MutationTaster - study a chromosomal position

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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 2.456406 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL10A1	disease_causing_automatic	0.999999542492878	simple_aae		affected	0	W651R	single base exchange	rs111033549		show file
COL10A1	disease_causing_automatic	0.999999542492878	simple_aae		affected	0	W651R	single base exchange	rs111033549		show file
NT5DC1	disease_causing_automatic	1	without_aae			0		single base exchange	rs111033549		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999542492878 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM952027)
known disease mutation: rs17474 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116441328A>GN/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.1951T>C
cDNA.2359T>C
g.38583T>C

AA changes

W651R Score: 101 explain score(s)

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

651

frameshift

known variant

Reference ID: rs111033549
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17474 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM952027)

known disease mutation at this position, please check HGMD for details (HGMD ID CM952027)
known disease mutation at this position, please check HGMD for details (HGMD ID CM952027)

regulatory features

H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.605	1
	4.881	1
(flanking)	-0.175	0.979

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	38578	wt: 0.8067 / mu: 0.8716 (marginal change - not scored)	wt: TGACCAGGTGTGGCT mu: TGACCAGGTGCGGCT	ACCA\|ggtg
Donor increased	38574	wt: 0.82 / mu: 0.91	wt: AAAATGACCAGGTGT mu: AAAATGACCAGGTGC	AATG\|acca

distance from splice site

1140

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

651

mutated

not conserved

651

Ptroglodytes

all identical

ENSPTRG00000018524

651

Mmulatta

all identical

ENSMMUG00000014642

651

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000039462

651

Ggallus

all identical

ENSGALG00000014965

645

Trubripes

all conserved

ENSTRUG00000006358

586

Drerio

all conserved

ENSDARG00000054753

626

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000033031

586

protein features

start (aa)	end (aa)	feature	details
520	680	REGION	Nonhelical region (NC1).	lost
547	680	DOMAIN	C1q.	lost
649	653	STRAND		lost
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

1951

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

2359

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

38583

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

116441328

original gDNA sequence snippet

TCACAGAAAATGACCAGGTGTGGCTCCAGCTTCCCAATGCC

altered gDNA sequence snippet

TCACAGAAAATGACCAGGTGCGGCTCCAGCTTCCCAATGCC

original cDNA sequence snippet

TCACAGAAAATGACCAGGTGTGGCTCCAGCTTCCCAATGCC

altered cDNA sequence snippet

TCACAGAAAATGACCAGGTGCGGCTCCAGCTTCCCAATGCC

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

speed

0.28 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: 0.999999542492878 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM952027)
known disease mutation: rs17474 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116441328A>GN/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.1951T>C
cDNA.2047T>C
g.38583T>C

AA changes

W651R Score: 101 explain score(s)

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

651

frameshift

known variant

regulatory features

H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.605	1
	4.881	1
(flanking)	-0.175	0.979

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	38578	wt: 0.8067 / mu: 0.8716 (marginal change - not scored)	wt: TGACCAGGTGTGGCT mu: TGACCAGGTGCGGCT	ACCA\|ggtg
Donor increased	38574	wt: 0.82 / mu: 0.91	wt: AAAATGACCAGGTGT mu: AAAATGACCAGGTGC	AATG\|acca

distance from splice site

1243

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

651

mutated

not conserved

651

Ptroglodytes

all identical

ENSPTRG00000018524

651

Mmulatta

all identical

ENSMMUG00000014642

651

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000039462

651

Ggallus

all identical

ENSGALG00000014965

645

Trubripes

all conserved

ENSTRUG00000006358

586

Drerio

all conserved

ENSDARG00000054753

626

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000033031

586

protein features

start (aa)	end (aa)	feature	details
520	680	REGION	Nonhelical region (NC1).	lost
547	680	DOMAIN	C1q.	lost
649	653	STRAND		lost
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

1951

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

2047

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

38583

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

116441328

original gDNA sequence snippet

TCACAGAAAATGACCAGGTGTGGCTCCAGCTTCCCAATGCC

altered gDNA sequence snippet

TCACAGAAAATGACCAGGTGCGGCTCCAGCTTCCCAATGCC

original cDNA sequence snippet

TCACAGAAAATGACCAGGTGTGGCTCCAGCTTCCCAATGCC

altered cDNA sequence snippet

TCACAGAAAATGACCAGGTGCGGCTCCAGCTTCCCAATGCC

wildtype AA sequence

mutated AA sequence

speed

0.20 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 CM952027)
known disease mutation: rs17474 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116441328A>GN/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.19317A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.605	1
	4.881	1
(flanking)	-0.175	0.979

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	19308	wt: 0.6002 / mu: 0.6070 (marginal change - not scored)	wt: GGGAAGCTGGAGCCA mu: GGGAAGCTGGAGCCG	GAAG\|ctgg

distance from splice site

2220

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)

19317

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

116441328

original gDNA sequence snippet

GGCATTGGGAAGCTGGAGCCACACCTGGTCATTTTCTGTGA

altered gDNA sequence snippet

GGCATTGGGAAGCTGGAGCCGCACCTGGTCATTTTCTGTGA

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

0.15 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