MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000282470
Querying Taster for transcript #2: ENST00000503414
Querying Taster for transcript #3: ENST00000535835
Querying Taster for transcript #4: ENST00000418378
MT speed 0 s - this script 3.087145 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPARCL1	polymorphism_automatic	3.99680288865056e-15	simple_aae				H106D	single base exchange	rs1049544		show file
SPARCL1	polymorphism_automatic	3.99680288865056e-15	simple_aae				H106D	single base exchange	rs1049544		show file
SPARCL1	polymorphism_automatic	3.42043935139813e-05	without_aae					single base exchange	rs1049544		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999996 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:88415636G>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.316C>G
cDNA.787C>G
g.36578C>G

AA changes

H106D Score: 81 explain score(s)

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

106

frameshift

known variant

Reference ID: rs1049544

database	homozygous (C/C)	heterozygous	allele carriers
1000G	944	995	1939
ExAC	13865	5037	18902

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.626	0.025
	1.089	0.026
(flanking)	0.271	0.018

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	36575	wt: 0.7143 / mu: 0.7197 (marginal change - not scored)	wt: GTGATGGTCACTTAA mu: GTGATGGTGACTTAA	GATG\|gtca

distance from splice site

115

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

106

mutated

not conserved

106

Ptroglodytes

not conserved

ENSPTRG00000016260

106

Mmulatta

not conserved

ENSMMUG00000019047

106

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029309

100

Ggallus

not conserved

ENSGALG00000010929

101

Trubripes

not conserved

ENSTRUG00000009856

Drerio

not conserved

ENSDARG00000074989

162

Dmelanogaster

no alignment

FBgn0026562

n/a

Celegans

no alignment

C44B12.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
103	119	REGION	O-glycosylated at two sites.	lost

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

316

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

787

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

36578

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

88415636

original gDNA sequence snippet

ATCAAGAGGACAGTGATGGTCACTTAAGTGTGAATTTGGAG

altered gDNA sequence snippet

ATCAAGAGGACAGTGATGGTGACTTAAGTGTGAATTTGGAG

original cDNA sequence snippet

ATCAAGAGGACAGTGATGGTCACTTAAGTGTGAATTTGGAG

altered cDNA sequence snippet

ATCAAGAGGACAGTGATGGTGACTTAAGTGTGAATTTGGAG

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 EDSDGDLSVN 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*

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

polymorphism

Model: simple_aae, prob: 0.999999999999996 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:88415636G>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.316C>G
cDNA.888C>G
g.36578C>G

AA changes

H106D Score: 81 explain score(s)

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

106

frameshift

known variant

Reference ID: rs1049544

database	homozygous (C/C)	heterozygous	allele carriers
1000G	944	995	1939
ExAC	13865	5037	18902

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.626	0.025
	1.089	0.026
(flanking)	0.271	0.018

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	36575	wt: 0.7143 / mu: 0.7197 (marginal change - not scored)	wt: GTGATGGTCACTTAA mu: GTGATGGTGACTTAA	GATG\|gtca

distance from splice site

115

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

106

mutated

not conserved

106

Ptroglodytes

not conserved

ENSPTRG00000016260

106

Mmulatta

not conserved

ENSMMUG00000019047

106

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029309

100

Ggallus

not conserved

ENSGALG00000010929

101

Trubripes

not conserved

ENSTRUG00000009856

Drerio

not conserved

ENSDARG00000074989

162

Dmelanogaster

no alignment

FBgn0026562

n/a

Celegans

no alignment

C44B12.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
103	119	REGION	O-glycosylated at two sites.	lost

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

316

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

888

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

36578

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

88415636

original gDNA sequence snippet

ATCAAGAGGACAGTGATGGTCACTTAAGTGTGAATTTGGAG

altered gDNA sequence snippet

ATCAAGAGGACAGTGATGGTGACTTAAGTGTGAATTTGGAG

original cDNA sequence snippet

ATCAAGAGGACAGTGATGGTCACTTAAGTGTGAATTTGGAG

altered cDNA sequence snippet

ATCAAGAGGACAGTGATGGTGACTTAAGTGTGAATTTGGAG

wildtype AA sequence

mutated AA sequence

speed

0.33 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999965795606486 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:88415636G>CN/A show variant in all transcripts IGV

HGNC symbol

SPARCL1

Ensembl transcript ID

ENST00000503414

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.484C>G
g.36578C>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1049544

database	homozygous (C/C)	heterozygous	allele carriers
1000G	944	995	1939
ExAC	13865	5037	18902

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.626	0.025
	1.089	0.026
(flanking)	0.271	0.018

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	36575	wt: 0.7143 / mu: 0.7197 (marginal change - not scored)	wt: GTGATGGTCACTTAA mu: GTGATGGTGACTTAA	GATG\|gtca

distance from splice site

115

Kozak consensus sequence altered?

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

544 / 544

chromosome

strand

-1

last intron/exon boundary

2135

theoretical NMD boundary in CDS

1541

length of CDS

1620

coding sequence (CDS) position

N/A

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

484

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

36578

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

88415636

original gDNA sequence snippet

ATCAAGAGGACAGTGATGGTCACTTAAGTGTGAATTTGGAG

altered gDNA sequence snippet

ATCAAGAGGACAGTGATGGTGACTTAAGTGTGAATTTGGAG

original cDNA sequence snippet

ATCAAGAGGACAGTGATGGTCACTTAAGTGTGAATTTGGAG

altered cDNA sequence snippet

ATCAAGAGGACAGTGATGGTGACTTAAGTGTGAATTTGGAG

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

N/A

speed

0.84 s

Problems

annotation problem

The chosen transcript ENST00000535835 on chromosome 4 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

back to results table