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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000222214
Querying Taster for transcript #2: ENST00000591470
Querying Taster for transcript #3: ENST00000457854
Querying Taster for transcript #4: ENST00000422947
Querying Taster for transcript #5: ENST00000293695
MT speed 0 s - this script 3.339508 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GCDH	disease_causing_automatic	0.999999999916678	simple_aae			0	A421V	single base exchange	rs121434367		show file
GCDH	disease_causing_automatic	0.999999999916678	simple_aae			0	A421V	single base exchange	rs121434367		show file
GCDH	disease_causing_automatic	0.999999999916678	simple_aae			0	A377V	single base exchange	rs121434367		show file
GCDH	disease_causing_automatic	1	without_aae			0		single base exchange	rs121434367		show file
SYCE2	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121434367		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999916678 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960722)
known disease mutation: rs2082 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13010300C>TN/A show variant in all transcripts IGV

HGNC symbol

GCDH

Ensembl transcript ID

ENST00000222214

Genbank transcript ID

NM_000159

UniProt peptide

Q92947

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1262C>T
cDNA.1473C>T
g.8461C>T

AA changes

A421V Score: 64 explain score(s)

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

421

frameshift

known variant

Reference ID: rs121434367

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	23	23

known disease mutation: rs2082 (pathogenic for Glutaric aciduria, type 1|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960722)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960722)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960722)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.605	1
	5.605	1
(flanking)	-2.749	0.021

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	8472	wt: 0.2675 / mu: 0.3327 (marginal change - not scored)	wt: ACATTCACGCCCTGATCCTTGGGAGAGCTATCACGGGAATC mu: ACATTCACGTCCTGATCCTTGGGAGAGCTATCACGGGAATC	cttg\|GGAG
Donor marginally increased	8454	wt: 0.9706 / mu: 0.9861 (marginal change - not scored)	wt: ATGACATTCACGCCC mu: ATGACATTCACGTCC	GACA\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

421

mutated

not conserved

421

Ptroglodytes

all identical

ENSPTRG00000010548

421

Mmulatta

all identical

ENSMMUG00000007043

421

Fcatus

all identical

ENSFCAG00000000477

421

Mmusculus

all identical

ENSMUSG00000003809

421

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008257

427

Drerio

no alignment

ENSDARG00000038361

n/a

Dmelanogaster

all identical

FBgn0031824

404

Celegans

all identical

F54D5.7

395

Xtropicalis

all identical

ENSXETG00000007932

423

protein features

start (aa)	end (aa)	feature	details
417	429	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1317 / 1317

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

439 / 439

position of stopcodon in wt / mu cDNA

1528 / 1528

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

212 / 212

chromosome

strand

last intron/exon boundary

1455

theoretical NMD boundary in CDS

1193

length of CDS

1317

coding sequence (CDS) position

1262

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

1473

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

8461

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

13010300

original gDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered gDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

original cDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered cDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

wildtype AA sequence

MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGTHDIH
ALILGRAITG IQAFTASK*

mutated AA sequence

speed

0.38 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

disease causing

Model: simple_aae, prob: 0.999999999916678 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960722)
known disease mutation: rs2082 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13010300C>TN/A show variant in all transcripts IGV

HGNC symbol

GCDH

Ensembl transcript ID

ENST00000591470

Genbank transcript ID

N/A

UniProt peptide

Q92947

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1262C>T
cDNA.1407C>T
g.8461C>T

AA changes

A421V Score: 64 explain score(s)

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

421

frameshift

known variant

Reference ID: rs121434367

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	23	23

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.605	1
	5.605	1
(flanking)	-2.749	0.021

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	8472	wt: 0.2675 / mu: 0.3327 (marginal change - not scored)	wt: ACATTCACGCCCTGATCCTTGGGAGAGCTATCACGGGAATC mu: ACATTCACGTCCTGATCCTTGGGAGAGCTATCACGGGAATC	cttg\|GGAG
Donor marginally increased	8454	wt: 0.9706 / mu: 0.9861 (marginal change - not scored)	wt: ATGACATTCACGCCC mu: ATGACATTCACGTCC	GACA\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

421

mutated

not conserved

421

Ptroglodytes

all identical

ENSPTRG00000010548

421

Mmulatta

all identical

ENSMMUG00000007043

421

Fcatus

all identical

ENSFCAG00000000477

421

Mmusculus

all identical

ENSMUSG00000003809

421

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008257

427

Drerio

no alignment

ENSDARG00000038361

n/a

Dmelanogaster

all identical

FBgn0031824

404

Celegans

all identical

F54D5.7

395

Xtropicalis

all identical

ENSXETG00000007932

423

protein features

start (aa)	end (aa)	feature	details
417	429	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1317 / 1317

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

439 / 439

position of stopcodon in wt / mu cDNA

1462 / 1462

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

146 / 146

chromosome

strand

last intron/exon boundary

1389

theoretical NMD boundary in CDS

1193

length of CDS

1317

coding sequence (CDS) position

1262

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

1407

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

8461

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

13010300

original gDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered gDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

original cDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered cDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

wildtype AA sequence

mutated AA sequence

speed

0.36 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999916678 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960722)
known disease mutation: rs2082 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13010300C>TN/A show variant in all transcripts IGV

HGNC symbol

GCDH

Ensembl transcript ID

ENST00000422947

Genbank transcript ID

N/A

UniProt peptide

Q92947

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1130C>T
cDNA.1388C>T
g.8461C>T

AA changes

A377V Score: 64 explain score(s)

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

377

frameshift

known variant

Reference ID: rs121434367

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	23	23

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.605	1
	5.605	1
(flanking)	-2.749	0.021

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	8472	wt: 0.2675 / mu: 0.3327 (marginal change - not scored)	wt: ACATTCACGCCCTGATCCTTGGGAGAGCTATCACGGGAATC mu: ACATTCACGTCCTGATCCTTGGGAGAGCTATCACGGGAATC	cttg\|GGAG
Donor marginally increased	8454	wt: 0.9706 / mu: 0.9861 (marginal change - not scored)	wt: ATGACATTCACGCCC mu: ATGACATTCACGTCC	GACA\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

377

mutated

not conserved

377

Ptroglodytes

all identical

ENSPTRG00000010548

421

Mmulatta

all identical

ENSMMUG00000007043

421

Fcatus

all identical

ENSFCAG00000000477

421

Mmusculus

all identical

ENSMUSG00000003809

421

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008257

427

Drerio

no alignment

ENSDARG00000038361

n/a

Dmelanogaster

all identical

FBgn0031824

404

Celegans

all identical

F54D5.7

395

Xtropicalis

all identical

ENSXETG00000007932

423

protein features

start (aa)	end (aa)	feature	details
364	388	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1185 / 1185

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

395 / 395

position of stopcodon in wt / mu cDNA

1443 / 1443

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

259 / 259

chromosome

strand

last intron/exon boundary

1370

theoretical NMD boundary in CDS

1061

length of CDS

1185

coding sequence (CDS) position

1130

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

1388

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

8461

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

13010300

original gDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered gDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

original cDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered cDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

wildtype AA sequence

MRSSSGTPSA PTARRDSCLA SCWPIATKSL ALLPRLECSG TILAHCKFCL PGSSDSPAST
PLVAGITGYG CAGVSSVAYG LLARELERVD SGYRSAMSVQ SSLVMHPIYA YGSEEQRQKY
LPQLAKGELL GCFGLTEPNS GSDPSSMETR AHYNSSNKSY TLNGTKTWIT NSPMADLFVV
WARCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*

mutated AA sequence

speed

0.76 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM960722)
known disease mutation: rs2082 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13010300C>TN/A show variant in all transcripts IGV

HGNC symbol

GCDH

Ensembl transcript ID

ENST00000457854

Genbank transcript ID

NM_013976

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.8461C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434367

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	23	23

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.605	1
	5.605	1
(flanking)	-2.749	0.021

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	8472	wt: 0.2675 / mu: 0.3327 (marginal change - not scored)	wt: ACATTCACGCCCTGATCCTTGGGAGAGCTATCACGGGAATC mu: ACATTCACGTCCTGATCCTTGGGAGAGCTATCACGGGAATC	cttg\|GGAG
Donor marginally increased	8454	wt: 0.9706 / mu: 0.9861 (marginal change - not scored)	wt: ATGACATTCACGCCC mu: ATGACATTCACGTCC	GACA\|ttca

distance from splice site

214

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

78 / 78

chromosome

strand

last intron/exon boundary

1321

theoretical NMD boundary in CDS

1193

length of CDS

1287

coding sequence (CDS) position

N/A

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

N/A

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

8461

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

13010300

original gDNA sequence snippet

AGGTACACATGACATTCACGCCCTGATCCTTGGGAGAGCTA

altered gDNA sequence snippet

AGGTACACATGACATTCACGTCCTGATCCTTGGGAGAGCTA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.18 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM960722)
known disease mutation: rs2082 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13010300C>TN/A show variant in all transcripts IGV

HGNC symbol

SYCE2

Ensembl transcript ID

ENST00000293695

Genbank transcript ID

NM_001105578

UniProt peptide

Q6PIF2

alteration type

single base exchange

alteration region

intron

DNA changes

g.19791G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434367

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	23	23

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.605	1
	5.605	1
(flanking)	-2.749	0.021

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	19783	wt: 0.61 / mu: 0.82	wt: CCCAAGGATCAGGGC mu: CCCAAGGATCAGGAC	CAAG\|gatc
Donor increased	19789	wt: 0.44 / mu: 0.76	wt: GATCAGGGCGTGAAT mu: GATCAGGACGTGAAT	TCAG\|ggcg
Donor increased	19792	wt: 0.68 / mu: 0.91	wt: CAGGGCGTGAATGTC mu: CAGGACGTGAATGTC	GGGC\|gtga
Donor gained	19793	0.53	mu: AGGACGTGAATGTCA	GACG\|tgaa
Donor gained	19787	0.60	mu: AGGATCAGGACGTGA	GATC\|agga

distance from splice site

101

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

no protein features affected

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

20 / 20

chromosome

strand

-1

last intron/exon boundary

632

theoretical NMD boundary in CDS

562

length of CDS

657

coding sequence (CDS) position

N/A

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

N/A

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

19791

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

13010300

original gDNA sequence snippet

TAGCTCTCCCAAGGATCAGGGCGTGAATGTCATGTGTACCT

altered gDNA sequence snippet

TAGCTCTCCCAAGGATCAGGACGTGAATGTCATGTGTACCT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MERQGVDVPH VKCKDQEPQP LGESKEHPRW EENCEEEAGG GPASASCQLT VLEGKSGLYF
SSLDSSIDIL QKRAQELIEN INKSRQKDHA LMTNFRNSLK TKVSDLTEKL EERIYQIYND
HNKIIQEKLQ EFTQKMAKIS HLETELKQVC HSVETVYKDL CLQPEQSLRL RWGPDHSRGK
SPPRPGNSQP PDVFVSSVAE TTSQATASEV QTNRDGEC*

mutated AA sequence

N/A

speed

0.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems