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 7 transcript(s)...
Querying Taster for transcript #1: ENST00000372991
Querying Taster for transcript #2: ENST00000511642
Querying Taster for transcript #3: ENST00000372987
Querying Taster for transcript #4: ENST00000372988
Querying Taster for transcript #5: ENST00000415497
Querying Taster for transcript #6: ENST00000414200
Querying Taster for transcript #7: ENST00000510503
MT speed 0 s - this script 6.135244 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CCND3	polymorphism_automatic	2.38997710511057e-12	simple_aae		affected		S259A	single base exchange	rs1051130		show file
CCND3	polymorphism_automatic	6.92101931321076e-12	simple_aae		affected		S187A	single base exchange	rs1051130		show file
CCND3	polymorphism_automatic	1.45670142615018e-11	simple_aae		affected		S178A	single base exchange	rs1051130		show file
CCND3	polymorphism_automatic	1.45670142615018e-11	simple_aae		affected		S178A	single base exchange	rs1051130		show file
CCND3	polymorphism_automatic	1.45670142615018e-11	simple_aae		affected		S209A	single base exchange	rs1051130		show file
CCND3	polymorphism_automatic	2.41909825504649e-11	simple_aae		affected		S63A	single base exchange	rs1051130		show file
CCND3	polymorphism_automatic	5.0810200491469e-10	simple_aae		affected		L132R	single base exchange	rs1051130		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999761 (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)

chr6:41903782A>CN/A show variant in all transcripts IGV

HGNC symbol

CCND3

Ensembl transcript ID

ENST00000372991

Genbank transcript ID

NM_001760

UniProt peptide

P30281

alteration type

single base exchange

alteration region

CDS

DNA changes

c.775T>G
cDNA.974T>G
g.114314T>G

AA changes

S259A Score: 99 explain score(s)

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

259

frameshift

known variant

Reference ID: rs1051130

database	homozygous (C/C)	heterozygous	allele carriers
1000G	936	1095	2031
ExAC	18016	-3265	14751

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.875	0.144
	-0.033	0.003
(flanking)	-1.762	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 marginally increased	114318	wt: 0.9237 / mu: 0.9307 (marginal change - not scored)	wt: CTCTCAGACCAGCTC mu: CGCTCAGACCAGCTC	CTCA\|gacc
Donor gained	114313	0.50	mu: GAAGCCGCTCAGACC	AGCC\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

259

mutated

all conserved

259

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000004419

259

Fcatus

all conserved

ENSFCAG00000004865

202

Mmusculus

all conserved

ENSMUSG00000034165

259

Ggallus

all identical

ENSGALG00000003485

261

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0010315

Celegans

all identical

Y38F1A.5

303

AEK

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
263	263	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

879 / 879

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

293 / 293

position of stopcodon in wt / mu cDNA

1078 / 1078

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

200 / 200

chromosome

strand

-1

last intron/exon boundary

911

theoretical NMD boundary in CDS

661

length of CDS

879

coding sequence (CDS) position

775

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

974

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

114314

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

41903782

original gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

original cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

wildtype AA sequence

MELLCCEGTR HAPRAGPDPR LLGDQRVLQS LLRLEERYVP RASYFQCVQR EIKPHMRKML
AYWMLEVCEE QRCEEEVFPL AMNYLDRYLS CVPTRKAQLQ LLGAVCMLLA SKLRETTPLT
IEKLCIYTDH AVSPRQLRDW EVLVLGKLKW DLAAVIAHDF LAFILHRLSL PRDRQALVKK
HAQTFLALCA TDYTFAMYPP SMIATGSIGA AVQGLGACSM SGDELTELLA GITGTEVDCL
RACQEQIEAA LRESLREASQ TSSSPAPKAP RGSSSQGPSQ TSTPTDVTAI HL*

mutated AA sequence

speed

0.45 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: 0.999999999993079 (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)

chr6:41903782A>CN/A show variant in all transcripts IGV

HGNC symbol

CCND3

Ensembl transcript ID

ENST00000414200

Genbank transcript ID

NM_001136125

UniProt peptide

P30281

alteration type

single base exchange

alteration region

CDS

DNA changes

c.559T>G
cDNA.665T>G
g.114314T>G

AA changes

S187A Score: 99 explain score(s)

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

187

frameshift

known variant

Reference ID: rs1051130

database	homozygous (C/C)	heterozygous	allele carriers
1000G	936	1095	2031
ExAC	18016	-3265	14751

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.875	0.144
	-0.033	0.003
(flanking)	-1.762	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 marginally increased	114318	wt: 0.9237 / mu: 0.9307 (marginal change - not scored)	wt: CTCTCAGACCAGCTC mu: CGCTCAGACCAGCTC	CTCA\|gacc
Donor gained	114313	0.50	mu: GAAGCCGCTCAGACC	AGCC\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

187

mutated

all conserved

187

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000004419

259

Fcatus

all conserved

ENSFCAG00000004865

202

Mmusculus

all conserved

ENSMUSG00000034165

259

Ggallus

all identical

ENSGALG00000003485

261

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0010315

n/a

Celegans

all identical

Y38F1A.5

303

AEK

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
175	191	HELIX		lost
193	195	HELIX		might get lost (downstream of altered splice site)
200	213	HELIX		might get lost (downstream of altered splice site)
222	233	HELIX		might get lost (downstream of altered splice site)
237	252	HELIX		might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

663 / 663

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

221 / 221

position of stopcodon in wt / mu cDNA

769 / 769

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

107 / 107

chromosome

strand

-1

last intron/exon boundary

602

theoretical NMD boundary in CDS

445

length of CDS

663

coding sequence (CDS) position

559

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

665

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

114314

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

41903782

original gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

original cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

wildtype AA sequence

MELLCCEGTR HAPRAGPDPR LLGDQRVLQS LLRLEERYVP RASYFQCVQR EIKPHMRKML
AYWMLEDWEV LVLGKLKWDL AAVIAHDFLA FILHRLSLPR DRQALVKKHA QTFLALCATD
YTFAMYPPSM IATGSIGAAV QGLGACSMSG DELTELLAGI TGTEVDCLRA CQEQIEAALR
ESLREASQTS SSPAPKAPRG SSSQGPSQTS TPTDVTAIHL *

mutated AA sequence

speed

1.27 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999985433 (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)

chr6:41903782A>CN/A show variant in all transcripts IGV

HGNC symbol

CCND3

Ensembl transcript ID

ENST00000511642

Genbank transcript ID

N/A

UniProt peptide

P30281

alteration type

single base exchange

alteration region

CDS

DNA changes

c.532T>G
cDNA.1284T>G
g.114314T>G

AA changes

S178A Score: 99 explain score(s)

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

178

frameshift

known variant

Reference ID: rs1051130

database	homozygous (C/C)	heterozygous	allele carriers
1000G	936	1095	2031
ExAC	18016	-3265	14751

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.875	0.144
	-0.033	0.003
(flanking)	-1.762	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 marginally increased	114318	wt: 0.9237 / mu: 0.9307 (marginal change - not scored)	wt: CTCTCAGACCAGCTC mu: CGCTCAGACCAGCTC	CTCA\|gacc
Donor gained	114313	0.50	mu: GAAGCCGCTCAGACC	AGCC\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

178

mutated

all conserved

178

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000004419

259

Fcatus

all conserved

ENSFCAG00000004865

202

Mmusculus

all conserved

ENSMUSG00000034165

259

Ggallus

all identical

ENSGALG00000003485

259

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0010315

Celegans

all identical

Y38F1A.5

303

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
175	191	HELIX		lost
193	195	HELIX		might get lost (downstream of altered splice site)
200	213	HELIX		might get lost (downstream of altered splice site)
222	233	HELIX		might get lost (downstream of altered splice site)
237	252	HELIX		might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

636 / 636

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

212 / 212

position of stopcodon in wt / mu cDNA

1388 / 1388

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

753 / 753

chromosome

strand

-1

last intron/exon boundary

1221

theoretical NMD boundary in CDS

418

length of CDS

636

coding sequence (CDS) position

532

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

1284

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

114314

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

41903782

original gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

original cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

wildtype AA sequence

MNYLDRYLSC VPTRKAQLQL LGAVCMLLAS KLRETTPLTI EKLCIYTDHA VSPRQLRDWE
VLVLGKLKWD LAAVIAHDFL AFILHRLSLP RDRQALVKKH AQTFLALCAT DYTFAMYPPS
MIATGSIGAA VQGLGACSMS GDELTELLAG ITGTEVDCLR ACQEQIEAAL RESLREASQT
SSSPAPKAPR GSSSQGPSQT STPTDVTAIH L*

mutated AA sequence

speed

0.98 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999985433 (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)

chr6:41903782A>CN/A show variant in all transcripts IGV

HGNC symbol

CCND3

Ensembl transcript ID

ENST00000372988

Genbank transcript ID

NM_001136017

UniProt peptide

P30281

alteration type

single base exchange

alteration region

CDS

DNA changes

c.532T>G
cDNA.1045T>G
g.114314T>G

AA changes

S178A Score: 99 explain score(s)

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

178

frameshift

known variant

Reference ID: rs1051130

database	homozygous (C/C)	heterozygous	allele carriers
1000G	936	1095	2031
ExAC	18016	-3265	14751

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.875	0.144
	-0.033	0.003
(flanking)	-1.762	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 marginally increased	114318	wt: 0.9237 / mu: 0.9307 (marginal change - not scored)	wt: CTCTCAGACCAGCTC mu: CGCTCAGACCAGCTC	CTCA\|gacc
Donor gained	114313	0.50	mu: GAAGCCGCTCAGACC	AGCC\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

178

mutated

all conserved

178

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000004419

259

Fcatus

all conserved

ENSFCAG00000004865

202

Mmusculus

all conserved

ENSMUSG00000034165

259

Ggallus

all identical

ENSGALG00000003485

259

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0010315

Celegans

all identical

Y38F1A.5

303

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
175	191	HELIX		lost
193	195	HELIX		might get lost (downstream of altered splice site)
200	213	HELIX		might get lost (downstream of altered splice site)
222	233	HELIX		might get lost (downstream of altered splice site)
237	252	HELIX		might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

636 / 636

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

212 / 212

position of stopcodon in wt / mu cDNA

1149 / 1149

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

514 / 514

chromosome

strand

-1

last intron/exon boundary

982

theoretical NMD boundary in CDS

418

length of CDS

636

coding sequence (CDS) position

532

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

1045

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

114314

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

41903782

original gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

original cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

wildtype AA sequence

mutated AA sequence

speed

1.52 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999985433 (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)

chr6:41903782A>CN/A show variant in all transcripts IGV

HGNC symbol

CCND3

Ensembl transcript ID

ENST00000372987

Genbank transcript ID

N/A

UniProt peptide

P30281

alteration type

single base exchange

alteration region

CDS

DNA changes

c.625T>G
cDNA.1145T>G
g.114314T>G

AA changes

S209A Score: 99 explain score(s)

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

209

frameshift

known variant

Reference ID: rs1051130

database	homozygous (C/C)	heterozygous	allele carriers
1000G	936	1095	2031
ExAC	18016	-3265	14751

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.875	0.144
	-0.033	0.003
(flanking)	-1.762	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 marginally increased	114318	wt: 0.9237 / mu: 0.9307 (marginal change - not scored)	wt: CTCTCAGACCAGCTC mu: CGCTCAGACCAGCTC	CTCA\|gacc
Donor gained	114313	0.50	mu: GAAGCCGCTCAGACC	AGCC\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

209

mutated

all conserved

209

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000004419

259

Fcatus

all conserved

ENSFCAG00000004865

202

Mmusculus

all conserved

ENSMUSG00000034165

259

Ggallus

all identical

ENSGALG00000003485

261

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0010315

Celegans

all identical

Y38F1A.5

303

AEK

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
200	213	HELIX		lost
222	233	HELIX		might get lost (downstream of altered splice site)
237	252	HELIX		might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

729 / 729

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

243 / 243

position of stopcodon in wt / mu cDNA

1249 / 1249

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

521 / 521

chromosome

strand

-1

last intron/exon boundary

1082

theoretical NMD boundary in CDS

511

length of CDS

729

coding sequence (CDS) position

625

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

1145

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

114314

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

41903782

original gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

original cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

wildtype AA sequence

MKSAGGSGRS LLPSPRVCEE QRCEEEVFPL AMNYLDRYLS CVPTRKAQLQ LLGAVCMLLA
SKLRETTPLT IEKLCIYTDH AVSPRQLRDW EVLVLGKLKW DLAAVIAHDF LAFILHRLSL
PRDRQALVKK HAQTFLALCA TDYTFAMYPP SMIATGSIGA AVQGLGACSM SGDELTELLA
GITGTEVDCL RACQEQIEAA LRESLREASQ TSSSPAPKAP RGSSSQGPSQ TSTPTDVTAI
HL*

mutated AA sequence

speed

1.35 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999975809 (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)

chr6:41903782A>CN/A show variant in all transcripts IGV

HGNC symbol

CCND3

Ensembl transcript ID

ENST00000415497

Genbank transcript ID

NM_001136126

UniProt peptide

P30281

alteration type

single base exchange

alteration region

CDS

DNA changes

c.187T>G
cDNA.755T>G
g.114314T>G

AA changes

S63A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs1051130

database	homozygous (C/C)	heterozygous	allele carriers
1000G	936	1095	2031
ExAC	18016	-3265	14751

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.875	0.144
	-0.033	0.003
(flanking)	-1.762	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 marginally increased	114318	wt: 0.9237 / mu: 0.9307 (marginal change - not scored)	wt: CTCTCAGACCAGCTC mu: CGCTCAGACCAGCTC	CTCA\|gacc
Donor gained	114313	0.50	mu: GAAGCCGCTCAGACC	AGCC\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000004419

259

Fcatus

all conserved

ENSFCAG00000004865

202

Mmusculus

all conserved

ENSMUSG00000034165

259

Ggallus

all identical

ENSGALG00000003485

261

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0010315

Celegans

all identical

Y38F1A.5

303

AEK

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
27	152	DOMAIN	Cyclin N-terminal.	lost
54	70	HELIX		lost
77	91	HELIX		might get lost (downstream of altered splice site)
96	98	HELIX		might get lost (downstream of altered splice site)
99	114	HELIX		might get lost (downstream of altered splice site)
123	127	HELIX		might get lost (downstream of altered splice site)
128	130	TURN		might get lost (downstream of altered splice site)
134	147	HELIX		might get lost (downstream of altered splice site)
148	150	TURN		might get lost (downstream of altered splice site)
157	160	HELIX		might get lost (downstream of altered splice site)
161	166	HELIX		might get lost (downstream of altered splice site)
172	174	TURN		might get lost (downstream of altered splice site)
175	191	HELIX		might get lost (downstream of altered splice site)
193	195	HELIX		might get lost (downstream of altered splice site)
200	213	HELIX		might get lost (downstream of altered splice site)
222	233	HELIX		might get lost (downstream of altered splice site)
237	252	HELIX		might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

291 / 291

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

97 / 97

position of stopcodon in wt / mu cDNA

859 / 859

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

569 / 569

chromosome

strand

-1

last intron/exon boundary

692

theoretical NMD boundary in CDS

length of CDS

291

coding sequence (CDS) position

187

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

755

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

114314

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

41903782

original gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

original cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

wildtype AA sequence

MYPPSMIATG SIGAAVQGLG ACSMSGDELT ELLAGITGTE VDCLRACQEQ IEAALRESLR
EASQTSSSPA PKAPRGSSSQ GPSQTSTPTD VTAIHL*

mutated AA sequence

MYPPSMIATG SIGAAVQGLG ACSMSGDELT ELLAGITGTE VDCLRACQEQ IEAALRESLR
EAAQTSSSPA PKAPRGSSSQ GPSQTSTPTD VTAIHL*

speed

1.39 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999491898 (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)

chr6:41903782A>CN/A show variant in all transcripts IGV

HGNC symbol

CCND3

Ensembl transcript ID

ENST00000510503

Genbank transcript ID

N/A

UniProt peptide

P30281

alteration type

single base exchange

alteration region

CDS

DNA changes

c.395T>G
cDNA.648T>G
g.114314T>G

AA changes

L132R Score: 102 explain score(s)

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

132

frameshift

known variant

Reference ID: rs1051130

database	homozygous (C/C)	heterozygous	allele carriers
1000G	936	1095	2031
ExAC	18016	-3265	14751

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.875	0.144
	-0.033	0.003
(flanking)	-1.762	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 marginally increased	114318	wt: 0.9237 / mu: 0.9307 (marginal change - not scored)	wt: CTCTCAGACCAGCTC mu: CGCTCAGACCAGCTC	CTCA\|gacc
Donor gained	114313	0.50	mu: GAAGCCGCTCAGACC	AGCC\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

132

mutated

not conserved

132

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000004419

222

CLRA

Fcatus

no alignment

ENSFCAG00000004865

n/a

Mmusculus

no alignment

ENSMUSG00000034165

n/a

Ggallus

no alignment

ENSGALG00000003485

n/a

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0010315

n/a

Celegans

no alignment

Y38F1A.5

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
27	152	DOMAIN	Cyclin N-terminal.	lost
134	147	HELIX		might get lost (downstream of altered splice site)
148	150	TURN		might get lost (downstream of altered splice site)
157	160	HELIX		might get lost (downstream of altered splice site)
161	166	HELIX		might get lost (downstream of altered splice site)
172	174	TURN		might get lost (downstream of altered splice site)
175	191	HELIX		might get lost (downstream of altered splice site)
193	195	HELIX		might get lost (downstream of altered splice site)
200	213	HELIX		might get lost (downstream of altered splice site)
222	233	HELIX		might get lost (downstream of altered splice site)
237	252	HELIX		might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

588 / 588

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

196 / 196

position of stopcodon in wt / mu cDNA

841 / 841

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

254 / 254

chromosome

strand

-1

last intron/exon boundary

585

theoretical NMD boundary in CDS

281

length of CDS

588

coding sequence (CDS) position

395

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

648

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

114314

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

41903782

original gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered gDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

original cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA

altered cDNA sequence snippet

GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA

wildtype AA sequence

MNYLDRYLSC VPTRKAQLQL LGAVCMLLAS KLRETTPLTI EKLCIYTDHA VSPRQLRDWE
VLVLGKLKWD LAAVIAHDFL AFILHRLSLP RDRQALVKKH AQTFLALCAT GLPAGLSGAD
RSCTQGEPQG SLSDQLQPSA QSPPGLQQPR AQPDQHSYRC HSHTPVALER PSGVATKQRR
GRCHPPPCLQ EPHHI*

mutated AA sequence

MNYLDRYLSC VPTRKAQLQL LGAVCMLLAS KLRETTPLTI EKLCIYTDHA VSPRQLRDWE
VLVLGKLKWD LAAVIAHDFL AFILHRLSLP RDRQALVKKH AQTFLALCAT GLPAGLSGAD
RSCTQGEPQG SRSDQLQPSA QSPPGLQQPR AQPDQHSYRC HSHTPVALER PSGVATKQRR
GRCHPPPCLQ EPHHI*

speed

0.37 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems