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: ENST00000336798
Querying Taster for transcript #2: ENST00000339394
MT speed 0 s - this script 3.433475 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SDC3	polymorphism_automatic	0.488712377746947	simple_aae		affected		T271I	single base exchange	rs2282440		show file
SDC3	polymorphism_automatic	0.793073929110232	simple_aae		affected		T329I	single base exchange	rs2282440		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.511287622253053 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM066224)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:31347320G>AN/A show variant in all transcripts IGV

HGNC symbol

SDC3

Ensembl transcript ID

ENST00000336798

Genbank transcript ID

N/A

UniProt peptide

O75056

alteration type

single base exchange

alteration region

CDS

DNA changes

c.812C>T
cDNA.2305C>T
g.34289C>T

AA changes

T271I Score: 89 explain score(s)

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

271

frameshift

known variant

Reference ID: rs2282440

database	homozygous (A/A)	heterozygous	allele carriers
1000G	159	489	648
ExAC	1756	6904	8660

known disease mutation at this position, please check HGMD for details (HGMD ID CM066224)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.459	0.971
	2.274	0.993
(flanking)	0.434	0.992

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	34294	wt: 0.8540 / mu: 0.8953 (marginal change - not scored)	wt: CAGCCAATGAGGTGG mu: TAGCCAATGAGGTGG	GCCA\|atga
Donor gained	34285	0.35	mu: AACCAGACATAGCCA	CCAG\|acat

distance from splice site

116

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

271

mutated

not conserved

271

Ptroglodytes

all identical

ENSPTRG00000000451

283

Mmulatta

all identical

ENSMMUG00000013519

320

Fcatus

all identical

ENSFCAG00000010378

282

Mmusculus

all identical

ENSMUSG00000025743

329

Ggallus

not conserved

ENSGALG00000000569

298

Trubripes

not conserved

ENSTRUG00000013115

139

Drerio

not conserved

ENSDARG00000088962

309

Dmelanogaster

not conserved

FBgn0010415

345

Celegans

all identical

F57C7.3

174

EDFF

Xtropicalis

not conserved

ENSXETG00000007104

274

VVPQTEPP

protein features

start (aa)	end (aa)	feature	details
1	387	TOPO_DOM	Extracellular (Potential).	lost
115	302	COMPBIAS	Ser/Thr-rich (mucin-like).	lost
314	314	CARBOHYD	O-linked (Xyl...) (glycosaminoglycan) (Potential).	might get lost (downstream of altered splice site)
367	367	CARBOHYD	O-linked (Xyl...) (glycosaminoglycan) (Potential).	might get lost (downstream of altered splice site)
383	384	SITE	Cleavage of ectodomain (Potential).	might get lost (downstream of altered splice site)
388	408	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
409	442	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
441	441	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1155 / 1155

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

385 / 385

position of stopcodon in wt / mu cDNA

2648 / 2648

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

1494 / 1494

chromosome

strand

-1

last intron/exon boundary

2482

theoretical NMD boundary in CDS

938

length of CDS

1155

coding sequence (CDS) position

812

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

2305

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

34289

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

31347320

original gDNA sequence snippet

AGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTG

altered gDNA sequence snippet

AGAGACCACACAACCAGACATAGCCAATGAGGTGGTAGCTG

original cDNA sequence snippet

AGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTG

altered cDNA sequence snippet

AGAGACCACACAACCAGACATAGCCAATGAGGTGGTAGCTG

wildtype AA sequence

MAIAYLGSSC PSQPPSSLAL SLSPTPSDFE QESGIETAMR FSPDVALAVS TTPAVLPTTN
IQPVGTPFEE LPSERPTLEP ATSPLVVTEV PEEPSQRATT VSTTMATTAA TSTGDPTVAT
VPATVATATP STPAAPPFTA TTAVIRTTGV RRLLPLPLTT VATARATTPE APSPPTTAAV
LDTEAPTPRL VSTATSRPRA LPRPATTQEP DIPERSTLPL GTTAPGPTEV AQTPTPETFL
TTIRDEPEVP VSGGPSGDFE LPEEETTQPD TANEVVAVGG AAAKASSPPG TLPKGARPGP
GLLDNAIDSG SSAAQLPQKS ILERKEVLVA VIVGGVVGAL FAAFLVTLLI YRMKKKDEGS
YTLEEPKQAS VTYQKPDKQE EFYA*

mutated AA sequence

MAIAYLGSSC PSQPPSSLAL SLSPTPSDFE QESGIETAMR FSPDVALAVS TTPAVLPTTN
IQPVGTPFEE LPSERPTLEP ATSPLVVTEV PEEPSQRATT VSTTMATTAA TSTGDPTVAT
VPATVATATP STPAAPPFTA TTAVIRTTGV RRLLPLPLTT VATARATTPE APSPPTTAAV
LDTEAPTPRL VSTATSRPRA LPRPATTQEP DIPERSTLPL GTTAPGPTEV AQTPTPETFL
TTIRDEPEVP VSGGPSGDFE LPEEETTQPD IANEVVAVGG AAAKASSPPG TLPKGARPGP
GLLDNAIDSG SSAAQLPQKS ILERKEVLVA VIVGGVVGAL FAAFLVTLLI YRMKKKDEGS
YTLEEPKQAS VTYQKPDKQE EFYA*

speed

0.71 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: 0.206926070889768 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM066224)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:31347320G>AN/A show variant in all transcripts IGV

HGNC symbol

SDC3

Ensembl transcript ID

ENST00000339394

Genbank transcript ID

NM_014654

UniProt peptide

O75056

alteration type

single base exchange

alteration region

CDS

DNA changes

c.986C>T
cDNA.1161C>T
g.34289C>T

AA changes

T329I Score: 89 explain score(s)

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

329

frameshift

known variant

Reference ID: rs2282440

database	homozygous (A/A)	heterozygous	allele carriers
1000G	159	489	648
ExAC	1756	6904	8660

known disease mutation at this position, please check HGMD for details (HGMD ID CM066224)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.459	0.971
	2.274	0.993
(flanking)	0.434	0.992

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	34294	wt: 0.8540 / mu: 0.8953 (marginal change - not scored)	wt: CAGCCAATGAGGTGG mu: TAGCCAATGAGGTGG	GCCA\|atga
Donor gained	34285	0.35	mu: AACCAGACATAGCCA	CCAG\|acat

distance from splice site

116

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

329

mutated

not conserved

329

Ptroglodytes

all identical

ENSPTRG00000000451

283

Mmulatta

all identical

ENSMMUG00000013519

320

Fcatus

all identical

ENSFCAG00000010378

283

Mmusculus

all identical

ENSMUSG00000025743

330

Ggallus

not conserved

ENSGALG00000000569

299

Trubripes

not conserved

ENSTRUG00000013115

139

Drerio

not conserved

ENSDARG00000088962

312

Dmelanogaster

not conserved

FBgn0010415

345

Celegans

all identical

F57C7.3

174

EDFF

Xtropicalis

not conserved

ENSXETG00000007104

281

protein features

start (aa)	end (aa)	feature	details
1	387	TOPO_DOM	Extracellular (Potential).	lost
367	367	CARBOHYD	O-linked (Xyl...) (glycosaminoglycan) (Potential).	might get lost (downstream of altered splice site)
383	384	SITE	Cleavage of ectodomain (Potential).	might get lost (downstream of altered splice site)
388	408	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
409	442	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
441	441	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1329 / 1329

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

443 / 443

position of stopcodon in wt / mu cDNA

1504 / 1504

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

176 / 176

chromosome

strand

-1

last intron/exon boundary

1338

theoretical NMD boundary in CDS

1112

length of CDS

1329

coding sequence (CDS) position

986

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

1161

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

34289

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

31347320

original gDNA sequence snippet

AGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTG

altered gDNA sequence snippet

AGAGACCACACAACCAGACATAGCCAATGAGGTGGTAGCTG

original cDNA sequence snippet

AGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTG

altered cDNA sequence snippet

AGAGACCACACAACCAGACATAGCCAATGAGGTGGTAGCTG

wildtype AA sequence

MKPGPPHRAG AAHGAGAGAG AAAGPGARGL LLPPLLLLLL AGRAAGAQRW RSENFERPVD
LEGSGDDDSF PDDELDDLYS GSGSGYFEQE SGIETAMRFS PDVALAVSTT PAVLPTTNIQ
PVGTPFEELP SERPTLEPAT SPLVVTEVPE EPSQRATTVS TTMATTAATS TGDPTVATVP
ATVATATPST PAAPPFTATT AVIRTTGVRR LLPLPLTTVA TARATTPEAP SPPTTAAVLD
TEAPTPRLVS TATSRPRALP RPATTQEPDI PERSTLPLGT TAPGPTEVAQ TPTPETFLTT
IRDEPEVPVS GGPSGDFELP EEETTQPDTA NEVVAVGGAA AKASSPPGTL PKGARPGPGL
LDNAIDSGSS AAQLPQKSIL ERKEVLVAVI VGGVVGALFA AFLVTLLIYR MKKKDEGSYT
LEEPKQASVT YQKPDKQEEF YA*

mutated AA sequence

MKPGPPHRAG AAHGAGAGAG AAAGPGARGL LLPPLLLLLL AGRAAGAQRW RSENFERPVD
LEGSGDDDSF PDDELDDLYS GSGSGYFEQE SGIETAMRFS PDVALAVSTT PAVLPTTNIQ
PVGTPFEELP SERPTLEPAT SPLVVTEVPE EPSQRATTVS TTMATTAATS TGDPTVATVP
ATVATATPST PAAPPFTATT AVIRTTGVRR LLPLPLTTVA TARATTPEAP SPPTTAAVLD
TEAPTPRLVS TATSRPRALP RPATTQEPDI PERSTLPLGT TAPGPTEVAQ TPTPETFLTT
IRDEPEVPVS GGPSGDFELP EEETTQPDIA NEVVAVGGAA AKASSPPGTL PKGARPGPGL
LDNAIDSGSS AAQLPQKSIL ERKEVLVAVI VGGVVGALFA AFLVTLLIYR MKKKDEGSYT
LEEPKQASVT YQKPDKQEEF YA*

speed

0.73 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems