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: ENST00000344577
Querying Taster for transcript #2: ENST00000536861
MT speed 0 s - this script 3.148054 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LIPI	polymorphism_automatic	0.060502204002636	simple_aae		affected		E452K	single base exchange	rs2822432		show file
LIPI	polymorphism_automatic	0.060502204002636	simple_aae		affected		E431K	single base exchange	rs2822432		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.939497795997364 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM166416)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr21:15516948C>TN/A show variant in all transcripts IGV

HGNC symbol

LIPI

Ensembl transcript ID

ENST00000344577

Genbank transcript ID

NM_198996

UniProt peptide

Q6XZB0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1354G>A
cDNA.1380G>A
g.66219G>A

AA changes

E452K Score: 56 explain score(s)

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

452

frameshift

known variant

Reference ID: rs2822432

database	homozygous (T/T)	heterozygous	allele carriers
1000G	333	923	1256
ExAC	6850	19067	25917

known disease mutation at this position, please check HGMD for details (HGMD ID CM166416)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.398	1
	3.212	1
(flanking)	0.343	1

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 marginally increased	66222	wt: 0.9974 / mu: 0.9982 (marginal change - not scored)	wt: CAGAAAGGTAAGAAA mu: CAAAAAGGTAAGAAA	GAAA\|ggta
Donor marginally increased	66216	wt: 0.5002 / mu: 0.5344 (marginal change - not scored)	wt: CATACCCAGAAAGGT mu: CATACCCAAAAAGGT	TACC\|caga
Donor marginally increased	66217	wt: 0.9339 / mu: 0.9556 (marginal change - not scored)	wt: ATACCCAGAAAGGTA mu: ATACCCAAAAAGGTA	ACCC\|agaa
Donor gained	66215	0.33	mu: ACATACCCAAAAAGG	ATAC\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

452

mutated

all conserved

452

Ptroglodytes

all identical

ENSPTRG00000013785

452

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000016924

425

Drerio

not conserved

ENSDARG00000005332

368

Dmelanogaster

no alignment

FBgn0034166

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
455	455	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1446 / 1446

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

482 / 482

position of stopcodon in wt / mu cDNA

1472 / 1472

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

27 / 27

chromosome

strand

-1

last intron/exon boundary

1385

theoretical NMD boundary in CDS

1308

length of CDS

1446

coding sequence (CDS) position

1354

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

1380

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

66219

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

15516948

original gDNA sequence snippet

TAAAATCACTTACATACCCAGAAAGGTAAGAAAATTAAATT

altered gDNA sequence snippet

TAAAATCACTTACATACCCAAAAAGGTAAGAAAATTAAATT

original cDNA sequence snippet

TAAAATCACTTACATACCCAGAAAGACCACCACTTTGCAGG

altered cDNA sequence snippet

TAAAATCACTTACATACCCAAAAAGACCACCACTTTGCAGG

wildtype AA sequence

MLLKCLHNNL CQKYSAHAFQ FSPRNVLWLL VVCLRSDNKR PCLEFSQLSV KDSFRDLFIP
RIETILMMYT RNNLNCAEPL FEQNNSLNVN FNTQKKTVWL IHGYRPVGSI PLWLQNFVRI
LLNEEDMNVI VVDWSRGATT FIYNRAVKNT RKVAVSLSVH IKNLLKHGAS LDNFHFIGVS
LGAHISGFVG KIFHGQLGRI TGLDPAGPRF SRKPPYSRLD YTDAKFVDVI HSDSNGLGIQ
EPLGHIDFYP NGGNKQPGCP KSIFSGIQFI KCNHQRAVHL FMASLETNCN FISFPCRSYK
DYKTSLCVDC DCFKEKSCPR LGYQAKLFKG VLKERMEGRP LRTTVFLDTS GTYPFCTYYF
VLSIIVPDKT MMDGSFSFKL LNQLGMIEEP RLYEKNKPFY KLQEVKILAQ FYNDFVNISS
IGLTYFQSSN LQCSTCTYKI QRLMLKSLTY PERPPLCRYN IVLKDREEVF LNPNTCTPKN
T*

mutated AA sequence

speed

0.88 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: 0.939497795997364 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM166416)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr21:15516948C>TN/A show variant in all transcripts IGV

HGNC symbol

LIPI

Ensembl transcript ID

ENST00000536861

Genbank transcript ID

N/A

UniProt peptide

Q6XZB0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1291G>A
cDNA.1291G>A
g.66219G>A

AA changes

E431K Score: 56 explain score(s)

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

431

frameshift

known variant

Reference ID: rs2822432

database	homozygous (T/T)	heterozygous	allele carriers
1000G	333	923	1256
ExAC	6850	19067	25917

known disease mutation at this position, please check HGMD for details (HGMD ID CM166416)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.398	1
	3.212	1
(flanking)	0.343	1

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 marginally increased	66222	wt: 0.9974 / mu: 0.9982 (marginal change - not scored)	wt: CAGAAAGGTAAGAAA mu: CAAAAAGGTAAGAAA	GAAA\|ggta
Donor marginally increased	66216	wt: 0.5002 / mu: 0.5344 (marginal change - not scored)	wt: CATACCCAGAAAGGT mu: CATACCCAAAAAGGT	TACC\|caga
Donor marginally increased	66217	wt: 0.9339 / mu: 0.9556 (marginal change - not scored)	wt: ATACCCAGAAAGGTA mu: ATACCCAAAAAGGTA	ACCC\|agaa
Donor gained	66215	0.33	mu: ACATACCCAAAAAGG	ATAC\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

431

mutated

all conserved

431

Ptroglodytes

all identical

ENSPTRG00000013785

452

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000016924

426

Drerio

not conserved

ENSDARG00000005332

368

Dmelanogaster

no alignment

FBgn0034166

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
436	436	DISULFID	By similarity.	might get lost (downstream of altered splice site)
455	455	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1383 / 1383

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

461 / 461

position of stopcodon in wt / mu cDNA

1383 / 1383

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

1296

theoretical NMD boundary in CDS

1245

length of CDS

1383

coding sequence (CDS) position

1291

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

1291

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

66219

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

15516948

original gDNA sequence snippet

TAAAATCACTTACATACCCAGAAAGGTAAGAAAATTAAATT

altered gDNA sequence snippet

TAAAATCACTTACATACCCAAAAAGGTAAGAAAATTAAATT

original cDNA sequence snippet

TAAAATCACTTACATACCCAGAAAGACCACCACTTTGCAGG

altered cDNA sequence snippet

TAAAATCACTTACATACCCAAAAAGACCACCACTTTGCAGG

wildtype AA sequence

MRVYIFLCLM CWVRSDNKRP CLEFSQLSVK DSFRDLFIPR IETILMMYTR NNLNCAEPLF
EQNNSLNVNF NTQKKTVWLI HGYRPVGSIP LWLQNFVRIL LNEEDMNVIV VDWSRGATTF
IYNRAVKNTR KVAVSLSVHI KNLLKHGASL DNFHFIGVSL GAHISGFVGK IFHGQLGRIT
GLDPAGPRFS RKPPYSRLDY TDAKFVDVIH SDSNGLGIQE PLGHIDFYPN GGNKQPGCPK
SIFSGIQFIK CNHQRAVHLF MASLETNCNF ISFPCRSYKD YKTSLCVDCD CFKEKSCPRL
GYQAKLFKGV LKERMEGRPL RTTVFLDTSG TYPFCTYYFV LSIIVPDKTM MDGSFSFKLL
NQLGMIEEPR LYEKNKPFYK LQEVKILAQF YNDFVNISSI GLTYFQSSNL QCSTCTYKIQ
RLMLKSLTYP ERPPLCRYNI VLKDREEVFL NPNTCTPKNT *

mutated AA sequence

speed

0.27 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems