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: ENST00000376217
Querying Taster for transcript #2: ENST00000315938
MT speed 0 s - this script 4.313592 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GDPD4	polymorphism_automatic	6.59472476627343e-14	simple_aae		affected		I390V	single base exchange	rs11237145		show file
GDPD4	polymorphism_automatic	6.59472476627343e-14	simple_aae		affected		I390V	single base exchange	rs11237145		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999934 (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)

chr11:76954812T>CN/A show variant in all transcripts IGV

HGNC symbol

GDPD4

Ensembl transcript ID

ENST00000376217

Genbank transcript ID

N/A

UniProt peptide

Q6W3E5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1168A>G
cDNA.1419A>G
g.57921A>G

AA changes

I390V Score: 29 explain score(s)

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

390

frameshift

known variant

Reference ID: rs11237145

database	homozygous (C/C)	heterozygous	allele carriers
1000G	215	844	1059
ExAC	6481	19805	26286

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.505	0.004
	-2.271	0
(flanking)	-0.625	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
Acc increased	57920	wt: 0.39 / mu: 0.56	wt: CATGTGGGCCGTTTAGTATCCATTGAAACCCTTGCTAAAAA mu: CATGTGGGCCGTTTAGTATCCGTTGAAACCCTTGCTAAAAA	atcc\|ATTG
Donor gained	57920	0.37	mu: GTATCCGTTGAAACC	ATCC\|gttg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

390

mutated

all conserved

390

Ptroglodytes

all conserved

ENSPTRG00000004100

390

Mmulatta

all conserved

ENSMMUG00000018188

390

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035582

466

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
184	468	TOPO_DOM	Extracellular (Potential).	lost
203	452	DOMAIN	GDPD.	lost
397	397	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
469	489	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
490	623	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1872 / 1872

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

624 / 624

position of stopcodon in wt / mu cDNA

2123 / 2123

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

252 / 252

chromosome

strand

-1

last intron/exon boundary

1792

theoretical NMD boundary in CDS

1490

length of CDS

1872

coding sequence (CDS) position

1168

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

1419

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

57921

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

76954812

original gDNA sequence snippet

ATGTGGGCCGTTTAGTATCCATTGAAACCCTTGCTAAAAAC

altered gDNA sequence snippet

ATGTGGGCCGTTTAGTATCCGTTGAAACCCTTGCTAAAAAC

original cDNA sequence snippet

ATGTGGGCCGTTTAGTATCCATTGAAACCCTTGCTAAAAAC

altered cDNA sequence snippet

ATGTGGGCCGTTTAGTATCCGTTGAAACCCTTGCTAAAAAC

wildtype AA sequence

MLLFLWIETS SEYFNFDWVT FLGTGYWFFW SIFILSLARI LTAYSSLLLL LGFLLLWERI
ELYLHLCHKI LILLVILLCV ILMFIICKFW KERWLVAGLS MQIFAPYVHL VSITVMVILF
WPVAFYVACL EREVRMRRYR MTHSEKKRLK QCNVITRLRG LQVPVGLPFL LILLGLYLMP
LGIYSPCIQE KENLGPKPTI FGHRGAPMLG PENTMMSFEK AVEHGAHGLE TDIHLSYDHV
PFLMHDFDLK RTTNIGEVQP ESACENPAFF NWDFLSTLNA GKWFVKPELR PFYNMKPLSE
ADKERARNQS IPTLADLLTL AEKERKFVIF DLHRPPPKHP LRHTFVRQVV SVILASKIEQ
HLIFWLPAHD RQYVRSVAPG FQHVGRLVSI ETLAKNNISI INVDYKKLFP NGLRDYKAAN
IHINVYTVNE PWLFSLAWCS RINSVTTDNI GLLSQLDHPH FFMTPKFYVF MWLLADIISV
LFIVAIFCFH WRRETEKEKL FETSSTRTDT QSGNLHIAMK PPVRVVEGPW TLAALYPALP
KSGKEHQGHF NFAAPSKKLL PIKNAVTPLK PGKHEIQPPM PTVVFELTQA PTRQATSEAT
FQTTLPTLKV DKPTMPSIEV PYP*

mutated AA sequence

MLLFLWIETS SEYFNFDWVT FLGTGYWFFW SIFILSLARI LTAYSSLLLL LGFLLLWERI
ELYLHLCHKI LILLVILLCV ILMFIICKFW KERWLVAGLS MQIFAPYVHL VSITVMVILF
WPVAFYVACL EREVRMRRYR MTHSEKKRLK QCNVITRLRG LQVPVGLPFL LILLGLYLMP
LGIYSPCIQE KENLGPKPTI FGHRGAPMLG PENTMMSFEK AVEHGAHGLE TDIHLSYDHV
PFLMHDFDLK RTTNIGEVQP ESACENPAFF NWDFLSTLNA GKWFVKPELR PFYNMKPLSE
ADKERARNQS IPTLADLLTL AEKERKFVIF DLHRPPPKHP LRHTFVRQVV SVILASKIEQ
HLIFWLPAHD RQYVRSVAPG FQHVGRLVSV ETLAKNNISI INVDYKKLFP NGLRDYKAAN
IHINVYTVNE PWLFSLAWCS RINSVTTDNI GLLSQLDHPH FFMTPKFYVF MWLLADIISV
LFIVAIFCFH WRRETEKEKL FETSSTRTDT QSGNLHIAMK PPVRVVEGPW TLAALYPALP
KSGKEHQGHF NFAAPSKKLL PIKNAVTPLK PGKHEIQPPM PTVVFELTQA PTRQATSEAT
FQTTLPTLKV DKPTMPSIEV PYP*

speed

1.37 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: 0.999999999999934 (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)

chr11:76954812T>CN/A show variant in all transcripts IGV

HGNC symbol

GDPD4

Ensembl transcript ID

ENST00000315938

Genbank transcript ID

NM_182833

UniProt peptide

Q6W3E5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1168A>G
cDNA.1419A>G
g.57921A>G

AA changes

I390V Score: 29 explain score(s)

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

390

frameshift

known variant

Reference ID: rs11237145

database	homozygous (C/C)	heterozygous	allele carriers
1000G	215	844	1059
ExAC	6481	19805	26286

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.505	0.004
	-2.271	0
(flanking)	-0.625	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
Acc increased	57920	wt: 0.39 / mu: 0.56	wt: CATGTGGGCCGTTTAGTATCCATTGAAACCCTTGCTAAAAA mu: CATGTGGGCCGTTTAGTATCCGTTGAAACCCTTGCTAAAAA	atcc\|ATTG
Donor gained	57920	0.37	mu: GTATCCGTTGAAACC	ATCC\|gttg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

390

mutated

all conserved

390

Ptroglodytes

all conserved

ENSPTRG00000004100

390

Mmulatta

all conserved

ENSMMUG00000018188

390

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035582

466

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
184	468	TOPO_DOM	Extracellular (Potential).	lost
203	452	DOMAIN	GDPD.	lost
397	397	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
469	489	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
490	623	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1563 / 1563

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

521 / 521

position of stopcodon in wt / mu cDNA

1814 / 1814

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

252 / 252

chromosome

strand

-1

last intron/exon boundary

1777

theoretical NMD boundary in CDS

1475

length of CDS

1563

coding sequence (CDS) position

1168

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

1419

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

57921

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

76954812

original gDNA sequence snippet

ATGTGGGCCGTTTAGTATCCATTGAAACCCTTGCTAAAAAC

altered gDNA sequence snippet

ATGTGGGCCGTTTAGTATCCGTTGAAACCCTTGCTAAAAAC

original cDNA sequence snippet

ATGTGGGCCGTTTAGTATCCATTGAAACCCTTGCTAAAAAC

altered cDNA sequence snippet

ATGTGGGCCGTTTAGTATCCGTTGAAACCCTTGCTAAAAAC

wildtype AA sequence

mutated AA sequence

MLLFLWIETS SEYFNFDWVT FLGTGYWFFW SIFILSLARI LTAYSSLLLL LGFLLLWERI
ELYLHLCHKI LILLVILLCV ILMFIICKFW KERWLVAGLS MQIFAPYVHL VSITVMVILF
WPVAFYVACL EREVRMRRYR MTHSEKKRLK QCNVITRLRG LQVPVGLPFL LILLGLYLMP
LGIYSPCIQE KENLGPKPTI FGHRGAPMLG PENTMMSFEK AVEHGAHGLE TDIHLSYDHV
PFLMHDFDLK RTTNIGEVQP ESACENPAFF NWDFLSTLNA GKWFVKPELR PFYNMKPLSE
ADKERARNQS IPTLADLLTL AEKERKFVIF DLHRPPPKHP LRHTFVRQVV SVILASKIEQ
HLIFWLPAHD RQYVRSVAPG FQHVGRLVSV ETLAKNNISI INVDYKKLFP NGLRDYKAAN
IHINVYTVNE PWLFSLAWCS RINSVTTDNI GLLSQLDHPH FFMTPKFYVF MWLLADIISV
LFIVAIFCFH WRRETEKEKL FETSSTRTDT QSGSKNEEDR *

speed

0.94 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems