta

all identical

ENSMMUG00000010555

318

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041247

313

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
28	381	TOPO_DOM	Lumenal (Potential).	lost
318	323	STRAND		lost
328	331	STRAND		might get lost (downstream of altered splice site)
337	339	STRAND		might get lost (downstream of altered splice site)
343	346	STRAND		might get lost (downstream of altered splice site)
348	363	STRAND		might get lost (downstream of altered splice site)
382	402	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
403	416	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1251 / 1251

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

417 / 417

position of stopcodon in wt / mu cDNA

1507 / 1507

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

257 / 257

chromosome

strand

-1

last intron/exon boundary

1374

theoretical NMD boundary in CDS

1067

length of CDS

1251

coding sequence (CDS) position

952

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

1208

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

27958

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

182853670

original gDNA sequence snippet

CTGTCACCTTTTCAGAGACAATTTACCAAGGAATCAAACAT

altered gDNA sequence snippet

CTGTCACCTTTTCAGAGACAGTTTACCAAGGAATCAAACAT

original cDNA sequence snippet

CCGTCTCAGATCCAGAGACAATTTACCAAGGAATCAAACAT

altered cDNA sequence snippet

CCGTCTCAGATCCAGAGACAGTTTACCAAGGAATCAAACAT

wildtype AA sequence

MPRQLSAAAA LFASLAVILH DGSQMRAKAF PETRDYSQPT AAATVQDIKK PVQQPAKQAP
HQTLAARFMD GHITFQTAAT VKIPTTTPAT TKNTATTSPI TYTLVTTQAT PNNSHTAPPV
TEVTVGPSLA PYSLPPTITP PAHTTGTSSS TVSHTTGNTT QPSNQTTLPA TLSIALHKST
TGQKPVQPTH APGTTAAAHN TTRTAAPAST VPGPTLAPQP SSVKTGIYQV LNGSRLCIKA
EMGIQLIVQD KESVFSPRRY FNIDPNATQA SGNCGTRKSN LLLNFQGGFV NLTFTKDEES
YYISEVGAYL TVSDPETIYQ GIKHAVVMFQ TAVGHSFKCV SEQSLQLSAH LQVKTTDVQL
QAFDFEDDHF GNVDECSSDY TIVLPVIGAI VVGLCLMGMG VYKIRLRCQS SGYQRI*

mutated AA sequence

MPRQLSAAAA LFASLAVILH DGSQMRAKAF PETRDYSQPT AAATVQDIKK PVQQPAKQAP
HQTLAARFMD GHITFQTAAT VKIPTTTPAT TKNTATTSPI TYTLVTTQAT PNNSHTAPPV
TEVTVGPSLA PYSLPPTITP PAHTTGTSSS TVSHTTGNTT QPSNQTTLPA TLSIALHKST
TGQKPVQPTH APGTTAAAHN TTRTAAPAST VPGPTLAPQP SSVKTGIYQV LNGSRLCIKA
EMGIQLIVQD KESVFSPRRY FNIDPNATQA SGNCGTRKSN LLLNFQGGFV NLTFTKDEES
YYISEVGAYL TVSDPETVYQ GIKHAVVMFQ TAVGHSFKCV SEQSLQLSAH LQVKTTDVQL
QAFDFEDDHF GNVDECSSDY TIVLPVIGAI VVGLCLMGMG VYKIRLRCQS SGYQRI*

speed

0.89 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: 0.999999999997849 (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)

chr3:182853670T>CN/A show variant in all transcripts IGV

HGNC symbol

LAMP3

Ensembl transcript ID

ENST00000466939

Genbank transcript ID

N/A

UniProt peptide

Q9UQV4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.880A>G
cDNA.998A>G
g.27958A>G

AA changes

I294V Score: 29 explain score(s)

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

294

frameshift

known variant

Reference ID: rs482912

database	homozygous (C/C)	heterozygous	allele carriers
1000G	714	1058	1772
ExAC	26741	-20715	6026

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.065	0
	-0.06	0
(flanking)	-0.275	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	27949	wt: 0.6039 / mu: 0.6178 (marginal change - not scored)	wt: TGCATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGA mu: TGCATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGA	tttt\|CAGA
Acc marginally increased	27952	wt: 0.9303 / mu: 0.9399 (marginal change - not scored)	wt: ATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAATC mu: ATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAATC	tcag\|AGAC
Acc marginally increased	27951	wt: 0.9780 / mu: 0.9855 (marginal change - not scored)	wt: CATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAAT mu: CATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAAT	ttca\|GAGA
Acc marginally increased	27953	wt: 0.5976 / mu: 0.6246 (marginal change - not scored)	wt: TCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAATCA mu: TCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAATCA	caga\|GACA
Acc increased	27950	wt: 0.68 / mu: 0.77	wt: GCATCTATCTGTCACCTTTTCAGAGACAATTTACCAAGGAA mu: GCATCTATCTGTCACCTTTTCAGAGACAGTTTACCAAGGAA	tttc\|AGAG
Donor marginally increased	27951	wt: 0.9015 / mu: 0.9024 (marginal change - not scored)	wt: TTTTCAGAGACAATT mu: TTTTCAGAGACAGTT	TTCA\|gaga
Donor gained	27957	0.31	mu: GAGACAGTTTACCAA	GACA\|gttt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

294

mutated

all conserved

294

Ptroglodytes

all identical

ENSPTRG00000015663

247

Mmulatta

all identical

ENSMMUG00000010555

318

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041247

313

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
28	381	TOPO_DOM	Lumenal (Potential).	lost
288	296	STRAND		lost
301	311	STRAND		might get lost (downstream of altered splice site)
313	315	STRAND		might get lost (downstream of altered splice site)
318	323	STRAND		might get lost (downstream of altered splice site)
328	331	STRAND		might get lost (downstream of altered splice site)
337	339	STRAND		might get lost (downstream of altered splice site)
343	346	STRAND		might get lost (downstream of altered splice site)
348	363	STRAND		might get lost (downstream of altered splice site)
382	402	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
403	416	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1179 / 1179

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

393 / 393

position of stopcodon in wt / mu cDNA

1297 / 1297

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

119 / 119

chromosome

strand

-1

last intron/exon boundary

1164

theoretical NMD boundary in CDS

995

length of CDS

1179

coding sequence (CDS) position

880

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

998

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

27958

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

182853670

original gDNA sequence snippet

CTGTCACCTTTTCAGAGACAATTTACCAAGGAATCAAACAT

altered gDNA sequence snippet

CTGTCACCTTTTCAGAGACAGTTTACCAAGGAATCAAACAT

original cDNA sequence snippet

CCGTCTCAGATCCAGAGACAATTTACCAAGGAATCAAACAT

altered cDNA sequence snippet

CCGTCTCAGATCCAGAGACAGTTTACCAAGGAATCAAACAT

wildtype AA sequence

MRAKAFPETR DYSQPTAAAT VQDIKKPVQQ PAKQAPHQTL AARFMDGHIT FQTAATVKIP
TTTPATTKNT ATTSPITYTL VTTQATPNNS HTAPPVTEVT VGPSLAPYSL PPTITPPAHT
TGTSSSTVSH TTGNTTQPSN QTTLPATLSI ALHKSTTGQK PVQPTHAPGT TAAAHNTTRT
AAPASTVPGP TLAPQPSSVK TGIYQVLNGS RLCIKAEMGI QLIVQDKESV FSPRRYFNID
PNATQASGNC GTRKSNLLLN FQGGFVNLTF TKDEESYYIS EVGAYLTVSD PETIYQGIKH
AVVMFQTAVG HSFKCVSEQS LQLSAHLQVK TTDVQLQAFD FEDDHFGNVD ECSSDYTIVL
PVIGAIVVGL CLMGMGVYKI RLRCQSSGYQ RI*

mutated AA sequence

MRAKAFPETR DYSQPTAAAT VQDIKKPVQQ PAKQAPHQTL AARFMDGHIT FQTAATVKIP
TTTPATTKNT ATTSPITYTL VTTQATPNNS HTAPPVTEVT VGPSLAPYSL PPTITPPAHT
TGTSSSTVSH TTGNTTQPSN QTTLPATLSI ALHKSTTGQK PVQPTHAPGT TAAAHNTTRT
AAPASTVPGP TLAPQPSSVK TGIYQVLNGS RLCIKAEMGI QLIVQDKESV FSPRRYFNID
PNATQASGNC GTRKSNLLLN FQGGFVNLTF TKDEESYYIS EVGAYLTVSD PETVYQGIKH
AVVMFQTAVG HSFKCVSEQS LQLSAHLQVK TTDVQLQAFD FEDDHFGNVD ECSSDYTIVL
PVIGAIVVGL CLMGMGVYKI RLRCQSSGYQ RI*

speed

0.92 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems