MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000261883
MT speed 0 s - this script 2.569279 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CILP	polymorphism_automatic	0.993562691767939	simple_aae		affected		I395T	single base exchange	rs2073711		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00643730823206106 (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 CM051412)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:65494212A>GN/A show variant in all transcripts IGV

HGNC symbol

CILP

Ensembl transcript ID

ENST00000261883

Genbank transcript ID

NM_003613

UniProt peptide

O75339

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1184T>C
cDNA.1351T>C
g.9615T>C

AA changes

I395T Score: 89 explain score(s)

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

395

frameshift

known variant

Reference ID: rs2073711

database	homozygous (G/G)	heterozygous	allele carriers
1000G	730	1027	1757
ExAC	19486	-6205	13281

known disease mutation at this position, please check HGMD for details (HGMD ID CM051412)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.248	0.999
	2.297	1
(flanking)	0.971	0.999

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	9617	sequence motif lost	-	wt: ATAG\|gtaa mu: ACAG.gtaa
Acc marginally decreased	9617	wt: 0.6249 / mu: 0.5663 (marginal change - not scored)	wt: TTGCCCAGCTGATTGTCATAGGTAAGCCTGTCTGGGTCCCT mu: TTGCCCAGCTGATTGTCACAGGTAAGCCTGTCTGGGTCCCT	atag\|GTAA
Donor marginally increased	9616	wt: 0.9964 / mu: 0.9987 (marginal change - not scored)	wt: GTCATAGGTAAGCCT mu: GTCACAGGTAAGCCT	CATA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

395

mutated

not conserved

395

Ptroglodytes

all identical

ENSPTRG00000007177

395

Mmulatta

all identical

ENSMMUG00000009659

395

Fcatus

all identical

ENSFCAG00000011462

395

Mmusculus

all identical

ENSMUSG00000042254

395

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000017280

337

Drerio

all identical

ENSDARG00000053362

386

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
309	395	DOMAIN	Ig-like C2-type.	lost
420	420	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
550	550	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
631	631	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1000	1000	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1056	1056	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3555 / 3555

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

1185 / 1185

position of stopcodon in wt / mu cDNA

3722 / 3722

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

168 / 168

chromosome

strand

-1

last intron/exon boundary

1354

theoretical NMD boundary in CDS

1136

length of CDS

3555

coding sequence (CDS) position

1184

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

1351

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

9615

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

65494212

original gDNA sequence snippet

GGTTGCCCAGCTGATTGTCATAGGTAAGCCTGTCTGGGTCC

altered gDNA sequence snippet

GGTTGCCCAGCTGATTGTCACAGGTAAGCCTGTCTGGGTCC

original cDNA sequence snippet

GGTTGCCCAGCTGATTGTCATAGCATCTGATGAGACTCCTT

altered cDNA sequence snippet

GGTTGCCCAGCTGATTGTCACAGCATCTGATGAGACTCCTT

wildtype AA sequence

MVGTKAWVFS FLVLEVTSVL GRQTMLTQSV RRVQPGKKNP SIFAKPADTL ESPGEWTTWF
NIDYPGGKGD YERLDAIRFY YGDRVCARPL RLEARTTDWT PAGSTGQVVH GSPREGFWCL
NREQRPGQNC SNYTVRFLCP PGSLRRDTER IWSPWSPWSK CSAACGQTGV QTRTRICLAE
MVSLCSEASE EGQHCMGQDC TACDLTCPMG QVNADCDACM CQDFMLHGAV SLPGGAPASG
AAIYLLTKTP KLLTQTDSDG RFRIPGLCPD GKSILKITKV KFAPIVLTMP KTSLKAATIK
AEFVRAETPY MVMNPETKAR RAGQSVSLCC KATGKPRPDK YFWYHNDTLL DPSLYKHESK
LVLRKLQQHQ AGEYFCKAQS DAGAVKSKVA QLIVIASDET PCNPVPESYL IRLPHDCFQN
ATNSFYYDVG RCPVKTCAGQ QDNGIRCRDA VQNCCGISKT EEREIQCSGY TLPTKVAKEC
SCQRCTETRS IVRGRVSAAD NGEPMRFGHV YMGNSRVSMT GYKGTFTLHV PQDTERLVLT
FVDRLQKFVN TTKVLPFNKK GSAVFHEIKM LRRKKPITLE AMETNIIPLG EVVGEDPMAE
LEIPSRSFYR QNGEPYIGKV KASVTFLDPR NISTATAAQT DLNFINDEGD TFPLRTYGMF
SVDFRDEVTS EPLNAGKVKV HLDSTQVKMP EHISTVKLWS LNPDTGLWEE EGDFKFENQR
RNKREDRTFL VGNLEIRERR LFNLDVPESR RCFVKVRAYR SERFLPSEQI QGVVISVINL
EPRTGFLSNP RAWGRFDSVI TGPNGACVPA FCDDQSPDAY SAYVLASLAG EELQAVESSP
KFNPNAIGVP QPYLNKLNYR RTDHEDPRVK KTAFQISMAK PRPNSAEESN GPIYAFENLR
ACEEAPPSAA HFRFYQIEGD RYDYNTVPFN EDDPMSWTED YLAWWPKPME FRACYIKVKI
VGPLEVNVRS RNMGGTHRQT VGKLYGIRDV RSTRDRDQPN VSAACLEFKC SGMLYDQDRV
DRTLVKVIPQ GSCRRASVNP MLHEYLVNHL PLAVNNDTSE YTMLAPLDPL GHNYGIYTVT
DQDPRTAKEI ALGRCFDGTS DGSSRIMKSN VGVALTFNCV ERQVGRQSAF QYLQSTPAQS
PAAGTVQGRV PSRRQQRASR GGQRQGGVVA SLRFPRVAQQ PLIN*

mutated AA sequence

MVGTKAWVFS FLVLEVTSVL GRQTMLTQSV RRVQPGKKNP SIFAKPADTL ESPGEWTTWF
NIDYPGGKGD YERLDAIRFY YGDRVCARPL RLEARTTDWT PAGSTGQVVH GSPREGFWCL
NREQRPGQNC SNYTVRFLCP PGSLRRDTER IWSPWSPWSK CSAACGQTGV QTRTRICLAE
MVSLCSEASE EGQHCMGQDC TACDLTCPMG QVNADCDACM CQDFMLHGAV SLPGGAPASG
AAIYLLTKTP KLLTQTDSDG RFRIPGLCPD GKSILKITKV KFAPIVLTMP KTSLKAATIK
AEFVRAETPY MVMNPETKAR RAGQSVSLCC KATGKPRPDK YFWYHNDTLL DPSLYKHESK
LVLRKLQQHQ AGEYFCKAQS DAGAVKSKVA QLIVTASDET PCNPVPESYL IRLPHDCFQN
ATNSFYYDVG RCPVKTCAGQ QDNGIRCRDA VQNCCGISKT EEREIQCSGY TLPTKVAKEC
SCQRCTETRS IVRGRVSAAD NGEPMRFGHV YMGNSRVSMT GYKGTFTLHV PQDTERLVLT
FVDRLQKFVN TTKVLPFNKK GSAVFHEIKM LRRKKPITLE AMETNIIPLG EVVGEDPMAE
LEIPSRSFYR QNGEPYIGKV KASVTFLDPR NISTATAAQT DLNFINDEGD TFPLRTYGMF
SVDFRDEVTS EPLNAGKVKV HLDSTQVKMP EHISTVKLWS LNPDTGLWEE EGDFKFENQR
RNKREDRTFL VGNLEIRERR LFNLDVPESR RCFVKVRAYR SERFLPSEQI QGVVISVINL
EPRTGFLSNP RAWGRFDSVI TGPNGACVPA FCDDQSPDAY SAYVLASLAG EELQAVESSP
KFNPNAIGVP QPYLNKLNYR RTDHEDPRVK KTAFQISMAK PRPNSAEESN GPIYAFENLR
ACEEAPPSAA HFRFYQIEGD RYDYNTVPFN EDDPMSWTED YLAWWPKPME FRACYIKVKI
VGPLEVNVRS RNMGGTHRQT VGKLYGIRDV RSTRDRDQPN VSAACLEFKC SGMLYDQDRV
DRTLVKVIPQ GSCRRASVNP MLHEYLVNHL PLAVNNDTSE YTMLAPLDPL GHNYGIYTVT
DQDPRTAKEI ALGRCFDGTS DGSSRIMKSN VGVALTFNCV ERQVGRQSAF QYLQSTPAQS
PAAGTVQGRV PSRRQQRASR GGQRQGGVVA SLRFPRVAQQ PLIN*

speed

0.51 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems