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: ENST00000319550
Querying Taster for transcript #2: ENST00000327673
Querying Taster for transcript #3: ENST00000243222
MT speed 0 s - this script 4.45787 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL10A1	disease_causing_automatic	0.996501425412234	simple_aae		affected	0	G18R	single base exchange	rs111033550		show file
COL10A1	disease_causing_automatic	0.996501425412234	simple_aae		affected	0	G18R	single base exchange	rs111033550		show file
NT5DC1	disease_causing_automatic	1	without_aae			0		single base exchange	rs111033550		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.996501425412234 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970341)
known disease mutation: rs17475 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116446604C>TN/A show variant in all transcripts IGV

HGNC symbol

COL10A1

Ensembl transcript ID

ENST00000327673

Genbank transcript ID

N/A

UniProt peptide

Q03692

alteration type

single base exchange

alteration region

CDS

DNA changes

c.52G>A
cDNA.460G>A
g.33307G>A

AA changes

G18R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs111033550
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17475 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970341)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970341)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970341)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.203	0.996
	3.073	1
(flanking)	0.541	1

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 increased	33304	wt: 0.35 / mu: 0.45	wt: TAGTATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAA mu: TAGTATCCTTGAACTTGGTTCATAGAGTGTTTTACGCTGAA	gttc\|ATGG
Acc marginally increased	33318	wt: 0.8640 / mu: 0.8737 (marginal change - not scored)	wt: TTGGTTCATGGAGTGTTTTACGCTGAACGATACCAAATGCC mu: TTGGTTCATAGAGTGTTTTACGCTGAACGATACCAAATGCC	ttac\|GCTG
Donor marginally increased	33304	wt: 0.8175 / mu: 0.8613 (marginal change - not scored)	wt: TGGTTCATGGAGTGT mu: TGGTTCATAGAGTGT	GTTC\|atgg

distance from splice site

103

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000018524

Mmulatta

all identical

ENSMMUG00000014642

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000039462

Ggallus

all identical

ENSGALG00000014965

SDG

Trubripes

no alignment

ENSTRUG00000006358

n/a

Drerio

all identical

ENSDARG00000054753

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000033031

n/a

protein features

start (aa)	end (aa)	feature	details
1	18	SIGNAL	Potential.	lost
19	56	REGION	Nonhelical region (NC2).	might get lost (downstream of altered splice site)
57	519	REGION	Triple-helical region.	might get lost (downstream of altered splice site)
500	500	CONFLICT	H -> P (in Ref. 1; CAA42933).	might get lost (downstream of altered splice site)
520	680	REGION	Nonhelical region (NC1).	might get lost (downstream of altered splice site)
547	680	DOMAIN	C1q.	might get lost (downstream of altered splice site)
553	557	STRAND		might get lost (downstream of altered splice site)
560	562	STRAND		might get lost (downstream of altered splice site)
573	576	STRAND		might get lost (downstream of altered splice site)
584	586	TURN		might get lost (downstream of altered splice site)
595	616	STRAND		might get lost (downstream of altered splice site)
619	626	STRAND		might get lost (downstream of altered splice site)
634	634	METAL	Calcium.	might get lost (downstream of altered splice site)
634	644	STRAND		might get lost (downstream of altered splice site)
649	653	STRAND		might get lost (downstream of altered splice site)
659	663	STRAND		might get lost (downstream of altered splice site)
666	668	STRAND		might get lost (downstream of altered splice site)
671	679	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2043 / 2043

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

681 / 681

position of stopcodon in wt / mu cDNA

2451 / 2451

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

409 / 409

chromosome

strand

-1

last intron/exon boundary

563

theoretical NMD boundary in CDS

104

length of CDS

2043

coding sequence (CDS) position

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

460

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

33307

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

116446604

original gDNA sequence snippet

TATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGA

altered gDNA sequence snippet

TATCCTTGAACTTGGTTCATAGAGTGTTTTACGCTGAACGA

original cDNA sequence snippet

TATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGA

altered cDNA sequence snippet

TATCCTTGAACTTGGTTCATAGAGTGTTTTACGCTGAACGA

wildtype AA sequence

MLPQIPFLLL VSLNLVHGVF YAERYQMPTG IKGPLPNTKT QFFIPYTIKS KGIAVRGEQG
TPGPPGPAGP RGHPGPSGPP GKPGYGSPGL QGEPGLPGPP GPSAVGKPGV PGLPGKPGER
GPYGPKGDVG PAGLPGPRGP PGPPGIPGPA GISVPGKPGQ QGPTGAPGPR GFPGEKGAPG
VPGMNGQKGE MGYGAPGRPG ERGLPGPQGP TGPSGPPGVG KRGENGVPGQ PGIKGDRGFP
GEMGPIGPPG PQGPPGERGP EGIGKPGAAG APGQPGIPGT KGLPGAPGIA GPPGPPGFGK
PGLPGLKGER GPAGLPGGPG AKGEQGPAGL PGKPGLTGPP GNMGPQGPKG IPGSHGLPGP
KGETGPAGPA GYPGAKGERG SPGSDGKPGY PGKPGLDGPK GNPGLPGPKG DPGVGGPPGL
PGPVGPAGAK GMPGHNGEAG PRGAPGIPGT RGPIGPPGIP GFPGSKGDPG SPGPPGPAGI
ATKGLNGPTG PPGPPGPRGH SGEPGLPGPP GPPGPPGQAV MPEGFIKAGQ RPSLSGTPLV
SANQGVTGMP VSAFTVILSK AYPAIGTPIP FDKILYNRQQ HYDPRTGIFT CQIPGIYYFS
YHVHVKGTHV WVGLYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN
GLYSSEYVHS SFSGFLVAPM *

mutated AA sequence

MLPQIPFLLL VSLNLVHRVF YAERYQMPTG IKGPLPNTKT QFFIPYTIKS KGIAVRGEQG
TPGPPGPAGP RGHPGPSGPP GKPGYGSPGL QGEPGLPGPP GPSAVGKPGV PGLPGKPGER
GPYGPKGDVG PAGLPGPRGP PGPPGIPGPA GISVPGKPGQ QGPTGAPGPR GFPGEKGAPG
VPGMNGQKGE MGYGAPGRPG ERGLPGPQGP TGPSGPPGVG KRGENGVPGQ PGIKGDRGFP
GEMGPIGPPG PQGPPGERGP EGIGKPGAAG APGQPGIPGT KGLPGAPGIA GPPGPPGFGK
PGLPGLKGER GPAGLPGGPG AKGEQGPAGL PGKPGLTGPP GNMGPQGPKG IPGSHGLPGP
KGETGPAGPA GYPGAKGERG SPGSDGKPGY PGKPGLDGPK GNPGLPGPKG DPGVGGPPGL
PGPVGPAGAK GMPGHNGEAG PRGAPGIPGT RGPIGPPGIP GFPGSKGDPG SPGPPGPAGI
ATKGLNGPTG PPGPPGPRGH SGEPGLPGPP GPPGPPGQAV MPEGFIKAGQ RPSLSGTPLV
SANQGVTGMP VSAFTVILSK AYPAIGTPIP FDKILYNRQQ HYDPRTGIFT CQIPGIYYFS
YHVHVKGTHV WVGLYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN
GLYSSEYVHS SFSGFLVAPM *

speed

0.64 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: 0.996501425412234 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970341)
known disease mutation: rs17475 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116446604C>TN/A show variant in all transcripts IGV

HGNC symbol

COL10A1

Ensembl transcript ID

ENST00000243222

Genbank transcript ID

NM_000493

UniProt peptide

Q03692

alteration type

single base exchange

alteration region

CDS

DNA changes

c.52G>A
cDNA.148G>A
g.33307G>A

AA changes

G18R Score: 125 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)	2.203	0.996
	3.073	1
(flanking)	0.541	1

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 increased	33304	wt: 0.35 / mu: 0.45	wt: TAGTATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAA mu: TAGTATCCTTGAACTTGGTTCATAGAGTGTTTTACGCTGAA	gttc\|ATGG
Acc marginally increased	33318	wt: 0.8640 / mu: 0.8737 (marginal change - not scored)	wt: TTGGTTCATGGAGTGTTTTACGCTGAACGATACCAAATGCC mu: TTGGTTCATAGAGTGTTTTACGCTGAACGATACCAAATGCC	ttac\|GCTG
Donor marginally increased	33304	wt: 0.8175 / mu: 0.8613 (marginal change - not scored)	wt: TGGTTCATGGAGTGT mu: TGGTTCATAGAGTGT	GTTC\|atgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000018524

Mmulatta

all identical

ENSMMUG00000014642

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000039462

Ggallus

all identical

ENSGALG00000014965

SDG

Trubripes

no alignment

ENSTRUG00000006358

n/a

Drerio

all identical

ENSDARG00000054753

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000033031

n/a

protein features

start (aa)	end (aa)	feature	details
1	18	SIGNAL	Potential.	lost
19	56	REGION	Nonhelical region (NC2).	might get lost (downstream of altered splice site)
57	519	REGION	Triple-helical region.	might get lost (downstream of altered splice site)
500	500	CONFLICT	H -> P (in Ref. 1; CAA42933).	might get lost (downstream of altered splice site)
520	680	REGION	Nonhelical region (NC1).	might get lost (downstream of altered splice site)
547	680	DOMAIN	C1q.	might get lost (downstream of altered splice site)
553	557	STRAND		might get lost (downstream of altered splice site)
560	562	STRAND		might get lost (downstream of altered splice site)
573	576	STRAND		might get lost (downstream of altered splice site)
584	586	TURN		might get lost (downstream of altered splice site)
595	616	STRAND		might get lost (downstream of altered splice site)
619	626	STRAND		might get lost (downstream of altered splice site)
634	634	METAL	Calcium.	might get lost (downstream of altered splice site)
634	644	STRAND		might get lost (downstream of altered splice site)
649	653	STRAND		might get lost (downstream of altered splice site)
659	663	STRAND		might get lost (downstream of altered splice site)
666	668	STRAND		might get lost (downstream of altered splice site)
671	679	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2043 / 2043

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

681 / 681

position of stopcodon in wt / mu cDNA

2139 / 2139

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

97 / 97

chromosome

strand

-1

last intron/exon boundary

251

theoretical NMD boundary in CDS

104

length of CDS

2043

coding sequence (CDS) position

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

148

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

33307

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

116446604

original gDNA sequence snippet

TATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGA

altered gDNA sequence snippet

TATCCTTGAACTTGGTTCATAGAGTGTTTTACGCTGAACGA

original cDNA sequence snippet

TATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGA

altered cDNA sequence snippet

TATCCTTGAACTTGGTTCATAGAGTGTTTTACGCTGAACGA

wildtype AA sequence

mutated AA sequence

speed

1.21 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM970341)
known disease mutation: rs17475 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116446604C>TN/A show variant in all transcripts IGV

HGNC symbol

NT5DC1

Ensembl transcript ID

ENST00000319550

Genbank transcript ID

NM_152729

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.24593C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.203	0.996
	3.073	1
(flanking)	0.541	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

7496

Kozak consensus sequence altered?

N/A

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

83 / 83

chromosome

strand

last intron/exon boundary

1335

theoretical NMD boundary in CDS

1202

length of CDS

1368

coding sequence (CDS) position

N/A

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

N/A

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

24593

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

116446604

original gDNA sequence snippet

TCGTTCAGCGTAAAACACTCCATGAACCAAGTTCAAGGATA

altered gDNA sequence snippet

TCGTTCAGCGTAAAACACTCTATGAACCAAGTTCAAGGATA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAQHFSLAAC DVVGFDLDHT LCRYNLPESA PLIYNSFAQF LVKEKGYDKE LLNVTPEDWD
FCCKGLALDL EDGNFLKLAN NGTVLRASHG TKMMTPEVLA EAYGKKEWKH FLSDTGMACR
SGKYYFYDNY FDLPGALLCA RVVDYLTKLN NGQKTFDFWK DIVAAIQHNY KMSAFKENCG
IYFPEIKRDP GRYLHSCPES VKKWLRQLKN AGKILLLITS SHSDYCRLLC EYILGNDFTD
LFDIVITNAL KPGFFSHLPS QRPFRTLEND EEQEALPSLD KPGWYSQGNA VHLYELLKKM
TGKPEPKVVY FGDSMHSDIF PARHYSNWET VLILEELRGD EGTRSQRPEE SEPLEKKGKY
EGPKAKPLNT SSKKWGSFFI DSVLGLENTE DSLVYTWSCK RISTYSTIAI PSIEAIAELP
LDYKFTRFSS SNSKTAGYYP NPPLVLSSDE TLISK*

mutated AA sequence

N/A

speed

0.51 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