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 3.393037 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL10A1	disease_causing	0.99999724019723	simple_aae		affected		S671P	single base exchange	rs111033552		show file
COL10A1	disease_causing	0.99999724019723	simple_aae		affected		S671P	single base exchange	rs111033552		show file
NT5DC1	disease_causing	1	without_aae		affected			single base exchange	rs111033552		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999724019723 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs17477 (probable pathogenic)
known disease mutation at this position (HGMD CM960316)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116441268A>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.2011T>C
cDNA.2419T>C
g.38643T>C

AA changes

S671P Score: 74 explain score(s)

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

671

frameshift

known variant

Reference ID: rs111033552
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs17477 (probable pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960316)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960316)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960316)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.31	1
	1.131	0.993
(flanking)	-0.187	0.965

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 marginally increased	38650	wt: 0.9043 / mu: 0.9148 (marginal change - not scored)	wt: GTATGTCCACTCCTCTTTCTCAGGATTCCTAGTGGCTCCAA mu: GTATGTCCACTCCCCTTTCTCAGGATTCCTAGTGGCTCCAA	tctc\|AGGA
Acc marginally increased	38644	wt: 0.2905 / mu: 0.3153 (marginal change - not scored)	wt: CTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTGG mu: CTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTGG	cctc\|TTTC
Acc gained	38635	0.34	mu: CCTATACTCCTCTGAGTATGTCCACTCCCCTTTCTCAGGAT	atgt\|CCAC

distance from splice site

1080

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

671

mutated

not conserved

671

Ptroglodytes

all identical

ENSPTRG00000018524

671

Mmulatta

all identical

ENSMMUG00000014642

671

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000039462

671

Ggallus

all identical

ENSGALG00000014965

665

Trubripes

all identical

ENSTRUG00000006358

606

Drerio

all identical

ENSDARG00000054753

646

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000033031

606

protein features

start (aa)	end (aa)	feature	details
520	680	REGION	Nonhelical region (NC1).	lost
547	680	DOMAIN	C1q.	lost
666	668	STRAND		might get lost (downstream of altered splice site)
671	679	STRAND		lost

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

2011

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

2419

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

38643

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

116441268

original gDNA sequence snippet

CCTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTG

altered gDNA sequence snippet

CCTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTG

original cDNA sequence snippet

CCTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTG

altered cDNA sequence snippet

CCTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTG

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

0.56 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: 0.99999724019723 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs17477 (probable pathogenic)
known disease mutation at this position (HGMD CM960316)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116441268A>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.2011T>C
cDNA.2107T>C
g.38643T>C

AA changes

S671P Score: 74 explain score(s)

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

671

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)	4.31	1
	1.131	0.993
(flanking)	-0.187	0.965

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 marginally increased	38650	wt: 0.9043 / mu: 0.9148 (marginal change - not scored)	wt: GTATGTCCACTCCTCTTTCTCAGGATTCCTAGTGGCTCCAA mu: GTATGTCCACTCCCCTTTCTCAGGATTCCTAGTGGCTCCAA	tctc\|AGGA
Acc marginally increased	38644	wt: 0.2905 / mu: 0.3153 (marginal change - not scored)	wt: CTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTGG mu: CTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTGG	cctc\|TTTC
Acc gained	38635	0.34	mu: CCTATACTCCTCTGAGTATGTCCACTCCCCTTTCTCAGGAT	atgt\|CCAC

distance from splice site

1183

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

671

mutated

not conserved

671

Ptroglodytes

all identical

ENSPTRG00000018524

671

Mmulatta

all identical

ENSMMUG00000014642

671

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000039462

671

Ggallus

all identical

ENSGALG00000014965

665

Trubripes

all identical

ENSTRUG00000006358

606

Drerio

all identical

ENSDARG00000054753

646

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000033031

606

protein features

start (aa)	end (aa)	feature	details
520	680	REGION	Nonhelical region (NC1).	lost
547	680	DOMAIN	C1q.	lost
666	668	STRAND		might get lost (downstream of altered splice site)
671	679	STRAND		lost

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

2011

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

2107

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

38643

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

116441268

original gDNA sequence snippet

CCTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTG

altered gDNA sequence snippet

CCTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTG

original cDNA sequence snippet

CCTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTG

altered cDNA sequence snippet

CCTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTG

wildtype AA sequence

mutated AA sequence

speed

0.85 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known as potential disease variant: rs17477 (probable pathogenic)
known disease mutation at this position (HGMD CM960316)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116441268A>GN/A show variant in all transcripts IGV

HGNC symbol

NT5DC1

Ensembl transcript ID

ENST00000319550

Genbank transcript ID

NM_152729

UniProt peptide

Q5TFE4

alteration type

single base exchange

alteration region

intron

DNA changes

g.19257A>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)	4.31	1
	1.131	0.993
(flanking)	-0.187	0.965

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	19250	wt: 0.9376 / mu: 0.9424 (marginal change - not scored)	wt: ATCCTGAGAAAGAGG mu: ATCCTGAGAAAGGGG	CCTG\|agaa
Donor marginally increased	19255	wt: 0.9955 / mu: 0.9956 (marginal change - not scored)	wt: GAGAAAGAGGAGTGG mu: GAGAAAGGGGAGTGG	GAAA\|gagg
Donor increased	19251	wt: 0.64 / mu: 0.98	wt: TCCTGAGAAAGAGGA mu: TCCTGAGAAAGGGGA	CTGA\|gaaa

distance from splice site

2160

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
313	313	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)

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)

19257

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

116441268

original gDNA sequence snippet

CACTAGGAATCCTGAGAAAGAGGAGTGGACATACTCAGAGG

altered gDNA sequence snippet

CACTAGGAATCCTGAGAAAGGGGAGTGGACATACTCAGAGG

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

0.45 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