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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000401850
Querying Taster for transcript #2: ENST00000249005
Querying Taster for transcript #3: ENST00000381278
MT speed 1.19 s - this script 2.872699 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
A4GALT	disease_causing	0.999977946410561	simple_aae		affected		G187D	single base exchange	rs28940572		show file
A4GALT	disease_causing	0.999977946410561	simple_aae		affected		G187D	single base exchange	rs28940572		show file
A4GALT	disease_causing	0.999977946410561	simple_aae		affected		G187D	single base exchange	rs28940572		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999977946410561 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004785)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:43089398C>TN/A show variant in all transcripts IGV

HGNC symbol

A4GALT

Ensembl transcript ID

ENST00000401850

Genbank transcript ID

N/A

UniProt peptide

Q9NPC4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.560G>A
cDNA.1050G>A
g.27907G>A

AA changes

G187D Score: 94 explain score(s)

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

187

frameshift

known variant

Reference ID: rs28940572

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation at this position, please check HGMD for details (HGMD ID CM004785)

known disease mutation at this position, please check HGMD for details (HGMD ID CM004785)
known disease mutation at this position, please check HGMD for details (HGMD ID CM004785)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.063	0.018
	4.049	0.993
(flanking)	4.049	0.998

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	27897	wt: 0.2645 / mu: 0.2973 (marginal change - not scored)	wt: CCTCCAGGATCGCACTCATGTGGAAGTTCGGCGGCATCTAC mu: CCTCCAGGATCGCACTCATGTGGAAGTTCGACGGCATCTAC	atgt\|GGAA
Donor increased	27908	wt: 0.22 / mu: 0.33	wt: TTCGGCGGCATCTAC mu: TTCGACGGCATCTAC	CGGC\|ggca

distance from splice site

606

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

187

mutated

not conserved

187

Ptroglodytes

all identical

ENSPTRG00000029414

183

Mmulatta

all identical

ENSMMUG00000010194

187

Fcatus

all identical

ENSFCAG00000008576

187

Mmusculus

all identical

ENSMUSG00000047878

193

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0031491

195

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
44	353	TOPO_DOM	Lumenal (Potential).	lost
192	194	MOTIF	DXD motif (By similarity).	might get lost (downstream of altered splice site)
203	203	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1062 / 1062

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

354 / 354

position of stopcodon in wt / mu cDNA

1552 / 1552

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

491 / 491

chromosome

strand

-1

last intron/exon boundary

445

theoretical NMD boundary in CDS

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

length of CDS

1062

coding sequence (CDS) position

560

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

1050

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

27907

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

43089398

original gDNA sequence snippet

CGCACTCATGTGGAAGTTCGGCGGCATCTACCTGGACACGG

altered gDNA sequence snippet

CGCACTCATGTGGAAGTTCGACGGCATCTACCTGGACACGG

original cDNA sequence snippet

CGCACTCATGTGGAAGTTCGGCGGCATCTACCTGGACACGG

altered cDNA sequence snippet

CGCACTCATGTGGAAGTTCGACGGCATCTACCTGGACACGG

wildtype AA sequence

MSKPPDLLLR LLRGAPRQRV CTLFIIGFKF TFFVSIMIYW HVVGEPKEKG QLYNLPAEIP
CPTLTPPTPP SHGPTPGNIF FLETSDRTNP NFLFMCSVES AARTHPESHV LVLMKGLPGG
NASLPRHLGI SLLSCFPNVQ MLPLDLRELF RDTPLADWYA AVQGRWEPYL LPVLSDASRI
ALMWKFGGIY LDTDFIVLKN LRNLTNVLGT QSRYVLNGAF LAFERRHEFM ALCMRDFVDH
YNGWIWGHQG PQLLTRVFKK WCSIRSLAES RACRGVTTLP PEAFYPIPWQ DWKKYFEDIN
PEELPRLLSA TYAVHVWNKK SQGTRFEATS RALLAQLHAR YCPTTHEAMK MYL*

mutated AA sequence

MSKPPDLLLR LLRGAPRQRV CTLFIIGFKF TFFVSIMIYW HVVGEPKEKG QLYNLPAEIP
CPTLTPPTPP SHGPTPGNIF FLETSDRTNP NFLFMCSVES AARTHPESHV LVLMKGLPGG
NASLPRHLGI SLLSCFPNVQ MLPLDLRELF RDTPLADWYA AVQGRWEPYL LPVLSDASRI
ALMWKFDGIY LDTDFIVLKN LRNLTNVLGT QSRYVLNGAF LAFERRHEFM ALCMRDFVDH
YNGWIWGHQG PQLLTRVFKK WCSIRSLAES RACRGVTTLP PEAFYPIPWQ DWKKYFEDIN
PEELPRLLSA TYAVHVWNKK SQGTRFEATS RALLAQLHAR YCPTTHEAMK MYL*

speed

0.44 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: 0.999977946410561 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004785)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:43089398C>TN/A show variant in all transcripts IGV

HGNC symbol

A4GALT

Ensembl transcript ID

ENST00000249005

Genbank transcript ID

NM_017436

UniProt peptide

Q9NPC4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.560G>A
cDNA.749G>A
g.27907G>A

AA changes

G187D Score: 94 explain score(s)

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

187

frameshift

known variant

Reference ID: rs28940572

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.063	0.018
	4.049	0.993
(flanking)	4.049	0.998

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	27897	wt: 0.2645 / mu: 0.2973 (marginal change - not scored)	wt: CCTCCAGGATCGCACTCATGTGGAAGTTCGGCGGCATCTAC mu: CCTCCAGGATCGCACTCATGTGGAAGTTCGACGGCATCTAC	atgt\|GGAA
Donor increased	27908	wt: 0.22 / mu: 0.33	wt: TTCGGCGGCATCTAC mu: TTCGACGGCATCTAC	CGGC\|ggca

distance from splice site

606

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

187

mutated

not conserved

187

Ptroglodytes

all identical

ENSPTRG00000029414

183

Mmulatta

all identical

ENSMMUG00000010194

187

Fcatus

all identical

ENSFCAG00000008576

187

Mmusculus

all identical

ENSMUSG00000047878

193

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0031491

195

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
44	353	TOPO_DOM	Lumenal (Potential).	lost
192	194	MOTIF	DXD motif (By similarity).	might get lost (downstream of altered splice site)
203	203	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1062 / 1062

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

354 / 354

position of stopcodon in wt / mu cDNA

1251 / 1251

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

190 / 190

chromosome

strand

-1

last intron/exon boundary

144

theoretical NMD boundary in CDS

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

length of CDS

1062

coding sequence (CDS) position

560

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

749

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

27907

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

43089398

original gDNA sequence snippet

CGCACTCATGTGGAAGTTCGGCGGCATCTACCTGGACACGG

altered gDNA sequence snippet

CGCACTCATGTGGAAGTTCGACGGCATCTACCTGGACACGG

original cDNA sequence snippet

CGCACTCATGTGGAAGTTCGGCGGCATCTACCTGGACACGG

altered cDNA sequence snippet

CGCACTCATGTGGAAGTTCGACGGCATCTACCTGGACACGG

wildtype AA sequence

mutated AA sequence

MSKPPDLLLR LLRGAPRQRV CTLFIIGFKF TFFVSIMIYW HVVGEPKEKG QLYNLPAEIP
CPTLTPPTPP SHGPTPGNIF FLETSDRTNP NFLFMCSVES AARTHPESHV LVLMKGLPGG
NASLPRHLGI SLLSCFPNVQ MLPLDLRELF RDTPLADWYA AVQGRWEPYL LPVLSDASRI
ALMWKFDGIY LDTDFIVLKN LRNLTNVLGT QSRYVLNGAF LAFERRHEFM ALCMRDFVDH
YNGWIWGHQG PQLLTRVFKK WCSIRSLAES RACRGVTTLP PEAFYPIPWQ DWKKYFEDIN
PEELPRLLSA TYAVHVWNKK SQGTRFEATS RALLAQLHAR YCPTTHEAMK MYL*

speed

0.41 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999977946410561 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004785)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:43089398C>TN/A show variant in all transcripts IGV

HGNC symbol

A4GALT

Ensembl transcript ID

ENST00000381278

Genbank transcript ID

N/A

UniProt peptide

Q9NPC4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.560G>A
cDNA.665G>A
g.27907G>A

AA changes

G187D Score: 94 explain score(s)

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

187

frameshift

known variant

Reference ID: rs28940572

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.063	0.018
	4.049	0.993
(flanking)	4.049	0.998

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	27897	wt: 0.2645 / mu: 0.2973 (marginal change - not scored)	wt: CCTCCAGGATCGCACTCATGTGGAAGTTCGGCGGCATCTAC mu: CCTCCAGGATCGCACTCATGTGGAAGTTCGACGGCATCTAC	atgt\|GGAA
Donor increased	27908	wt: 0.22 / mu: 0.33	wt: TTCGGCGGCATCTAC mu: TTCGACGGCATCTAC	CGGC\|ggca

distance from splice site

606

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

187

mutated

not conserved

187

Ptroglodytes

all identical

ENSPTRG00000029414

183

Mmulatta

all identical

ENSMMUG00000010194

187

Fcatus

all identical

ENSFCAG00000008576

187

Mmusculus

all identical

ENSMUSG00000047878

193

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0031491

195

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
44	353	TOPO_DOM	Lumenal (Potential).	lost
192	194	MOTIF	DXD motif (By similarity).	might get lost (downstream of altered splice site)
203	203	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1062 / 1062

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

354 / 354

position of stopcodon in wt / mu cDNA

1167 / 1167

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

106 / 106

chromosome

strand

-1

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

1062

coding sequence (CDS) position

560

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

665

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

27907

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

43089398

original gDNA sequence snippet

CGCACTCATGTGGAAGTTCGGCGGCATCTACCTGGACACGG

altered gDNA sequence snippet

CGCACTCATGTGGAAGTTCGACGGCATCTACCTGGACACGG

original cDNA sequence snippet

CGCACTCATGTGGAAGTTCGGCGGCATCTACCTGGACACGG

altered cDNA sequence snippet

CGCACTCATGTGGAAGTTCGACGGCATCTACCTGGACACGG

wildtype AA sequence

mutated AA sequence

MSKPPDLLLR LLRGAPRQRV CTLFIIGFKF TFFVSIMIYW HVVGEPKEKG QLYNLPAEIP
CPTLTPPTPP SHGPTPGNIF FLETSDRTNP NFLFMCSVES AARTHPESHV LVLMKGLPGG
NASLPRHLGI SLLSCFPNVQ MLPLDLRELF RDTPLADWYA AVQGRWEPYL LPVLSDASRI
ALMWKFDGIY LDTDFIVLKN LRNLTNVLGT QSRYVLNGAF LAFERRHEFM ALCMRDFVDH
YNGWIWGHQG PQLLTRVFKK WCSIRSLAES RACRGVTTLP PEAFYPIPWQ DWKKYFEDIN
PEELPRLLSA TYAVHVWNKK SQGTRFEATS RALLAQLHAR YCPTTHEAMK MYL*

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

Problems