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: ENST00000259883
Querying Taster for transcript #2: ENST00000405948
MT speed 0 s - this script 3.354094 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PGBD1	polymorphism_automatic	2.19782106958277e-07	simple_aae		affected		I678V	single base exchange	rs1997660		show file
PGBD1	polymorphism_automatic	2.19782106958277e-07	simple_aae		affected		I678V	single base exchange	rs1997660		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999780217893 (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)

chr6:28269663A>GN/A show variant in all transcripts IGV

HGNC symbol

PGBD1

Ensembl transcript ID

ENST00000259883

Genbank transcript ID

NM_001184743

UniProt peptide

Q96JS3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2032A>G
cDNA.2437A>G
g.20350A>G

AA changes

I678V Score: 29 explain score(s)

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

678

frameshift

known variant

Reference ID: rs1997660

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1027	909	1936
ExAC	11717	9333	21050

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.061	0.871
	0.806	0.902
(flanking)	2.311	0.913

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
Acc marginally increased	20349	wt: 0.9323 / mu: 0.9653 (marginal change - not scored)	wt: AGAGGGTATTTTGATTTCCGAATAGAAGAAAACAATGAGAT mu: AGAGGGTATTTTGATTTCCGAGTAGAAGAAAACAATGAGAT	ccga\|ATAG
Donor gained	20344	0.48	mu: TTGATTTCCGAGTAG	GATT\|tccg
Donor gained	20349	0.83	mu: TTCCGAGTAGAAGAA	CCGA\|gtag

distance from splice site

664

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

678

mutated

all conserved

678

Ptroglodytes

all conserved

ENSPTRG00000017873

678

Mmulatta

all conserved

ENSMMUG00000007228

678

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000055313

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2430 / 2430

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

810 / 810

position of stopcodon in wt / mu cDNA

2835 / 2835

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

406 / 406

chromosome

strand

last intron/exon boundary

1275

theoretical NMD boundary in CDS

819

length of CDS

2430

coding sequence (CDS) position

2032

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

2437

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

20350

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

28269663

original gDNA sequence snippet

GAGGGTATTTTGATTTCCGAATAGAAGAAAACAATGAGATA

altered gDNA sequence snippet

GAGGGTATTTTGATTTCCGAGTAGAAGAAAACAATGAGATA

original cDNA sequence snippet

GAGGGTATTTTGATTTCCGAATAGAAGAAAACAATGAGATA

altered cDNA sequence snippet

GAGGGTATTTTGATTTCCGAGTAGAAGAAAACAATGAGATA

wildtype AA sequence

MYEALPGPAP ENEDGLVKVK EEDPTWEQVC NSQEGSSHTQ EICRLRFRHF CYQEAHGPQE
ALAQLRELCH QWLRPEMHTK EQIMELLVLE QFLTILPKEL QPCVKTYPLE SGEEAVTVLE
NLETGSGDTG QQASVYIQGQ DMHPMVAEYQ GVSLECQSLQ LLPGITTLKC EPPQRPQGNP
QEVSGPVPHG SAHLQEKNPR DKAVVPVFNP VRSQTLVKTE EETAQAVAAE KWSHLSLTRR
NLCGNSAQET VMSLSPMTEE IVTKDRLFKA KQETSEEMEQ SGEASGKPNR ECAPQIPCST
PIATERTVAH LNTLKDRHPG DLWARMHISS LEYAAGDITR KGRKKDKARV SELLQGLSFS
GDSDVEKDNE PEIQPAQKKL KVSCFPEKSW TKRDIKPNFP SWSALDSGLL NLKSEKLNPV
ELFELFFDDE TFNLIVNETN NYASQKNVSL EVTVQEMRCV FGVLLLSGFM RHPRREMYWE
VSDTDQNLVR DAIRRDRFEL IFSNLHFADN GHLDQKDKFT KLRPLIKQMN KNFLLYAPLE
EYYCFDKSMC ECFDSDQFLN GKPIRIGYKI WCGTTTQGYL VWFEPYQEES TMKVDEDPDL
GLGGNLVMNF ADVLLERGQY PYHLCFDSFF TSVKLLSALK KKGVRATGTI RENRTEKCPL
MNVEHMKKMK RGYFDFRIEE NNEIILCRWY GDGIISLCSN AVGIEPVNEV SCCDADNEEI
PQISQPSIVK VYDECKEGVA KMDQIISKYR VRIRSKKWYS ILVSYMIDVA MNNAWQLHRA
CNPGASLDPL DFRRFVAHFY LEHNAHLSD*

mutated AA sequence

MYEALPGPAP ENEDGLVKVK EEDPTWEQVC NSQEGSSHTQ EICRLRFRHF CYQEAHGPQE
ALAQLRELCH QWLRPEMHTK EQIMELLVLE QFLTILPKEL QPCVKTYPLE SGEEAVTVLE
NLETGSGDTG QQASVYIQGQ DMHPMVAEYQ GVSLECQSLQ LLPGITTLKC EPPQRPQGNP
QEVSGPVPHG SAHLQEKNPR DKAVVPVFNP VRSQTLVKTE EETAQAVAAE KWSHLSLTRR
NLCGNSAQET VMSLSPMTEE IVTKDRLFKA KQETSEEMEQ SGEASGKPNR ECAPQIPCST
PIATERTVAH LNTLKDRHPG DLWARMHISS LEYAAGDITR KGRKKDKARV SELLQGLSFS
GDSDVEKDNE PEIQPAQKKL KVSCFPEKSW TKRDIKPNFP SWSALDSGLL NLKSEKLNPV
ELFELFFDDE TFNLIVNETN NYASQKNVSL EVTVQEMRCV FGVLLLSGFM RHPRREMYWE
VSDTDQNLVR DAIRRDRFEL IFSNLHFADN GHLDQKDKFT KLRPLIKQMN KNFLLYAPLE
EYYCFDKSMC ECFDSDQFLN GKPIRIGYKI WCGTTTQGYL VWFEPYQEES TMKVDEDPDL
GLGGNLVMNF ADVLLERGQY PYHLCFDSFF TSVKLLSALK KKGVRATGTI RENRTEKCPL
MNVEHMKKMK RGYFDFRVEE NNEIILCRWY GDGIISLCSN AVGIEPVNEV SCCDADNEEI
PQISQPSIVK VYDECKEGVA KMDQIISKYR VRIRSKKWYS ILVSYMIDVA MNNAWQLHRA
CNPGASLDPL DFRRFVAHFY LEHNAHLSD*

speed

0.69 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: 0.999999780217893 (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)

chr6:28269663A>GN/A show variant in all transcripts IGV

HGNC symbol

PGBD1

Ensembl transcript ID

ENST00000405948

Genbank transcript ID

NM_032507

UniProt peptide

Q96JS3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2032A>G
cDNA.2452A>G
g.20350A>G

AA changes

I678V Score: 29 explain score(s)

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

678

frameshift

known variant

Reference ID: rs1997660

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1027	909	1936
ExAC	11717	9333	21050

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.061	0.871
	0.806	0.902
(flanking)	2.311	0.913

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
Acc marginally increased	20349	wt: 0.9323 / mu: 0.9653 (marginal change - not scored)	wt: AGAGGGTATTTTGATTTCCGAATAGAAGAAAACAATGAGAT mu: AGAGGGTATTTTGATTTCCGAGTAGAAGAAAACAATGAGAT	ccga\|ATAG
Donor gained	20344	0.48	mu: TTGATTTCCGAGTAG	GATT\|tccg
Donor gained	20349	0.83	mu: TTCCGAGTAGAAGAA	CCGA\|gtag

distance from splice site

663

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

678

mutated

all conserved

678

Ptroglodytes

all conserved

ENSPTRG00000017873

678

Mmulatta

all conserved

ENSMMUG00000007228

678

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000055313

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2430 / 2430

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

810 / 810

position of stopcodon in wt / mu cDNA

2850 / 2850

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

421 / 421

chromosome

strand

last intron/exon boundary

1290

theoretical NMD boundary in CDS

819

length of CDS

2430

coding sequence (CDS) position

2032

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

2452

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

20350

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

28269663

original gDNA sequence snippet

GAGGGTATTTTGATTTCCGAATAGAAGAAAACAATGAGATA

altered gDNA sequence snippet

GAGGGTATTTTGATTTCCGAGTAGAAGAAAACAATGAGATA

original cDNA sequence snippet

GAGGGTATTTTGATTTCCGAATAGAAGAAAACAATGAGATA

altered cDNA sequence snippet

GAGGGTATTTTGATTTCCGAGTAGAAGAAAACAATGAGATA

wildtype AA sequence

mutated AA sequence

MYEALPGPAP ENEDGLVKVK EEDPTWEQVC NSQEGSSHTQ EICRLRFRHF CYQEAHGPQE
ALAQLRELCH QWLRPEMHTK EQIMELLVLE QFLTILPKEL QPCVKTYPLE SGEEAVTVLE
NLETGSGDTG QQASVYIQGQ DMHPMVAEYQ GVSLECQSLQ LLPGITTLKC EPPQRPQGNP
QEVSGPVPHG SAHLQEKNPR DKAVVPVFNP VRSQTLVKTE EETAQAVAAE KWSHLSLTRR
NLCGNSAQET VMSLSPMTEE IVTKDRLFKA KQETSEEMEQ SGEASGKPNR ECAPQIPCST
PIATERTVAH LNTLKDRHPG DLWARMHISS LEYAAGDITR KGRKKDKARV SELLQGLSFS
GDSDVEKDNE PEIQPAQKKL KVSCFPEKSW TKRDIKPNFP SWSALDSGLL NLKSEKLNPV
ELFELFFDDE TFNLIVNETN NYASQKNVSL EVTVQEMRCV FGVLLLSGFM RHPRREMYWE
VSDTDQNLVR DAIRRDRFEL IFSNLHFADN GHLDQKDKFT KLRPLIKQMN KNFLLYAPLE
EYYCFDKSMC ECFDSDQFLN GKPIRIGYKI WCGTTTQGYL VWFEPYQEES TMKVDEDPDL
GLGGNLVMNF ADVLLERGQY PYHLCFDSFF TSVKLLSALK KKGVRATGTI RENRTEKCPL
MNVEHMKKMK RGYFDFRVEE NNEIILCRWY GDGIISLCSN AVGIEPVNEV SCCDADNEEI
PQISQPSIVK VYDECKEGVA KMDQIISKYR VRIRSKKWYS ILVSYMIDVA MNNAWQLHRA
CNPGASLDPL DFRRFVAHFY LEHNAHLSD*

speed

0.68 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems