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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000433076
Querying Taster for transcript #2: ENST00000442966
Querying Taster for transcript #3: ENST00000428040
Querying Taster for transcript #4: ENST00000436442
MT speed 4.38 s - this script 4.405406 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RPP21	polymorphism_automatic	1.47599710231816e-11	simple_aae		affected		Q149K	single base exchange	rs974963		show file
RPP21	polymorphism_automatic	1.47599710231816e-11	simple_aae		affected		Q157K	single base exchange	rs974963		show file
RPP21	polymorphism_automatic	1.47599710231816e-11	simple_aae		affected		Q172K	single base exchange	rs974963		show file
RPP21	polymorphism_automatic	1.16120253201846e-06	without_aae		affected			single base exchange	rs974963		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999998524 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30314567C>AN/A show variant in all transcripts IGV

HGNC symbol

RPP21

Ensembl transcript ID

ENST00000442966

Genbank transcript ID

NM_024839

UniProt peptide

Q9H633

alteration type

single base exchange

alteration region

CDS

DNA changes

c.445C>A
cDNA.458C>A
g.1660C>A

AA changes

Q149K Score: 53 explain score(s)

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

149

frameshift

known variant

Reference ID: rs974963

database	homozygous (A/A)	heterozygous	allele carriers
1000G	363	1140	1503
ExAC	5759	21249	27008

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.011	0
	0.92	0.001
(flanking)	-0.968	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	1655	wt: 0.34 / mu: 0.42	wt: AATGCAGACTCAGGG mu: AATGCAGACTAAGGG	TGCA\|gact
Donor marginally increased	1657	wt: 0.5616 / mu: 0.6297 (marginal change - not scored)	wt: TGCAGACTCAGGGTT mu: TGCAGACTAAGGGTT	CAGA\|ctca
Donor gained	1656	0.95	mu: ATGCAGACTAAGGGT	GCAG\|acta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

149

mutated

all conserved

149

Ptroglodytes

all identical

ENSPTRG00000017924

172

Mmulatta

all identical

ENSMMUG00000011680

171

Fcatus

all conserved

ENSFCAG00000002035

170

Mmusculus

all identical

ENSMUSG00000024446

149

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000043404

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000026230

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

465 / 465

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

155 / 155

position of stopcodon in wt / mu cDNA

478 / 478

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

14 / 14

chromosome

strand

last intron/exon boundary

381

theoretical NMD boundary in CDS

317

length of CDS

465

coding sequence (CDS) position

445

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

458

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

1660

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

30314567

original gDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered gDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

original cDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered cDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

wildtype AA sequence

MAGPVKDREA FQRLNFLYQA AHCVLAQDPE NQALARFYCY TERTIAKRLV LRRDPSVKRT
LCRGCSSLLV PGLTCTQRQR RCRGQRWTVQ TCLTCQRSQR FLNDPGHLLW GDRPEAQLGS
QADSKPLQPL PNTAHSISDR LPEEKMQTQG SSNQ*

mutated AA sequence

MAGPVKDREA FQRLNFLYQA AHCVLAQDPE NQALARFYCY TERTIAKRLV LRRDPSVKRT
LCRGCSSLLV PGLTCTQRQR RCRGQRWTVQ TCLTCQRSQR FLNDPGHLLW GDRPEAQLGS
QADSKPLQPL PNTAHSISDR LPEEKMQTKG SSNQ*

speed

1.10 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: 0.99999999998524 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30314567C>AN/A show variant in all transcripts IGV

HGNC symbol

RPP21

Ensembl transcript ID

ENST00000433076

Genbank transcript ID

NM_001199120

UniProt peptide

Q9H633

alteration type

single base exchange

alteration region

CDS

DNA changes

c.469C>A
cDNA.510C>A
g.1660C>A

AA changes

Q157K Score: 53 explain score(s)

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

157

frameshift

known variant

Reference ID: rs974963

database	homozygous (A/A)	heterozygous	allele carriers
1000G	363	1140	1503
ExAC	5759	21249	27008

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.011	0
	0.92	0.001
(flanking)	-0.968	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	1655	wt: 0.34 / mu: 0.42	wt: AATGCAGACTCAGGG mu: AATGCAGACTAAGGG	TGCA\|gact
Donor marginally increased	1657	wt: 0.5616 / mu: 0.6297 (marginal change - not scored)	wt: TGCAGACTCAGGGTT mu: TGCAGACTAAGGGTT	CAGA\|ctca
Donor gained	1656	0.95	mu: ATGCAGACTAAGGGT	GCAG\|acta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

157

mutated

all conserved

157

Ptroglodytes

all identical

ENSPTRG00000017924

172

Mmulatta

all identical

ENSMMUG00000011680

171

Fcatus

all conserved

ENSFCAG00000002035

170

Mmusculus

all identical

ENSMUSG00000024446

149

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000043404

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000026230

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

489 / 489

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

163 / 163

position of stopcodon in wt / mu cDNA

530 / 530

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

42 / 42

chromosome

strand

last intron/exon boundary

433

theoretical NMD boundary in CDS

341

length of CDS

489

coding sequence (CDS) position

469

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

510

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

1660

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

30314567

original gDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered gDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

original cDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered cDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

wildtype AA sequence

MAGPVKDREA FQRLNFLYQA AHCVLAQDPE NQALARFYCY TERTIAKRLV LRRPLSSSAP
RDPSVKRTLC RGCSSLLVPG LTCTQRQRRC RGQRWTVQTC LTCQRSQRFL NDPGHLLWGD
RPEAQLGSQA DSKPLQPLPN TAHSISDRLP EEKMQTQGSS NQ*

mutated AA sequence

MAGPVKDREA FQRLNFLYQA AHCVLAQDPE NQALARFYCY TERTIAKRLV LRRPLSSSAP
RDPSVKRTLC RGCSSLLVPG LTCTQRQRRC RGQRWTVQTC LTCQRSQRFL NDPGHLLWGD
RPEAQLGSQA DSKPLQPLPN TAHSISDRLP EEKMQTKGSS NQ*

speed

1.10 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999998524 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30314567C>AN/A show variant in all transcripts IGV

HGNC symbol

RPP21

Ensembl transcript ID

ENST00000428040

Genbank transcript ID

N/A

UniProt peptide

Q9H633

alteration type

single base exchange

alteration region

CDS

DNA changes

c.514C>A
cDNA.527C>A
g.1660C>A

AA changes

Q172K Score: 53 explain score(s)

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

172

frameshift

known variant

Reference ID: rs974963

database	homozygous (A/A)	heterozygous	allele carriers
1000G	363	1140	1503
ExAC	5759	21249	27008

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.011	0
	0.92	0.001
(flanking)	-0.968	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	1655	wt: 0.34 / mu: 0.42	wt: AATGCAGACTCAGGG mu: AATGCAGACTAAGGG	TGCA\|gact
Donor marginally increased	1657	wt: 0.5616 / mu: 0.6297 (marginal change - not scored)	wt: TGCAGACTCAGGGTT mu: TGCAGACTAAGGGTT	CAGA\|ctca
Donor gained	1656	0.95	mu: ATGCAGACTAAGGGT	GCAG\|acta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

172

mutated

all conserved

172

Ptroglodytes

all identical

ENSPTRG00000017924

172

Mmulatta

all identical

ENSMMUG00000011680

171

Fcatus

all conserved

ENSFCAG00000002035

170

Mmusculus

all identical

ENSMUSG00000024446

149

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000043404

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000026230

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

534 / 534

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

178 / 178

position of stopcodon in wt / mu cDNA

547 / 547

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

14 / 14

chromosome

strand

last intron/exon boundary

450

theoretical NMD boundary in CDS

386

length of CDS

534

coding sequence (CDS) position

514

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

527

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

1660

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

30314567

original gDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered gDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

original cDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered cDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

wildtype AA sequence

MAGPVKDREA FQRLNFLYQV SLRQGPHGDG ARRPRVTAPL PQAAHCVLAQ DPENQALARF
YCYTERTIAK RLVLRRDPSV KRTLCRGCSS LLVPGLTCTQ RQRRCRGQRW TVQTCLTCQR
SQRFLNDPGH LLWGDRPEAQ LGSQADSKPL QPLPNTAHSI SDRLPEEKMQ TQGSSNQ*

mutated AA sequence

MAGPVKDREA FQRLNFLYQV SLRQGPHGDG ARRPRVTAPL PQAAHCVLAQ DPENQALARF
YCYTERTIAK RLVLRRDPSV KRTLCRGCSS LLVPGLTCTQ RQRRCRGQRW TVQTCLTCQR
SQRFLNDPGH LLWGDRPEAQ LGSQADSKPL QPLPNTAHSI SDRLPEEKMQ TKGSSNQ*

speed

1.13 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999998838797468 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30314567C>AN/A show variant in all transcripts IGV

HGNC symbol

RPP21

Ensembl transcript ID

ENST00000436442

Genbank transcript ID

NM_001199121

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.455C>A
g.1660C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs974963

database	homozygous (A/A)	heterozygous	allele carriers
1000G	363	1140	1503
ExAC	5759	21249	27008

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.011	0
	0.92	0.001
(flanking)	-0.968	0

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

splice sites

splice site change occurs after stopcodon (at aa 149)

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	1655	wt: 0.34 / mu: 0.42	wt: AATGCAGACTCAGGG mu: AATGCAGACTAAGGG	TGCA\|gact
Donor marginally increased	1657	wt: 0.5616 / mu: 0.6297 (marginal change - not scored)	wt: TGCAGACTCAGGGTT mu: TGCAGACTAAGGGTT	CAGA\|ctca
Donor gained	1656	0.95	mu: ATGCAGACTAAGGGT	GCAG\|acta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

4 / 4

chromosome

strand

last intron/exon boundary

378

theoretical NMD boundary in CDS

324

length of CDS

435

coding sequence (CDS) position

N/A

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

455

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

1660

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

30314567

original gDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered gDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

original cDNA sequence snippet

CTGAGGAGAAAATGCAGACTCAGGGTTCCAGTAACCAGTGA

altered cDNA sequence snippet

CTGAGGAGAAAATGCAGACTAAGGGTTCCAGTAACCAGTGA

wildtype AA sequence

MAGPVKDREA FQRLNFLYQA AHCVLAQDPE NQALARFYCY TERTIAKRLV LRRDPSVKRT
LCRGCSSLLV PGLTCTQRQR RCRGQRWTVQ TCLTCQRSQR FLNDPGHLLW GDRPEAQLGS
QAGERFQTTT TLAKHSPLHF RPPS*

mutated AA sequence

N/A

speed

1.05 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

Problems