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: ENST00000282470
Querying Taster for transcript #2: ENST00000503414
Querying Taster for transcript #3: ENST00000418378
MT speed 0 s - this script 2.949091 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPARCL1	polymorphism_automatic	5.09203790244328e-12	simple_aae		affected		T419A	single base exchange	rs1130643		show file
SPARCL1	polymorphism_automatic	5.09203790244328e-12	simple_aae		affected		T294A	single base exchange	rs1130643		show file
SPARCL1	polymorphism_automatic	5.09203790244328e-12	simple_aae		affected		T419A	single base exchange	rs1130643		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999994908 (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)

chr4:88412806T>CN/A show variant in all transcripts IGV

HGNC symbol

SPARCL1

Ensembl transcript ID

ENST00000282470

Genbank transcript ID

NM_004684

UniProt peptide

Q14515

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1255A>G
cDNA.1726A>G
g.39408A>G

AA changes

T419A Score: 58 explain score(s)

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

419

frameshift

known variant

Reference ID: rs1130643

database	homozygous (C/C)	heterozygous	allele carriers
1000G	204	693	897
ExAC	1949	13554	15503

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.563	0
(flanking)	-1.285	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
Donor gained	39402	0.85	mu: ATGAGGAGGAAGCGT	GAGG\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

419

mutated

not conserved

419

Ptroglodytes

all identical

ENSPTRG00000016260

419

Mmulatta

all identical

ENSMMUG00000019047

416

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029309

406

Ggallus

all conserved

ENSGALG00000010929

411

Trubripes

all identical

ENSTRUG00000009856

368

RRAGKWGSIVGMNPVQIRATVDLYPSTRSALAGH

Drerio

not conserved

ENSDARG00000074989

340

TMDLYPDVRLTRHSNGQGVPA

Dmelanogaster

no alignment

FBgn0026562

n/a

Celegans

not conserved

C44B12.2

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
432	454	DOMAIN	Follistatin-like.	might get lost (downstream of altered splice site)
433	433	DISULFID	By similarity.	might get lost (downstream of altered splice site)
438	438	DISULFID	By similarity.	might get lost (downstream of altered splice site)
444	444	DISULFID	By similarity.	might get lost (downstream of altered splice site)
450	511	DOMAIN	Kazal-like.	might get lost (downstream of altered splice site)
454	454	DISULFID	By similarity.	might get lost (downstream of altered splice site)
456	456	DISULFID	By similarity.	might get lost (downstream of altered splice site)
462	462	DISULFID	By similarity.	might get lost (downstream of altered splice site)
472	472	DISULFID	By similarity.	might get lost (downstream of altered splice site)
476	476	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
483	483	DISULFID	By similarity.	might get lost (downstream of altered splice site)
490	490	DISULFID	By similarity.	might get lost (downstream of altered splice site)
509	509	DISULFID	By similarity.	might get lost (downstream of altered splice site)
515	515	DISULFID	By similarity.	might get lost (downstream of altered splice site)
622	657	DOMAIN	EF-hand.	might get lost (downstream of altered splice site)
626	626	DISULFID	By similarity.	might get lost (downstream of altered splice site)
634	634	DISULFID	By similarity.	might get lost (downstream of altered splice site)
635	646	CA_BIND	Potential.	might get lost (downstream of altered splice site)
650	650	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1995 / 1995

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

665 / 665

position of stopcodon in wt / mu cDNA

2466 / 2466

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

472 / 472

chromosome

strand

-1

last intron/exon boundary

2438

theoretical NMD boundary in CDS

1916

length of CDS

1995

coding sequence (CDS) position

1255

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

1726

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

39408

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

88412806

original gDNA sequence snippet

ACTCATCAAATGAGGAGGAAACGTCAAGTGAAGGCAACATG

altered gDNA sequence snippet

ACTCATCAAATGAGGAGGAAGCGTCAAGTGAAGGCAACATG

original cDNA sequence snippet

ACTCATCAAATGAGGAGGAAACGTCAAGTGAAGGCAACATG

altered cDNA sequence snippet

ACTCATCAAATGAGGAGGAAGCGTCAAGTGAAGGCAACATG

wildtype AA sequence

MKTGLFFLCL LGTAAAIPTN ARLLSDHSKP TAETVAPDNT AIPSLRAEAE ENEKETAVST
EDDSHHKAEK SSVLKSKEES HEQSAEQGKS SSQELGLKDQ EDSDGHLSVN LEYAPTEGTL
DIKEDMSEPQ EKKLSENTDF LAPGVSSFTD SNQQESITKR EENQEQPRNY SHHQLNRSSK
HSQGLRDQGN QEQDPNISNG EEEEEKEPGE VGTHNDNQER KTELPREHAN SKQEEDNTQS
DDILEESDQP TQVSKMQEDE FDQGNQEQED NSNAEMEEEN ASNVNKHIQE TEWQSQEGKT
GLEAISNHKE TEEKTVSEAL LMEPTDDGNT TPRNHGVDDD GDDDGDDGGT DGPRHSASDD
YFIPSQAFLE AERAQSIAYH LKIEEQREKV HENENIGTTE PGEHQEAKKA ENSSNEEETS
SEGNMRVHAV DSCMSFQCKR GHICKADQQG KPHCVCQDPV TCPPTKPLDQ VCGTDNQTYA
SSCHLFATKC RLEGTKKGHQ LQLDYFGACK SIPTCTDFEV IQFPLRMRDW LKNILMQLYE
ANSEHAGYLN EKQRNKVKKI YLDEKRLLAG DHPIDLLLRD FKKNYHMYVY PVHWQFSELD
QHPMDRVLTH SELAPLRASL VPMEHCITRF FEECDPNKDK HITLKEWGHC FGIKEEDIDE
NLLF*

mutated AA sequence

MKTGLFFLCL LGTAAAIPTN ARLLSDHSKP TAETVAPDNT AIPSLRAEAE ENEKETAVST
EDDSHHKAEK SSVLKSKEES HEQSAEQGKS SSQELGLKDQ EDSDGHLSVN LEYAPTEGTL
DIKEDMSEPQ EKKLSENTDF LAPGVSSFTD SNQQESITKR EENQEQPRNY SHHQLNRSSK
HSQGLRDQGN QEQDPNISNG EEEEEKEPGE VGTHNDNQER KTELPREHAN SKQEEDNTQS
DDILEESDQP TQVSKMQEDE FDQGNQEQED NSNAEMEEEN ASNVNKHIQE TEWQSQEGKT
GLEAISNHKE TEEKTVSEAL LMEPTDDGNT TPRNHGVDDD GDDDGDDGGT DGPRHSASDD
YFIPSQAFLE AERAQSIAYH LKIEEQREKV HENENIGTTE PGEHQEAKKA ENSSNEEEAS
SEGNMRVHAV DSCMSFQCKR GHICKADQQG KPHCVCQDPV TCPPTKPLDQ VCGTDNQTYA
SSCHLFATKC RLEGTKKGHQ LQLDYFGACK SIPTCTDFEV IQFPLRMRDW LKNILMQLYE
ANSEHAGYLN EKQRNKVKKI YLDEKRLLAG DHPIDLLLRD FKKNYHMYVY PVHWQFSELD
QHPMDRVLTH SELAPLRASL VPMEHCITRF FEECDPNKDK HITLKEWGHC FGIKEEDIDE
NLLF*

speed

0.45 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: 0.999999999994908 (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)

chr4:88412806T>CN/A show variant in all transcripts IGV

HGNC symbol

SPARCL1

Ensembl transcript ID

ENST00000503414

Genbank transcript ID

N/A

UniProt peptide

Q14515

alteration type

single base exchange

alteration region

CDS

DNA changes

c.880A>G
cDNA.1423A>G
g.39408A>G

AA changes

T294A Score: 58 explain score(s)

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

294

frameshift

known variant

Reference ID: rs1130643

database	homozygous (C/C)	heterozygous	allele carriers
1000G	204	693	897
ExAC	1949	13554	15503

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.563	0
(flanking)	-1.285	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
Donor gained	39402	0.85	mu: ATGAGGAGGAAGCGT	GAGG\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

294

mutated

not conserved

294

Ptroglodytes

all identical

ENSPTRG00000016260

419

Mmulatta

all identical

ENSMMUG00000019047

416

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029309

406

Ggallus

all conserved

ENSGALG00000010929

407

Trubripes

all identical

ENSTRUG00000009856

368

Drerio

not conserved

ENSDARG00000074989

340

TMDLYPDVRLTRHSNGQGVPA

Dmelanogaster

no alignment

FBgn0026562

n/a

Celegans

not conserved

C44B12.2

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
398	398	CARBOHYD	O-linked (GalNAc...) (Probable).	might get lost (downstream of altered splice site)
399	399	CARBOHYD	O-linked (GalNAc...) (Probable).	might get lost (downstream of altered splice site)
412	412	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
432	454	DOMAIN	Follistatin-like.	might get lost (downstream of altered splice site)
433	433	DISULFID	By similarity.	might get lost (downstream of altered splice site)
438	438	DISULFID	By similarity.	might get lost (downstream of altered splice site)
444	444	DISULFID	By similarity.	might get lost (downstream of altered splice site)
450	511	DOMAIN	Kazal-like.	might get lost (downstream of altered splice site)
454	454	DISULFID	By similarity.	might get lost (downstream of altered splice site)
456	456	DISULFID	By similarity.	might get lost (downstream of altered splice site)
462	462	DISULFID	By similarity.	might get lost (downstream of altered splice site)
472	472	DISULFID	By similarity.	might get lost (downstream of altered splice site)
476	476	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
483	483	DISULFID	By similarity.	might get lost (downstream of altered splice site)
490	490	DISULFID	By similarity.	might get lost (downstream of altered splice site)
509	509	DISULFID	By similarity.	might get lost (downstream of altered splice site)
515	515	DISULFID	By similarity.	might get lost (downstream of altered splice site)
622	657	DOMAIN	EF-hand.	might get lost (downstream of altered splice site)
626	626	DISULFID	By similarity.	might get lost (downstream of altered splice site)
634	634	DISULFID	By similarity.	might get lost (downstream of altered splice site)
635	646	CA_BIND	Potential.	might get lost (downstream of altered splice site)
650	650	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1620 / 1620

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

540 / 540

position of stopcodon in wt / mu cDNA

2163 / 2163

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

544 / 544

chromosome

strand

-1

last intron/exon boundary

2135

theoretical NMD boundary in CDS

1541

length of CDS

1620

coding sequence (CDS) position

880

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

1423

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

39408

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

88412806

original gDNA sequence snippet

ACTCATCAAATGAGGAGGAAACGTCAAGTGAAGGCAACATG

altered gDNA sequence snippet

ACTCATCAAATGAGGAGGAAGCGTCAAGTGAAGGCAACATG

original cDNA sequence snippet

ACTCATCAAATGAGGAGGAAACGTCAAGTGAAGGCAACATG

altered cDNA sequence snippet

ACTCATCAAATGAGGAGGAAGCGTCAAGTGAAGGCAACATG

wildtype AA sequence

MSEPQEKKLS ENTDFLAPGV SSFTDSNQQE SITKREENQE QPRNYSHHQL NRSSKHSQGL
RDQGNQEQDP NISNGEEEEE KEPGEVGTHN DNQERKTELP REHANSKQEE DNTQSDDILE
ESDQPTQVSK MQEDEFDQGN QEQEDNSNAE MEEENASNVN KHIQETEWQS QEGKTGLEAI
SNHKETEEKT VSEALLMEPT DDGNTTPRNH GVDDDGDDDG DDGGTDGPRH SASDDYFIPS
QAFLEAERAQ SIAYHLKIEE QREKVHENEN IGTTEPGEHQ EAKKAENSSN EEETSSEGNM
RVHAVDSCMS FQCKRGHICK ADQQGKPHCV CQDPVTCPPT KPLDQVCGTD NQTYASSCHL
FATKCRLEGT KKGHQLQLDY FGACKSIPTC TDFEVIQFPL RMRDWLKNIL MQLYEANSEH
AGYLNEKQRN KVKKIYLDEK RLLAGDHPID LLLRDFKKNY HMYVYPVHWQ FSELDQHPMD
RVLTHSELAP LRASLVPMEH CITRFFEECD PNKDKHITLK EWGHCFGIKE EDIDENLLF*

mutated AA sequence

MSEPQEKKLS ENTDFLAPGV SSFTDSNQQE SITKREENQE QPRNYSHHQL NRSSKHSQGL
RDQGNQEQDP NISNGEEEEE KEPGEVGTHN DNQERKTELP REHANSKQEE DNTQSDDILE
ESDQPTQVSK MQEDEFDQGN QEQEDNSNAE MEEENASNVN KHIQETEWQS QEGKTGLEAI
SNHKETEEKT VSEALLMEPT DDGNTTPRNH GVDDDGDDDG DDGGTDGPRH SASDDYFIPS
QAFLEAERAQ SIAYHLKIEE QREKVHENEN IGTTEPGEHQ EAKKAENSSN EEEASSEGNM
RVHAVDSCMS FQCKRGHICK ADQQGKPHCV CQDPVTCPPT KPLDQVCGTD NQTYASSCHL
FATKCRLEGT KKGHQLQLDY FGACKSIPTC TDFEVIQFPL RMRDWLKNIL MQLYEANSEH
AGYLNEKQRN KVKKIYLDEK RLLAGDHPID LLLRDFKKNY HMYVYPVHWQ FSELDQHPMD
RVLTHSELAP LRASLVPMEH CITRFFEECD PNKDKHITLK EWGHCFGIKE EDIDENLLF*

speed

0.48 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999994908 (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)

chr4:88412806T>CN/A show variant in all transcripts IGV

HGNC symbol

SPARCL1

Ensembl transcript ID

ENST00000418378

Genbank transcript ID

NM_001128310

UniProt peptide

Q14515

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1255A>G
cDNA.1827A>G
g.39408A>G

AA changes

T419A Score: 58 explain score(s)

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

419

frameshift

known variant

Reference ID: rs1130643

database	homozygous (C/C)	heterozygous	allele carriers
1000G	204	693	897
ExAC	1949	13554	15503

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.563	0
(flanking)	-1.285	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
Donor gained	39402	0.85	mu: ATGAGGAGGAAGCGT	GAGG\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

419

mutated

not conserved

419

Ptroglodytes

all identical

ENSPTRG00000016260

419

Mmulatta

all identical

ENSMMUG00000019047

416

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029309

406

Ggallus

all conserved

ENSGALG00000010929

411

Trubripes

all identical

ENSTRUG00000009856

368

RRAGKWGSIVGMNPVQIRATVDLYPSTRSALAGH

Drerio

not conserved

ENSDARG00000074989

340

TMDLYPDVRLTRHSNGQGVPA

Dmelanogaster

no alignment

FBgn0026562

n/a

Celegans

not conserved

C44B12.2

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
432	454	DOMAIN	Follistatin-like.	might get lost (downstream of altered splice site)
433	433	DISULFID	By similarity.	might get lost (downstream of altered splice site)
438	438	DISULFID	By similarity.	might get lost (downstream of altered splice site)
444	444	DISULFID	By similarity.	might get lost (downstream of altered splice site)
450	511	DOMAIN	Kazal-like.	might get lost (downstream of altered splice site)
454	454	DISULFID	By similarity.	might get lost (downstream of altered splice site)
456	456	DISULFID	By similarity.	might get lost (downstream of altered splice site)
462	462	DISULFID	By similarity.	might get lost (downstream of altered splice site)
472	472	DISULFID	By similarity.	might get lost (downstream of altered splice site)
476	476	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
483	483	DISULFID	By similarity.	might get lost (downstream of altered splice site)
490	490	DISULFID	By similarity.	might get lost (downstream of altered splice site)
509	509	DISULFID	By similarity.	might get lost (downstream of altered splice site)
515	515	DISULFID	By similarity.	might get lost (downstream of altered splice site)
622	657	DOMAIN	EF-hand.	might get lost (downstream of altered splice site)
626	626	DISULFID	By similarity.	might get lost (downstream of altered splice site)
634	634	DISULFID	By similarity.	might get lost (downstream of altered splice site)
635	646	CA_BIND	Potential.	might get lost (downstream of altered splice site)
650	650	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1995 / 1995

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

665 / 665

position of stopcodon in wt / mu cDNA

2567 / 2567

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

573 / 573

chromosome

strand

-1

last intron/exon boundary

2539

theoretical NMD boundary in CDS

1916

length of CDS

1995

coding sequence (CDS) position

1255

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

1827

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

39408

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

88412806

original gDNA sequence snippet

ACTCATCAAATGAGGAGGAAACGTCAAGTGAAGGCAACATG

altered gDNA sequence snippet

ACTCATCAAATGAGGAGGAAGCGTCAAGTGAAGGCAACATG

original cDNA sequence snippet

ACTCATCAAATGAGGAGGAAACGTCAAGTGAAGGCAACATG

altered cDNA sequence snippet

ACTCATCAAATGAGGAGGAAGCGTCAAGTGAAGGCAACATG

wildtype AA sequence

mutated AA sequence

MKTGLFFLCL LGTAAAIPTN ARLLSDHSKP TAETVAPDNT AIPSLRAEAE ENEKETAVST
EDDSHHKAEK SSVLKSKEES HEQSAEQGKS SSQELGLKDQ EDSDGHLSVN LEYAPTEGTL
DIKEDMSEPQ EKKLSENTDF LAPGVSSFTD SNQQESITKR EENQEQPRNY SHHQLNRSSK
HSQGLRDQGN QEQDPNISNG EEEEEKEPGE VGTHNDNQER KTELPREHAN SKQEEDNTQS
DDILEESDQP TQVSKMQEDE FDQGNQEQED NSNAEMEEEN ASNVNKHIQE TEWQSQEGKT
GLEAISNHKE TEEKTVSEAL LMEPTDDGNT TPRNHGVDDD GDDDGDDGGT DGPRHSASDD
YFIPSQAFLE AERAQSIAYH LKIEEQREKV HENENIGTTE PGEHQEAKKA ENSSNEEEAS
SEGNMRVHAV DSCMSFQCKR GHICKADQQG KPHCVCQDPV TCPPTKPLDQ VCGTDNQTYA
SSCHLFATKC RLEGTKKGHQ LQLDYFGACK SIPTCTDFEV IQFPLRMRDW LKNILMQLYE
ANSEHAGYLN EKQRNKVKKI YLDEKRLLAG DHPIDLLLRD FKKNYHMYVY PVHWQFSELD
QHPMDRVLTH SELAPLRASL VPMEHCITRF FEECDPNKDK HITLKEWGHC FGIKEEDIDE
NLLF*

speed

0.35 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems