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: ENST00000342740
Querying Taster for transcript #2: ENST00000334420
MT speed 0 s - this script 3.564074 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CARMIL3	polymorphism_automatic	1.00159896160301e-05	simple_aae		affected		L1022M	single base exchange	rs10146906		show file
CARMIL3	polymorphism_automatic	4.16261537760088e-05	simple_aae		affected		L118M	single base exchange	rs10146906		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999989984010384 (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)

chr14:24533539C>AN/A show variant in all transcripts IGV

HGNC symbol

CARMIL3

Ensembl transcript ID

ENST00000342740

Genbank transcript ID

NM_138360

UniProt peptide

Q8ND23

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3064C>A
cDNA.3218C>A
g.12334C>A

AA changes

L1022M Score: 15 explain score(s)

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

1022

frameshift

known variant

Reference ID: rs10146906

database	homozygous (A/A)	heterozygous	allele carriers
1000G	373	1000	1373
ExAC	9727	13313	23040

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.38	1
	1.33	1
(flanking)	3.683	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 gained	12330	0.97	mu: CGAAGGGTCATGGAG	AAGG\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1022

mutated

all conserved

1022

Ptroglodytes

all conserved

ENSPTRG00000006188

1022

Mmulatta

all conserved

ENSMMUG00000007357

1023

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000022211

1021

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000086990

1006

Dmelanogaster

no alignment

FBgn0033212

n/a

Celegans

no alignment

K07G5.1

n/a

Xtropicalis

no alignment

ENSXETG00000022577

n/a

protein features

start (aa)	end (aa)	feature	details
1062	1062	CONFLICT	R -> W (in Ref. 2; CAD38886).	might get lost (downstream of altered splice site)
1070	1098	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
1204	1208	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4119 / 4119

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

1373 / 1373

position of stopcodon in wt / mu cDNA

4273 / 4273

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

155 / 155

chromosome

strand

last intron/exon boundary

4248

theoretical NMD boundary in CDS

4043

length of CDS

4119

coding sequence (CDS) position

3064

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

3218

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

12334

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

24533539

original gDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCCTGGAGGAAAGTTCTAGGTGT

altered gDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCATGGAGGAAAGTTCTAGGTGT

original cDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCCTGGAGGAAAGTTCTAGCTAC

altered cDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCATGGAGGAAAGTTCTAGCTAC

wildtype AA sequence

MAKPSVELTR ELQDSIRRCL SQGAVLQQHH VKLETKPKKF EDRVLALTSW RLHLFLLKVP
AKVESSFNVL EIRAFNTLSQ NQILVETERG MVSMRLPSAE SVDQVTRHVS SALSKVCPGP
GCLIRRGNAD TPEGPRDTSP NSETSTSTTH SVCGGFSETY AALCDYNGLH CREEVQWDVD
TIYHAEDNRE FNLLDFSHLE SRDLALMVAA LAYNQWFTKL YCKDLRLGSE VLEQVLHTLS
KSGSLEELVL DNAGLKTDFV QKLAGVFGEN GSCVLHALTL SHNPIEDKGF LSLSQQLLCF
PSGLTKLCLA KTAISPRGLQ ALGQTFGANP AFASSLRYLD LSKNPGLLAT DEANALYSFL
AQPNALVHLD LSGTDCVIDL LLGALLHGCC SHLTYLNLAR NSCSHRKGRE APPAFKQFFS
SAYTLSHVNL SATKLPLEAL RALLQGLSLN SHLSDLHLDL SSCELRSAGA QALQEQLGAV
TCVGSLDLSD NGFDSDLLTL VPALGKNKSL KHLFLGKNFN VKAKTLEEIL HKLVQLIQEE
DCSLQSLSVA DSRLKLRTSI LINALGSNTC LAKVDLSGNG MEDIGAKMLS KALQINSSLR
TILWDRNNTS ALGFLDIARA LESNHTLRFM SFPVSDISQA YRSAPERTED VWQKIQWCLV
RNNHSQTCPQ EQAFRLQQGL VTSSAEQMLQ RLCGRVQEEV RALRLCPLEP VQDELLYARD
LIKDAKNSRA LFPSLYELGH VLANDGPVRQ RLESVASEVS KAVDKELQVI LESMVSLTQE
LCPVAMRVAE GHNKMLSNVA ERVTVPRNFI RGALLEQAGQ DIQNKLDEVK LSVVTYLTSS
IVDEILQELY HSHKSLARHL TQLRTLSDPP GCPGQGQDLS SRGRGRNHDH EETTDDELGT
NIDTMAIKKQ KRCRKIRPVS AFISGSPQDM ESQLGNLGIP PGWFSGLGGS QPTASGSWEG
LSELPTHGYK LRHQTQGRPR PPRTTPPGPG RPSMPAPGTR QENGMATRLD EGLEDFFSRR
VLEESSSYPR TLRTVRPGLS EAPLPPLQKK RRRGLFHFRR PRSFKGDRGP GSPTTGLLLP
PPPPPPPTQE SPPSPDPPSL GNNSSPCWSP EEESSLLPGF GGGRGPSFRR KMGTEGSEPG
EGGPAPGTAQ QPRVHGVALP GLERAKGWSF DGKREGPGPD QEGSTQAWQK RRSSDDAGPG
SWKPPPPPQS TKPSFSAMRR AEATWHIAEE SAPNHSCQSP SPASQDGEEE KEGTLFPERT
LPARNAKLQD PALAPWPPKP VAVPRGRQPP QEPGVREEAE AGDAAPGVNK PRLRLSSQQD
QEEPEVQGPP DPGRRTAPLK PKRTRRAQSC DKLEPDRRRP PDPTGTSEPG TD*

mutated AA sequence

MAKPSVELTR ELQDSIRRCL SQGAVLQQHH VKLETKPKKF EDRVLALTSW RLHLFLLKVP
AKVESSFNVL EIRAFNTLSQ NQILVETERG MVSMRLPSAE SVDQVTRHVS SALSKVCPGP
GCLIRRGNAD TPEGPRDTSP NSETSTSTTH SVCGGFSETY AALCDYNGLH CREEVQWDVD
TIYHAEDNRE FNLLDFSHLE SRDLALMVAA LAYNQWFTKL YCKDLRLGSE VLEQVLHTLS
KSGSLEELVL DNAGLKTDFV QKLAGVFGEN GSCVLHALTL SHNPIEDKGF LSLSQQLLCF
PSGLTKLCLA KTAISPRGLQ ALGQTFGANP AFASSLRYLD LSKNPGLLAT DEANALYSFL
AQPNALVHLD LSGTDCVIDL LLGALLHGCC SHLTYLNLAR NSCSHRKGRE APPAFKQFFS
SAYTLSHVNL SATKLPLEAL RALLQGLSLN SHLSDLHLDL SSCELRSAGA QALQEQLGAV
TCVGSLDLSD NGFDSDLLTL VPALGKNKSL KHLFLGKNFN VKAKTLEEIL HKLVQLIQEE
DCSLQSLSVA DSRLKLRTSI LINALGSNTC LAKVDLSGNG MEDIGAKMLS KALQINSSLR
TILWDRNNTS ALGFLDIARA LESNHTLRFM SFPVSDISQA YRSAPERTED VWQKIQWCLV
RNNHSQTCPQ EQAFRLQQGL VTSSAEQMLQ RLCGRVQEEV RALRLCPLEP VQDELLYARD
LIKDAKNSRA LFPSLYELGH VLANDGPVRQ RLESVASEVS KAVDKELQVI LESMVSLTQE
LCPVAMRVAE GHNKMLSNVA ERVTVPRNFI RGALLEQAGQ DIQNKLDEVK LSVVTYLTSS
IVDEILQELY HSHKSLARHL TQLRTLSDPP GCPGQGQDLS SRGRGRNHDH EETTDDELGT
NIDTMAIKKQ KRCRKIRPVS AFISGSPQDM ESQLGNLGIP PGWFSGLGGS QPTASGSWEG
LSELPTHGYK LRHQTQGRPR PPRTTPPGPG RPSMPAPGTR QENGMATRLD EGLEDFFSRR
VMEESSSYPR TLRTVRPGLS EAPLPPLQKK RRRGLFHFRR PRSFKGDRGP GSPTTGLLLP
PPPPPPPTQE SPPSPDPPSL GNNSSPCWSP EEESSLLPGF GGGRGPSFRR KMGTEGSEPG
EGGPAPGTAQ QPRVHGVALP GLERAKGWSF DGKREGPGPD QEGSTQAWQK RRSSDDAGPG
SWKPPPPPQS TKPSFSAMRR AEATWHIAEE SAPNHSCQSP SPASQDGEEE KEGTLFPERT
LPARNAKLQD PALAPWPPKP VAVPRGRQPP QEPGVREEAE AGDAAPGVNK PRLRLSSQQD
QEEPEVQGPP DPGRRTAPLK PKRTRRAQSC DKLEPDRRRP PDPTGTSEPG TD*

speed

0.84 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: 0.999958373846224 (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)

chr14:24533539C>AN/A show variant in all transcripts IGV

HGNC symbol

CARMIL3

Ensembl transcript ID

ENST00000334420

Genbank transcript ID

N/A

UniProt peptide

Q8ND23

alteration type

single base exchange

alteration region

CDS

DNA changes

c.352C>A
cDNA.3221C>A
g.12334C>A

AA changes

L118M Score: 15 explain score(s)

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

118

frameshift

known variant

Reference ID: rs10146906

database	homozygous (A/A)	heterozygous	allele carriers
1000G	373	1000	1373
ExAC	9727	13313	23040

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.38	1
	1.33	1
(flanking)	3.683	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 gained	12330	0.97	mu: CGAAGGGTCATGGAG	AAGG\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

118

mutated

all conserved

118

Ptroglodytes

all conserved

ENSPTRG00000006188

1022

Mmulatta

all conserved

ENSMMUG00000007357

1023

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000022211

1021

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000086990

1010

Dmelanogaster

no alignment

FBgn0033212

n/a

Celegans

all conserved

K07G5.1

861

Xtropicalis

no alignment

ENSXETG00000022577

n/a

protein features

start (aa)	end (aa)	feature	details
244	264	REPEAT	LRR 1.	might get lost (downstream of altered splice site)
274	295	REPEAT	LRR 2.	might get lost (downstream of altered splice site)
303	323	REPEAT	LRR 3.	might get lost (downstream of altered splice site)
335	357	REPEAT	LRR 4.	might get lost (downstream of altered splice site)
365	385	REPEAT	LRR 5.	might get lost (downstream of altered splice site)
392	413	REPEAT	LRR 6.	might get lost (downstream of altered splice site)
424	444	REPEAT	LRR 7.	might get lost (downstream of altered splice site)
455	475	REPEAT	LRR 8.	might get lost (downstream of altered splice site)
482	501	REPEAT	LRR 9.	might get lost (downstream of altered splice site)
509	530	REPEAT	LRR 10.	might get lost (downstream of altered splice site)
1062	1062	CONFLICT	R -> W (in Ref. 2; CAD38886).	might get lost (downstream of altered splice site)
1070	1098	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
1204	1208	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1278 / 1278

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

426 / 426

position of stopcodon in wt / mu cDNA

4147 / 4147

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

2870 / 2870

chromosome

strand

last intron/exon boundary

4122

theoretical NMD boundary in CDS

1202

length of CDS

1278

coding sequence (CDS) position

352

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

3221

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

12334

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

24533539

original gDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCCTGGAGGAAAGTTCTAGGTGT

altered gDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCATGGAGGAAAGTTCTAGGTGT

original cDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCCTGGAGGAAAGTTCTAGCTAC

altered cDNA sequence snippet

ACTTCTTCAGCCGAAGGGTCATGGAGGAAAGTTCTAGCTAC

wildtype AA sequence

MAIKKQKRCR KIRPVSAFIS GSPQDMESQL GNLGIPPGWF SGLGGSQPTA SGSWEGLSEL
PTHGYKLRHQ TQGRPRPPRT TPPGPGRPSM PAPGTRQENG MATRLDEGLE DFFSRRVLEE
SSSYPRTLRT VRPGLSEAPL PPLQKKRRRG LFHFRRPRSF KGDRGPGSPT TGLLLPPPPP
PPPTQESPPS PDPPSLGNNS SPCWSPEEES SLLPGFGGGR GPSFRRKMGP GPDQEGSTQA
WQKRRSSDDA GPGSWKPPPP PQSTKPSFSA MRRAEATWHI AEESAPNHSC QSPSPASQDG
EEEKEGTLFP ERTLPARNAK LQDPALAPWP PKPVAVPRGR QPPQEPGVRE EAEAGDAAPG
VNKPRLRLSS QQDQEEPEVQ GPPDPGRRTA PLKPKRTRRA QSCDKLEPDR RRPPDPTGTS
EPGTD*

mutated AA sequence

MAIKKQKRCR KIRPVSAFIS GSPQDMESQL GNLGIPPGWF SGLGGSQPTA SGSWEGLSEL
PTHGYKLRHQ TQGRPRPPRT TPPGPGRPSM PAPGTRQENG MATRLDEGLE DFFSRRVMEE
SSSYPRTLRT VRPGLSEAPL PPLQKKRRRG LFHFRRPRSF KGDRGPGSPT TGLLLPPPPP
PPPTQESPPS PDPPSLGNNS SPCWSPEEES SLLPGFGGGR GPSFRRKMGP GPDQEGSTQA
WQKRRSSDDA GPGSWKPPPP PQSTKPSFSA MRRAEATWHI AEESAPNHSC QSPSPASQDG
EEEKEGTLFP ERTLPARNAK LQDPALAPWP PKPVAVPRGR QPPQEPGVRE EAEAGDAAPG
VNKPRLRLSS QQDQEEPEVQ GPPDPGRRTA PLKPKRTRRA QSCDKLEPDR RRPPDPTGTS
EPGTD*

speed

0.73 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems