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: ENST00000423345
Querying Taster for transcript #2: ENST00000255612
MT speed 0 s - this script 4.116727 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PRAM1	polymorphism_automatic	2.89768209427166e-14	simple_aae		affected		G135E	single base exchange	rs58466313		show file
PRAM1	polymorphism_automatic	2.89768209427166e-14	simple_aae		affected		G135E	single base exchange	rs58466313		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999971 (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)

chr19:8564288C>TN/A show variant in all transcripts IGV

HGNC symbol

PRAM1

Ensembl transcript ID

ENST00000423345

Genbank transcript ID

NM_032152

UniProt peptide

Q96QH2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.404G>A
cDNA.451G>A
g.3235G>A

AA changes

G135E Score: 98 explain score(s)

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

135

frameshift

known variant

Reference ID: rs58466313

database	homozygous (T/T)	heterozygous	allele carriers
1000G	221	371	592
ExAC	1113	3085	4198

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.758	0.006
	0.285	0.003
(flanking)	0.443	0.002

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	3230	0.87	mu: CCACAGCTGGAGGCC	ACAG\|ctgg
Donor gained	3236	0.35	mu: CTGGAGGCCACTCCG	GGAG\|gcca

distance from splice site

377

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

135

mutated

not conserved

135

Ptroglodytes

not conserved

ENSPTRG00000010425

111

Mmulatta

not conserved

ENSMMUG00000018808

136

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000032739

133

Ggallus

no alignment

ENSGALG00000021886

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000088017

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
27	511	COMPBIAS	Pro-rich.	lost
70	165	REGION	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.	lost
130	141	REPEAT	6.	lost
142	153	REPEAT	7.	might get lost (downstream of altered splice site)
154	165	REPEAT	8.	might get lost (downstream of altered splice site)
382	382	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
622	696	DOMAIN	SH3.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2013 / 2013

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

671 / 671

position of stopcodon in wt / mu cDNA

2060 / 2060

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

48 / 48

chromosome

strand

-1

last intron/exon boundary

2023

theoretical NMD boundary in CDS

1925

length of CDS

2013

coding sequence (CDS) position

404

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

451

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

3235

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

8564288

original gDNA sequence snippet

CAAGAAGTTCCCACAGCTGGGGGCCACTCCGTTTCCAAGGA

altered gDNA sequence snippet

CAAGAAGTTCCCACAGCTGGAGGCCACTCCGTTTCCAAGGA

original cDNA sequence snippet

CAAGAAGTTCCCACAGCTGGGGGCCACTCCGTTTCCAAGGA

altered cDNA sequence snippet

CAAGAAGTTCCCACAGCTGGAGGCCACTCCGTTTCCAAGGA

wildtype AA sequence

MAHHLPAAME SHQDFRSIKA KFQASQPEPS DLPKKPPKPE FGKLKKFSQP ELSEHPKKAP
LPEFGAVSLK PPPPEVTDLP KKPPPPEVTD LPKKPPPPEV TDLPKKPPPP EVTDLPKKPS
KLELSDLSKK FPQLGATPFP RKPLQPEVGE APLKASLPEP GAPARKPLQP DELSHPARPP
SEPKSGAFPR KLWQPEAGEA TPRSPQPELS TFPKKPAQPE FNVYPKKPPQ PQVGGLPKKS
VPQPEFSEAA QTPLWKPQSS EPKRDSSAFP KKASQPPLSD FPKKPPQPEL GDLTRTSSEP
EVSVLPKRPR PAEFKALSKK PPQPELGGLP RTSSEPEFNS LPRKLLQPER RGPPRKFSQP
EPSAVLKRHP QPEFFGDLPR KPPLPSSASE SSLPAAVAGF SSRHPLSPGF GAAGTPRWRS
GGLVHSGGAR PGLRPSHPPR RRPLPPASSL GHPPAKPPLP PGPVDMQSFR RPSAASIDLR
RTRSAAGLHF QDRQPEDIPQ VPDEIYELYD DVEPRDDSSP SPKGRDEAPS VQQAARRPPQ
DPALRKEKDP QPQQLPPMDP KLLKQLRKAE KAEREFRKKF KFEGEIVVHT KMMIDPNAKT
RRGGGKHLGI RRGEILEVIE FTSNEEMLCR DPKGKYGYVP RTALLPLETE VYDDVDFCDP
LENQPLPLGR *

mutated AA sequence

MAHHLPAAME SHQDFRSIKA KFQASQPEPS DLPKKPPKPE FGKLKKFSQP ELSEHPKKAP
LPEFGAVSLK PPPPEVTDLP KKPPPPEVTD LPKKPPPPEV TDLPKKPPPP EVTDLPKKPS
KLELSDLSKK FPQLEATPFP RKPLQPEVGE APLKASLPEP GAPARKPLQP DELSHPARPP
SEPKSGAFPR KLWQPEAGEA TPRSPQPELS TFPKKPAQPE FNVYPKKPPQ PQVGGLPKKS
VPQPEFSEAA QTPLWKPQSS EPKRDSSAFP KKASQPPLSD FPKKPPQPEL GDLTRTSSEP
EVSVLPKRPR PAEFKALSKK PPQPELGGLP RTSSEPEFNS LPRKLLQPER RGPPRKFSQP
EPSAVLKRHP QPEFFGDLPR KPPLPSSASE SSLPAAVAGF SSRHPLSPGF GAAGTPRWRS
GGLVHSGGAR PGLRPSHPPR RRPLPPASSL GHPPAKPPLP PGPVDMQSFR RPSAASIDLR
RTRSAAGLHF QDRQPEDIPQ VPDEIYELYD DVEPRDDSSP SPKGRDEAPS VQQAARRPPQ
DPALRKEKDP QPQQLPPMDP KLLKQLRKAE KAEREFRKKF KFEGEIVVHT KMMIDPNAKT
RRGGGKHLGI RRGEILEVIE FTSNEEMLCR DPKGKYGYVP RTALLPLETE VYDDVDFCDP
LENQPLPLGR *

speed

1.12 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: 0.999999999999971 (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)

chr19:8564288C>TN/A show variant in all transcripts IGV

HGNC symbol

PRAM1

Ensembl transcript ID

ENST00000255612

Genbank transcript ID

N/A

UniProt peptide

Q96QH2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.404G>A
cDNA.424G>A
g.3235G>A

AA changes

G135E Score: 98 explain score(s)

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

135

frameshift

known variant

Reference ID: rs58466313

database	homozygous (T/T)	heterozygous	allele carriers
1000G	221	371	592
ExAC	1113	3085	4198

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.758	0.006
	0.285	0.003
(flanking)	0.443	0.002

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	3230	0.87	mu: CCACAGCTGGAGGCC	ACAG\|ctgg
Donor gained	3236	0.35	mu: CTGGAGGCCACTCCG	GGAG\|gcca

distance from splice site

377

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

135

mutated

not conserved

135

Ptroglodytes

not conserved

ENSPTRG00000010425

111

Mmulatta

not conserved

ENSMMUG00000018808

136

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000032739

133

Ggallus

no alignment

ENSGALG00000021886

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000088017

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
27	511	COMPBIAS	Pro-rich.	lost
70	165	REGION	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.	lost
130	141	REPEAT	6.	lost
142	153	REPEAT	7.	might get lost (downstream of altered splice site)
154	165	REPEAT	8.	might get lost (downstream of altered splice site)
382	382	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
622	696	DOMAIN	SH3.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2010 / 2010

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

670 / 670

position of stopcodon in wt / mu cDNA

2030 / 2030

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

21 / 21

chromosome

strand

-1

last intron/exon boundary

1993

theoretical NMD boundary in CDS

1922

length of CDS

2010

coding sequence (CDS) position

404

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

424

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

3235

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

8564288

original gDNA sequence snippet

CAAGAAGTTCCCACAGCTGGGGGCCACTCCGTTTCCAAGGA

altered gDNA sequence snippet

CAAGAAGTTCCCACAGCTGGAGGCCACTCCGTTTCCAAGGA

original cDNA sequence snippet

CAAGAAGTTCCCACAGCTGGGGGCCACTCCGTTTCCAAGGA

altered cDNA sequence snippet

CAAGAAGTTCCCACAGCTGGAGGCCACTCCGTTTCCAAGGA

wildtype AA sequence

MAHHLPAAME SHQDFRSIKA KFQASQPEPS DLPKKPPKPE FGKLKKFSQP ELSEHPKKAP
LPEFGAVSLK PPPPEVTDLP KKPPPPEVTD LPKKPPPPEV TDLPKKPPPP EVTDLPKKPS
KLELSDLSKK FPQLGATPFP RKPLQPEVGE APLKASLPEP GAPARKPLQP DELSHPARPP
SEPKSGAFPR KLWQPEAGEA TPRSPQPELS TFPKKPAQPE FNVYPKKPPQ PQVGGLPKKS
VPQPEFSEAA QTPLWKPQSS EPKRDSSAFP KKASQPPLSD FPKKPPQPEL GDLTRTSSEP
EVSVLPKRPR PAEFKALSKK PPQPELGGLP RTSSEPEFNS LPRKLLQPER RGPPRKFSQP
EPSAVLKRHP QPEFFGDLPR KPPLPSSASE SSLPAAVAGF SSRHPLSPGF GAAGTPRWRS
GGLVHSGGAR PGLRPSHPPR RRPLPPASSL GHPPAKPPLP PGPVDMQSFR RPSAASIDLR
RTRSAAGLHF QDRQPEDIPV PDEIYELYDD VEPRDDSSPS PKGRDEAPSV QQAARRPPQD
PALRKEKDPQ PQQLPPMDPK LLKQLRKAEK AEREFRKKFK FEGEIVVHTK MMIDPNAKTR
RGGGKHLGIR RGEILEVIEF TSNEEMLCRD PKGKYGYVPR TALLPLETEV YDDVDFCDPL
ENQPLPLGR*

mutated AA sequence

MAHHLPAAME SHQDFRSIKA KFQASQPEPS DLPKKPPKPE FGKLKKFSQP ELSEHPKKAP
LPEFGAVSLK PPPPEVTDLP KKPPPPEVTD LPKKPPPPEV TDLPKKPPPP EVTDLPKKPS
KLELSDLSKK FPQLEATPFP RKPLQPEVGE APLKASLPEP GAPARKPLQP DELSHPARPP
SEPKSGAFPR KLWQPEAGEA TPRSPQPELS TFPKKPAQPE FNVYPKKPPQ PQVGGLPKKS
VPQPEFSEAA QTPLWKPQSS EPKRDSSAFP KKASQPPLSD FPKKPPQPEL GDLTRTSSEP
EVSVLPKRPR PAEFKALSKK PPQPELGGLP RTSSEPEFNS LPRKLLQPER RGPPRKFSQP
EPSAVLKRHP QPEFFGDLPR KPPLPSSASE SSLPAAVAGF SSRHPLSPGF GAAGTPRWRS
GGLVHSGGAR PGLRPSHPPR RRPLPPASSL GHPPAKPPLP PGPVDMQSFR RPSAASIDLR
RTRSAAGLHF QDRQPEDIPV PDEIYELYDD VEPRDDSSPS PKGRDEAPSV QQAARRPPQD
PALRKEKDPQ PQQLPPMDPK LLKQLRKAEK AEREFRKKFK FEGEIVVHTK MMIDPNAKTR
RGGGKHLGIR RGEILEVIEF TSNEEMLCRD PKGKYGYVPR TALLPLETEV YDDVDFCDPL
ENQPLPLGR*

speed

0.97 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems