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: ENST00000332272
Querying Taster for transcript #2: ENST00000390664
MT speed 0 s - this script 3.509462 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHST6	disease_causing_automatic	0.999970317866074	simple_aae		affected	0	R93S	single base exchange	rs121917826		show file
CHST6	disease_causing_automatic	0.999970317866074	simple_aae		affected	0	R93S	single base exchange	rs121917826		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999970317866074 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040695)
known disease mutation: rs5079 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:75513450G>TN/A show variant in all transcripts IGV

HGNC symbol

CHST6

Ensembl transcript ID

ENST00000332272

Genbank transcript ID

NM_021615

UniProt peptide

Q9GZX3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.277C>A
cDNA.457C>A
g.15833C>A

AA changes

R93S Score: 110 explain score(s)

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

frameshift

known variant

Reference ID: rs121917826
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5079 (pathogenic for Macular corneal dystrophy, type II) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040695)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040695)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040695)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.078	1
	1.349	1
(flanking)	0.122	0.996

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	15833	wt: 0.3336 / mu: 0.3620 (marginal change - not scored)	wt: CAACGCTGCACATGGCTGTGCGCGACCTGGTGCGCTCCGTC mu: CAACGCTGCACATGGCTGTGAGCGACCTGGTGCGCTCCGTC	gtgc\|GCGA
Donor increased	15833	wt: 0.26 / mu: 0.77	wt: CTGTGCGCGACCTGG mu: CTGTGAGCGACCTGG	GTGC\|gcga

distance from splice site

293

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000042548

Mmulatta

all identical

ENSMMUG00000001563

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031952

Ggallus

all identical

ENSGALG00000000913

Trubripes

no homologue

Drerio

all identical

ENSDARG00000061357

133

Dmelanogaster

all conserved

FBgn0051637

235

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003576

protein features

start (aa)	end (aa)	feature	details
27	395	TOPO_DOM	Lumenal (Potential).	lost
116	116	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
202	210	NP_BIND	PAPS (By similarity).	might get lost (downstream of altered splice site)
229	229	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
328	328	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

1188 / 1188

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

396 / 396

position of stopcodon in wt / mu cDNA

1368 / 1368

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

181 / 181

chromosome

strand

-1

last intron/exon boundary

165

theoretical NMD boundary in CDS

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

length of CDS

1188

coding sequence (CDS) position

277

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

457

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

15833

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

75513450

original gDNA sequence snippet

CAACGCTGCACATGGCTGTGCGCGACCTGGTGCGCTCCGTC

altered gDNA sequence snippet

CAACGCTGCACATGGCTGTGAGCGACCTGGTGCGCTCCGTC

original cDNA sequence snippet

CAACGCTGCACATGGCTGTGCGCGACCTGGTGCGCTCCGTC

altered cDNA sequence snippet

CAACGCTGCACATGGCTGTGAGCGACCTGGTGCGCTCCGTC

wildtype AA sequence

MWLPRVSSTA VTALLLAQTF LLLFLVSRPG PSSPAGGEAR VHVLVLSSWR SGSSFVGQLF
NQHPDVFYLM EPAWHVWTTL SQGSAATLHM AVRDLVRSVF LCDMDVFDAY LPWRRNLSDL
FQWAVSRALC SPPACSAFPR GAISSEAVCK PLCARQSFTL AREACRSYSH VVLKEVRFFN
LQVLYPLLSD PALNLRIVHL VRDPRAVLRS REQTAKALAR DNGIVLGTNG TWVEADPGLR
VVREVCRSHV RIAEAATLKP PPFLRGRYRL VRFEDLAREP LAEIRALYAF TGLSLTPQLE
AWIHNITHGS GPGARREAFK TSSRNALNVS QAWRHALPFA KIRRVQELCA GALQLLGYRP
VYSEDEQRNL ALDLVLPRGL NGFTWASSTA SHPRN*

mutated AA sequence

MWLPRVSSTA VTALLLAQTF LLLFLVSRPG PSSPAGGEAR VHVLVLSSWR SGSSFVGQLF
NQHPDVFYLM EPAWHVWTTL SQGSAATLHM AVSDLVRSVF LCDMDVFDAY LPWRRNLSDL
FQWAVSRALC SPPACSAFPR GAISSEAVCK PLCARQSFTL AREACRSYSH VVLKEVRFFN
LQVLYPLLSD PALNLRIVHL VRDPRAVLRS REQTAKALAR DNGIVLGTNG TWVEADPGLR
VVREVCRSHV RIAEAATLKP PPFLRGRYRL VRFEDLAREP LAEIRALYAF TGLSLTPQLE
AWIHNITHGS GPGARREAFK TSSRNALNVS QAWRHALPFA KIRRVQELCA GALQLLGYRP
VYSEDEQRNL ALDLVLPRGL NGFTWASSTA SHPRN*

speed

1.10 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: 0.999970317866074 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040695)
known disease mutation: rs5079 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:75513450G>TN/A show variant in all transcripts IGV

HGNC symbol

CHST6

Ensembl transcript ID

ENST00000390664

Genbank transcript ID

N/A

UniProt peptide

Q9GZX3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.277C>A
cDNA.969C>A
g.15833C>A

AA changes

R93S Score: 110 explain score(s)

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

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.078	1
	1.349	1
(flanking)	0.122	0.996

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	15833	wt: 0.3336 / mu: 0.3620 (marginal change - not scored)	wt: CAACGCTGCACATGGCTGTGCGCGACCTGGTGCGCTCCGTC mu: CAACGCTGCACATGGCTGTGAGCGACCTGGTGCGCTCCGTC	gtgc\|GCGA
Donor increased	15833	wt: 0.26 / mu: 0.77	wt: CTGTGCGCGACCTGG mu: CTGTGAGCGACCTGG	GTGC\|gcga

distance from splice site

293

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000042548

Mmulatta

all identical

ENSMMUG00000001563

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031952

Ggallus

all identical

ENSGALG00000000913

Trubripes

no homologue

Drerio

all identical

ENSDARG00000061357

133

Dmelanogaster

all conserved

FBgn0051637

235

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003576

protein features

start (aa)	end (aa)	feature	details
27	395	TOPO_DOM	Lumenal (Potential).	lost
116	116	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
202	210	NP_BIND	PAPS (By similarity).	might get lost (downstream of altered splice site)
229	229	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
328	328	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

1188 / 1188

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

396 / 396

position of stopcodon in wt / mu cDNA

1880 / 1880

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

693 / 693

chromosome

strand

-1

last intron/exon boundary

677

theoretical NMD boundary in CDS

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

length of CDS

1188

coding sequence (CDS) position

277

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

969

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

15833

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

75513450

original gDNA sequence snippet

CAACGCTGCACATGGCTGTGCGCGACCTGGTGCGCTCCGTC

altered gDNA sequence snippet

CAACGCTGCACATGGCTGTGAGCGACCTGGTGCGCTCCGTC

original cDNA sequence snippet

CAACGCTGCACATGGCTGTGCGCGACCTGGTGCGCTCCGTC

altered cDNA sequence snippet

CAACGCTGCACATGGCTGTGAGCGACCTGGTGCGCTCCGTC

wildtype AA sequence

mutated AA sequence

speed

0.46 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems