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: ENST00000558017
Querying Taster for transcript #2: ENST00000329600
MT speed 0 s - this script 3.317208 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GDPGP1	polymorphism_automatic	5.99520433297585e-15	simple_aae		affected		M37T	single base exchange	rs7171194		show file
GDPGP1	polymorphism_automatic	5.99520433297585e-15	simple_aae		affected		M37T	single base exchange	rs7171194		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999994 (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)

chr15:90784250T>CN/A show variant in all transcripts IGV

HGNC symbol

GDPGP1

Ensembl transcript ID

ENST00000558017

Genbank transcript ID

NM_001013657

UniProt peptide

Q6ZNW5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110T>C
cDNA.530T>C
g.7211T>C

AA changes

M37T Score: 81 explain score(s)

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

frameshift

known variant

Reference ID: rs7171194

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1740	629	2369
ExAC	30584	-28401	2183

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.197	0
	0.211	0
(flanking)	-0.584	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	7213	wt: 0.8512 / mu: 0.9169 (marginal change - not scored)	wt: TCATGGCAGAAGGGA mu: TCACGGCAGAAGGGA	ATGG\|caga
Donor gained	7212	0.31	mu: CTCACGGCAGAAGGG	CACG\|gcag

distance from splice site

119

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000023568

Mmulatta

all identical

ENSMMUG00000029504

Fcatus

all conserved

ENSFCAG00000005271

Mmusculus

all conserved

ENSMUSG00000050973

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0035999

n/a

Celegans

no alignment

C10F3.4

n/a

Xtropicalis

all conserved

ENSXETG00000012962

protein features

start (aa)	end (aa)	feature	details
218	218	ACT_SITE	Tele-GMP-histidine intermediate (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1158 / 1158

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

386 / 386

position of stopcodon in wt / mu cDNA

1578 / 1578

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

412

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1158

coding sequence (CDS) position

110

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

530

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

7211

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

90784250

original gDNA sequence snippet

TTATGGGCAGAAGGATCTCATGGCAGAAGGGATTCAGTGGC

altered gDNA sequence snippet

TTATGGGCAGAAGGATCTCACGGCAGAAGGGATTCAGTGGC

original cDNA sequence snippet

TTATGGGCAGAAGGATCTCATGGCAGAAGGGATTCAGTGGC

altered cDNA sequence snippet

TTATGGGCAGAAGGATCTCACGGCAGAAGGGATTCAGTGGC

wildtype AA sequence

MALPHDSNET SYLLPPNNED WGRQTIPDFV YGQKDLMAEG IQWPRNAPGI PDALPQSPFD
AALCSAWKQR VELGLFRYRL RELQTQILPG AVGFVAQLNV ERGVQRRPPQ TIKSVRQAFD
PVQFNFNKIR PGEVLFRLHR EPDLPGTLLQ EDILVVINVS PLEWGHVLLV PEPARQLPQR
LLPGALRAGI EAVLLSLHPG FRVGFNSLGG LASVNHLHLH GYYLAHRLPV EQAPSEPLDP
GGHLHLLQDL PAPGFLFYTR GPGPDLESLI SRVCRATDYL TDHEIAHNLF VTRGAPPGKT
SPSSALTGVR VILWARKSSF GIKDGEAFNV ALCELAGHLP VKTSQDFSSL TEAAAVALIQ
DCRLPPSQAE DVQAALVALM SQEEQ*

mutated AA sequence

MALPHDSNET SYLLPPNNED WGRQTIPDFV YGQKDLTAEG IQWPRNAPGI PDALPQSPFD
AALCSAWKQR VELGLFRYRL RELQTQILPG AVGFVAQLNV ERGVQRRPPQ TIKSVRQAFD
PVQFNFNKIR PGEVLFRLHR EPDLPGTLLQ EDILVVINVS PLEWGHVLLV PEPARQLPQR
LLPGALRAGI EAVLLSLHPG FRVGFNSLGG LASVNHLHLH GYYLAHRLPV EQAPSEPLDP
GGHLHLLQDL PAPGFLFYTR GPGPDLESLI SRVCRATDYL TDHEIAHNLF VTRGAPPGKT
SPSSALTGVR VILWARKSSF GIKDGEAFNV ALCELAGHLP VKTSQDFSSL TEAAAVALIQ
DCRLPPSQAE DVQAALVALM SQEEQ*

speed

0.80 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: 0.999999999999994 (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)

chr15:90784250T>CN/A show variant in all transcripts IGV

HGNC symbol

GDPGP1

Ensembl transcript ID

ENST00000329600

Genbank transcript ID

N/A

UniProt peptide

Q6ZNW5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110T>C
cDNA.110T>C
g.7211T>C

AA changes

M37T Score: 81 explain score(s)

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

frameshift

known variant

Reference ID: rs7171194

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1740	629	2369
ExAC	30584	-28401	2183

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.197	0
	0.211	0
(flanking)	-0.584	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	7213	wt: 0.8512 / mu: 0.9169 (marginal change - not scored)	wt: TCATGGCAGAAGGGA mu: TCACGGCAGAAGGGA	ATGG\|caga
Donor gained	7212	0.31	mu: CTCACGGCAGAAGGG	CACG\|gcag

distance from splice site

110

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000023568

Mmulatta

all identical

ENSMMUG00000029504

Fcatus

all conserved

ENSFCAG00000005271

Mmusculus

all conserved

ENSMUSG00000050973

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0035999

n/a

Celegans

no alignment

C10F3.4

n/a

Xtropicalis

all conserved

ENSXETG00000012962

protein features

start (aa)	end (aa)	feature	details
218	218	ACT_SITE	Tele-GMP-histidine intermediate (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1158 / 1158

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

386 / 386

position of stopcodon in wt / mu cDNA

1158 / 1158

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

1 / 1

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1158

coding sequence (CDS) position

110

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

110

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

7211

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

90784250

original gDNA sequence snippet

TTATGGGCAGAAGGATCTCATGGCAGAAGGGATTCAGTGGC

altered gDNA sequence snippet

TTATGGGCAGAAGGATCTCACGGCAGAAGGGATTCAGTGGC

original cDNA sequence snippet

TTATGGGCAGAAGGATCTCATGGCAGAAGGGATTCAGTGGC

altered cDNA sequence snippet

TTATGGGCAGAAGGATCTCACGGCAGAAGGGATTCAGTGGC

wildtype AA sequence

mutated AA sequence

speed

0.52 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems