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: ENST00000368764
Querying Taster for transcript #2: ENST00000392667
MT speed 1.79 s - this script 4.079351 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
IVL	polymorphism_automatic	1.72972747236599e-13	simple_aae		affected		Q237E	single base exchange	rs7520711		show file
IVL	polymorphism_automatic	2.7210456110538e-12	simple_aae		affected		Q91E	single base exchange	rs7520711		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999827 (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)

chr1:152882982C>GN/A show variant in all transcripts IGV

HGNC symbol

IVL

Ensembl transcript ID

ENST00000368764

Genbank transcript ID

NM_005547

UniProt peptide

P07476

alteration type

single base exchange

alteration region

CDS

DNA changes

c.709C>G
cDNA.773C>G
g.1962C>G

AA changes

Q237E Score: 29 explain score(s)

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

237

frameshift

known variant

Reference ID: rs7520711

database	homozygous (G/G)	heterozygous	allele carriers
1000G	580	965	1545
ExAC	-	-	-

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.573	0
	-0.891	0
(flanking)	-1.12	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 increased	1961	wt: 0.36 / mu: 0.98	wt: CTCCCACAGCAGCAG mu: CTCCCAGAGCAGCAG	CCCA\|cagc
Donor marginally increased	1966	wt: 0.2168 / mu: 0.2226 (marginal change - not scored)	wt: ACAGCAGCAGGAGGG mu: AGAGCAGCAGGAGGG	AGCA\|gcag
Donor gained	1958	0.54	mu: GAGCTCCCAGAGCAG	GCTC\|ccag

distance from splice site

728

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

237

mutated

all conserved

237

Ptroglodytes

all conserved

ENSPTRG00000030382

204

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000049128

210

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0031820

347

KNTAIG

EPLG

Celegans

all identical

Y75B8A.8

191

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
153	542	REGION	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].	lost
233	242	REPEAT	9.	lost
243	252	REPEAT	10.	might get lost (downstream of altered splice site)
253	262	REPEAT	11.	might get lost (downstream of altered splice site)
263	272	REPEAT	12.	might get lost (downstream of altered splice site)
273	282	REPEAT	13.	might get lost (downstream of altered splice site)
283	292	REPEAT	14.	might get lost (downstream of altered splice site)
293	302	REPEAT	15.	might get lost (downstream of altered splice site)
303	312	REPEAT	16.	might get lost (downstream of altered splice site)
313	318	HELIX		might get lost (downstream of altered splice site)
313	322	REPEAT	17.	might get lost (downstream of altered splice site)
323	328	HELIX		might get lost (downstream of altered splice site)
323	332	REPEAT	18.	might get lost (downstream of altered splice site)
333	338	HELIX		might get lost (downstream of altered splice site)
333	342	REPEAT	19.	might get lost (downstream of altered splice site)
343	348	HELIX		might get lost (downstream of altered splice site)
343	352	REPEAT	20.	might get lost (downstream of altered splice site)
353	358	HELIX		might get lost (downstream of altered splice site)
353	362	REPEAT	21.	might get lost (downstream of altered splice site)
363	372	REPEAT	22.	might get lost (downstream of altered splice site)
373	382	REPEAT	23.	might get lost (downstream of altered splice site)
383	392	REPEAT	24; approximate.	might get lost (downstream of altered splice site)
393	402	REPEAT	25.	might get lost (downstream of altered splice site)
403	412	REPEAT	26.	might get lost (downstream of altered splice site)
413	422	REPEAT	27.	might get lost (downstream of altered splice site)
423	432	REPEAT	28.	might get lost (downstream of altered splice site)
433	442	REPEAT	29.	might get lost (downstream of altered splice site)
443	452	REPEAT	30.	might get lost (downstream of altered splice site)
453	462	REPEAT	31.	might get lost (downstream of altered splice site)
463	472	REPEAT	32.	might get lost (downstream of altered splice site)
473	482	REPEAT	33.	might get lost (downstream of altered splice site)
483	492	REPEAT	34.	might get lost (downstream of altered splice site)
493	502	REPEAT	35.	might get lost (downstream of altered splice site)
496	496	CROSSLNK	Isoglutamyl lysine isopeptide (Gln-Lys) (interchain with K-? in other proteins).	might get lost (downstream of altered splice site)
503	512	REPEAT	36; approximate.	might get lost (downstream of altered splice site)
513	522	REPEAT	37.	might get lost (downstream of altered splice site)
523	532	REPEAT	38.	might get lost (downstream of altered splice site)
533	542	REPEAT	39; approximate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1758 / 1758

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

586 / 586

position of stopcodon in wt / mu cDNA

1822 / 1822

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

65 / 65

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1758

coding sequence (CDS) position

709

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

773

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

1962

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

152882982

original gDNA sequence snippet

AGGGGCAGCTGGAGCTCCCACAGCAGCAGGAGGGGCAGCTG

altered gDNA sequence snippet

AGGGGCAGCTGGAGCTCCCAGAGCAGCAGGAGGGGCAGCTG

original cDNA sequence snippet

AGGGGCAGCTGGAGCTCCCACAGCAGCAGGAGGGGCAGCTG

altered cDNA sequence snippet

AGGGGCAGCTGGAGCTCCCAGAGCAGCAGGAGGGGCAGCTG

wildtype AA sequence

MSQQHTLPVT LSPALSQELL KTVPPPVNTH QEQMKQPTPL PPPCQKVPVE LPVEVPSKQE
EKHMTAVKGL PEQECEQQQK EPQEQELQQQ HWEQHEEYQK AENPEQQLKQ EKTQRDQQLN
KQLEEEKKLL DQQLDQELVK RDEQLGMKKE QLLELPEQQE GHLKHLEQQE GQLKHPEQQE
GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPQQQE
GQLELSEQQE GQLELSEQQE GQLKHLEHQE GQLEVPEEQM GQLKYLEQQE GQLKHLDQQE
KQPELPEQQM GQLKHLEQQE GQPKHLEQQE GQLEQLEEQE GQLKHLEQQE GQLEHLEHQE
GQLGLPEQQV LQLKQLEKQQ GQPKHLEEEE GQLKHLVQQE GQLKHLVQQE GQLEQQERQV
EHLEQQVGQL KHLEEQEGQL KHLEQQQGQL EVPEQQVGQP KNLEQEEKQL ELPEQQEGQV
KHLEKQEAQL ELPEQQVGQP KHLEQQEKHL EHPEQQDGQL KHLEQQEGQL KDLEQQKGQL
EQPVFAPAPG QVQDIQPALP TKGEVLLPVE HQQQKQEVQW PPKHK*

mutated AA sequence

MSQQHTLPVT LSPALSQELL KTVPPPVNTH QEQMKQPTPL PPPCQKVPVE LPVEVPSKQE
EKHMTAVKGL PEQECEQQQK EPQEQELQQQ HWEQHEEYQK AENPEQQLKQ EKTQRDQQLN
KQLEEEKKLL DQQLDQELVK RDEQLGMKKE QLLELPEQQE GHLKHLEQQE GQLKHPEQQE
GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE
GQLELSEQQE GQLELSEQQE GQLKHLEHQE GQLEVPEEQM GQLKYLEQQE GQLKHLDQQE
KQPELPEQQM GQLKHLEQQE GQPKHLEQQE GQLEQLEEQE GQLKHLEQQE GQLEHLEHQE
GQLGLPEQQV LQLKQLEKQQ GQPKHLEEEE GQLKHLVQQE GQLKHLVQQE GQLEQQERQV
EHLEQQVGQL KHLEEQEGQL KHLEQQQGQL EVPEQQVGQP KNLEQEEKQL ELPEQQEGQV
KHLEKQEAQL ELPEQQVGQP KHLEQQEKHL EHPEQQDGQL KHLEQQEGQL KDLEQQKGQL
EQPVFAPAPG QVQDIQPALP TKGEVLLPVE HQQQKQEVQW PPKHK*

speed

1.02 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: 0.999999999997279 (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)

chr1:152882982C>GN/A show variant in all transcripts IGV

HGNC symbol

IVL

Ensembl transcript ID

ENST00000392667

Genbank transcript ID

N/A

UniProt peptide

P07476

alteration type

single base exchange

alteration region

CDS

DNA changes

c.271C>G
cDNA.637C>G
g.1962C>G

AA changes

Q91E Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs7520711

database	homozygous (G/G)	heterozygous	allele carriers
1000G	580	965	1545
ExAC	-	-	-

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.573	0
	-0.891	0
(flanking)	-1.12	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 increased	1961	wt: 0.36 / mu: 0.98	wt: CTCCCACAGCAGCAG mu: CTCCCAGAGCAGCAG	CCCA\|cagc
Donor marginally increased	1966	wt: 0.2168 / mu: 0.2226 (marginal change - not scored)	wt: ACAGCAGCAGGAGGG mu: AGAGCAGCAGGAGGG	AGCA\|gcag
Donor gained	1958	0.54	mu: GAGCTCCCAGAGCAG	GCTC\|ccag

distance from splice site

445

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000030382

197

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000049128

139

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0031820

345

KNTAIG

EPLG

Celegans

all identical

Y75B8A.8

144

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
90	90	LIPID	Omega-hydroxyceramide glutamate ester (Probable).	might get lost (downstream of altered splice site)
118	118	LIPID	Omega-hydroxyceramide glutamate ester (Probable).	might get lost (downstream of altered splice site)
133	133	LIPID	Omega-hydroxyceramide glutamate ester (Probable).	might get lost (downstream of altered splice site)
153	162	REPEAT	1.	might get lost (downstream of altered splice site)
153	542	REGION	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].	might get lost (downstream of altered splice site)
163	172	REPEAT	2.	might get lost (downstream of altered splice site)
173	182	REPEAT	3.	might get lost (downstream of altered splice site)
183	192	REPEAT	4.	might get lost (downstream of altered splice site)
193	202	REPEAT	5.	might get lost (downstream of altered splice site)
203	212	REPEAT	6.	might get lost (downstream of altered splice site)
213	222	REPEAT	7.	might get lost (downstream of altered splice site)
223	232	REPEAT	8.	might get lost (downstream of altered splice site)
233	242	REPEAT	9.	might get lost (downstream of altered splice site)
243	252	REPEAT	10.	might get lost (downstream of altered splice site)
253	262	REPEAT	11.	might get lost (downstream of altered splice site)
263	272	REPEAT	12.	might get lost (downstream of altered splice site)
273	282	REPEAT	13.	might get lost (downstream of altered splice site)
283	292	REPEAT	14.	might get lost (downstream of altered splice site)
293	302	REPEAT	15.	might get lost (downstream of altered splice site)
303	312	REPEAT	16.	might get lost (downstream of altered splice site)
313	318	HELIX		might get lost (downstream of altered splice site)
313	322	REPEAT	17.	might get lost (downstream of altered splice site)
323	328	HELIX		might get lost (downstream of altered splice site)
323	332	REPEAT	18.	might get lost (downstream of altered splice site)
333	338	HELIX		might get lost (downstream of altered splice site)
333	342	REPEAT	19.	might get lost (downstream of altered splice site)
343	348	HELIX		might get lost (downstream of altered splice site)
343	352	REPEAT	20.	might get lost (downstream of altered splice site)
353	358	HELIX		might get lost (downstream of altered splice site)
353	362	REPEAT	21.	might get lost (downstream of altered splice site)
363	372	REPEAT	22.	might get lost (downstream of altered splice site)
373	382	REPEAT	23.	might get lost (downstream of altered splice site)
383	392	REPEAT	24; approximate.	might get lost (downstream of altered splice site)
393	402	REPEAT	25.	might get lost (downstream of altered splice site)
403	412	REPEAT	26.	might get lost (downstream of altered splice site)
413	422	REPEAT	27.	might get lost (downstream of altered splice site)
423	432	REPEAT	28.	might get lost (downstream of altered splice site)
433	442	REPEAT	29.	might get lost (downstream of altered splice site)
443	452	REPEAT	30.	might get lost (downstream of altered splice site)
453	462	REPEAT	31.	might get lost (downstream of altered splice site)
463	472	REPEAT	32.	might get lost (downstream of altered splice site)
473	482	REPEAT	33.	might get lost (downstream of altered splice site)
483	492	REPEAT	34.	might get lost (downstream of altered splice site)
493	502	REPEAT	35.	might get lost (downstream of altered splice site)
496	496	CROSSLNK	Isoglutamyl lysine isopeptide (Gln-Lys) (interchain with K-? in other proteins).	might get lost (downstream of altered splice site)
503	512	REPEAT	36; approximate.	might get lost (downstream of altered splice site)
513	522	REPEAT	37.	might get lost (downstream of altered splice site)
523	532	REPEAT	38.	might get lost (downstream of altered splice site)
533	542	REPEAT	39; approximate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1320 / 1320

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

440 / 440

position of stopcodon in wt / mu cDNA

1686 / 1686

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

367 / 367

chromosome

strand

last intron/exon boundary

193

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1320

coding sequence (CDS) position

271

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

637

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

1962

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

152882982

original gDNA sequence snippet

AGGGGCAGCTGGAGCTCCCACAGCAGCAGGAGGGGCAGCTG

altered gDNA sequence snippet

AGGGGCAGCTGGAGCTCCCAGAGCAGCAGGAGGGGCAGCTG

original cDNA sequence snippet

AGGGGCAGCTGGAGCTCCCACAGCAGCAGGAGGGGCAGCTG

altered cDNA sequence snippet

AGGGGCAGCTGGAGCTCCCAGAGCAGCAGGAGGGGCAGCTG

wildtype AA sequence

MKKEQLLELP EQQEGHLKHL EQQEGQLKHP EQQEGQLELP EQQEGQLELP EQQEGQLELP
EQQEGQLELP EQQEGQLELP EQQEGQLELP QQQEGQLELS EQQEGQLELS EQQEGQLKHL
EHQEGQLEVP EEQMGQLKYL EQQEGQLKHL DQQEKQPELP EQQMGQLKHL EQQEGQPKHL
EQQEGQLEQL EEQEGQLKHL EQQEGQLEHL EHQEGQLGLP EQQVLQLKQL EKQQGQPKHL
EEEEGQLKHL VQQEGQLKHL VQQEGQLEQQ ERQVEHLEQQ VGQLKHLEEQ EGQLKHLEQQ
QGQLEVPEQQ VGQPKNLEQE EKQLELPEQQ EGQVKHLEKQ EAQLELPEQQ VGQPKHLEQQ
EKHLEHPEQQ DGQLKHLEQQ EGQLKDLEQQ KGQLEQPVFA PAPGQVQDIQ PALPTKGEVL
LPVEHQQQKQ EVQWPPKHK*

mutated AA sequence

MKKEQLLELP EQQEGHLKHL EQQEGQLKHP EQQEGQLELP EQQEGQLELP EQQEGQLELP
EQQEGQLELP EQQEGQLELP EQQEGQLELP EQQEGQLELS EQQEGQLELS EQQEGQLKHL
EHQEGQLEVP EEQMGQLKYL EQQEGQLKHL DQQEKQPELP EQQMGQLKHL EQQEGQPKHL
EQQEGQLEQL EEQEGQLKHL EQQEGQLEHL EHQEGQLGLP EQQVLQLKQL EKQQGQPKHL
EEEEGQLKHL VQQEGQLKHL VQQEGQLEQQ ERQVEHLEQQ VGQLKHLEEQ EGQLKHLEQQ
QGQLEVPEQQ VGQPKNLEQE EKQLELPEQQ EGQVKHLEKQ EAQLELPEQQ VGQPKHLEQQ
EKHLEHPEQQ DGQLKHLEQQ EGQLKDLEQQ KGQLEQPVFA PAPGQVQDIQ PALPTKGEVL
LPVEHQQQKQ EVQWPPKHK*

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems