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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000417816
Querying Taster for transcript #2: ENST00000534331
Querying Taster for transcript #3: ENST00000529198
Querying Taster for transcript #4: ENST00000377118
MT speed 3.23 s - this script 4.683094 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C10orf113	polymorphism_automatic	5.25519318960166e-05	simple_aae		affected		D110H	single base exchange	rs625223		show file
C10orf113	polymorphism_automatic	5.25519318960166e-05	simple_aae		affected		D100H	single base exchange	rs625223		show file
C10orf113	polymorphism_automatic	0.707211757514295	without_aae		affected			single base exchange	rs625223		show file
NEBL	polymorphism_automatic	0.707211757514295	without_aae		affected			single base exchange	rs625223		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999947448068104 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:21414892C>GN/A show variant in all transcripts IGV

HGNC symbol

C10orf113

Ensembl transcript ID

ENST00000534331

Genbank transcript ID

NM_001010896

UniProt peptide

Q5VZT2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.328G>C
cDNA.379G>C
g.20597G>C

AA changes

D110H Score: 81 explain score(s)

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

110

frameshift

known variant

Reference ID: rs625223

database	homozygous (G/G)	heterozygous	allele carriers
1000G	814	1091	1905
ExAC	11090	10587	21677

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	0.71
	0.769	0.549
(flanking)	-0.598	0.182

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 increased	20592	wt: 0.22 / mu: 0.76	wt: TCCTGAACCAGATCC mu: TCCTGAACCACATCC	CTGA\|acca
Donor increased	20598	wt: 0.57 / mu: 0.82	wt: ACCAGATCCAGGCAA mu: ACCACATCCAGGCAA	CAGA\|tcca

distance from splice site

161

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

110

mutated

not conserved

110

Ptroglodytes

all identical

ENSPTRG00000029923

110

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

468 / 468

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

156 / 156

position of stopcodon in wt / mu cDNA

519 / 519

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

52 / 52

chromosome

strand

-1

last intron/exon boundary

219

theoretical NMD boundary in CDS

117

length of CDS

468

coding sequence (CDS) position

328

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

379

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

20597

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

21414892

original gDNA sequence snippet

TCCAGGCAGCTCCTGAACCAGATCCAGGCAACTGGGCCAAG

altered gDNA sequence snippet

TCCAGGCAGCTCCTGAACCACATCCAGGCAACTGGGCCAAG

original cDNA sequence snippet

TCCAGGCAGCTCCTGAACCAGATCCAGGCAACTGGGCCAAG

altered cDNA sequence snippet

TCCAGGCAGCTCCTGAACCACATCCAGGCAACTGGGCCAAG

wildtype AA sequence

MAKSERRIYS MESMAPEISE DIGCPLAYMR ESVCALLINQ SFFSCVAEMY IPDMNRPGKA
ERRAEKGLRP PRKLVGETRR LQSWPTLARW LRRVSFSLYK PPIQAAPEPD PGNWAKSPRL
SLGPEGITKG KHGFKFQGIK EKFNVSKKVL KMTFL*

mutated AA sequence

MAKSERRIYS MESMAPEISE DIGCPLAYMR ESVCALLINQ SFFSCVAEMY IPDMNRPGKA
ERRAEKGLRP PRKLVGETRR LQSWPTLARW LRRVSFSLYK PPIQAAPEPH PGNWAKSPRL
SLGPEGITKG KHGFKFQGIK EKFNVSKKVL KMTFL*

speed

0.82 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: 0.999947448068104 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:21414892C>GN/A show variant in all transcripts IGV

HGNC symbol

C10orf113

Ensembl transcript ID

ENST00000377118

Genbank transcript ID

N/A

UniProt peptide

Q5VZT2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.298G>C
cDNA.379G>C
g.20597G>C

AA changes

D100H Score: 81 explain score(s)

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

100

frameshift

known variant

Reference ID: rs625223

database	homozygous (G/G)	heterozygous	allele carriers
1000G	814	1091	1905
ExAC	11090	10587	21677

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	0.71
	0.769	0.549
(flanking)	-0.598	0.182

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 increased	20592	wt: 0.22 / mu: 0.76	wt: TCCTGAACCAGATCC mu: TCCTGAACCACATCC	CTGA\|acca
Donor increased	20598	wt: 0.57 / mu: 0.82	wt: ACCAGATCCAGGCAA mu: ACCACATCCAGGCAA	CAGA\|tcca

distance from splice site

161

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

not conserved

100

Ptroglodytes

all identical

ENSPTRG00000029923

110

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

438 / 438

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

146 / 146

position of stopcodon in wt / mu cDNA

519 / 519

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

82 / 82

chromosome

strand

-1

last intron/exon boundary

219

theoretical NMD boundary in CDS

length of CDS

438

coding sequence (CDS) position

298

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

379

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

20597

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

21414892

original gDNA sequence snippet

TCCAGGCAGCTCCTGAACCAGATCCAGGCAACTGGGCCAAG

altered gDNA sequence snippet

TCCAGGCAGCTCCTGAACCACATCCAGGCAACTGGGCCAAG

original cDNA sequence snippet

TCCAGGCAGCTCCTGAACCAGATCCAGGCAACTGGGCCAAG

altered cDNA sequence snippet

TCCAGGCAGCTCCTGAACCACATCCAGGCAACTGGGCCAAG

wildtype AA sequence

MESMAPEISE DIGCPLAYMR ESVCALLINQ SFFSCVAEMY IPDMNRPGKA ERRAEKGLRP
PRKLVGETRR LQSWPTLARW LRRVSFSLYK PPIQAAPEPD PGNWAKSPRL SLGPEGITKG
KHGFKFQGIK EKFNVSKKVL KMTFL*

mutated AA sequence

MESMAPEISE DIGCPLAYMR ESVCALLINQ SFFSCVAEMY IPDMNRPGKA ERRAEKGLRP
PRKLVGETRR LQSWPTLARW LRRVSFSLYK PPIQAAPEPH PGNWAKSPRL SLGPEGITKG
KHGFKFQGIK EKFNVSKKVL KMTFL*

speed

0.78 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.292788242485705 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:21414892C>GN/A show variant in all transcripts IGV

HGNC symbol

C10orf113

Ensembl transcript ID

ENST00000529198

Genbank transcript ID

NM_001177483

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.414G>C
g.20597G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs625223

database	homozygous (G/G)	heterozygous	allele carriers
1000G	814	1091	1905
ExAC	11090	10587	21677

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	0.71
	0.769	0.549
(flanking)	-0.598	0.182

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

splice sites

splice site change occurs after stopcodon (at aa 120) splice site change occurs after stopcodon (at aa 122)

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	20592	wt: 0.22 / mu: 0.76	wt: TCCTGAACCAGATCC mu: TCCTGAACCACATCC	CTGA\|acca
Donor increased	20598	wt: 0.57 / mu: 0.82	wt: ACCAGATCCAGGCAA mu: ACCACATCCAGGCAA	CAGA\|tcca

distance from splice site

196

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

52 / 52

chromosome

strand

-1

last intron/exon boundary

219

theoretical NMD boundary in CDS

117

length of CDS

240

coding sequence (CDS) position

N/A

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

414

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

20597

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

21414892

original gDNA sequence snippet

TCCAGGCAGCTCCTGAACCAGATCCAGGCAACTGGGCCAAG

altered gDNA sequence snippet

TCCAGGCAGCTCCTGAACCACATCCAGGCAACTGGGCCAAG

original cDNA sequence snippet

TCCAGGCAGCTCCTGAACCAGATCCAGGCAACTGGGCCAAG

altered cDNA sequence snippet

TCCAGGCAGCTCCTGAACCACATCCAGGCAACTGGGCCAAG

wildtype AA sequence

MAKSERRIYS MESMAPEISE DIGCPLAYMR ESVCALLINQ SFFSCVAEMY IPDMNRLEER
TAALYPIGLV RQNGEPRRA*

mutated AA sequence

N/A

speed

0.98 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.292788242485705 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr10:21414892C>GN/A show variant in all transcripts IGV

HGNC symbol

NEBL

Ensembl transcript ID

ENST00000417816

Genbank transcript ID

NM_213569

UniProt peptide

O76041

alteration type

single base exchange

alteration region

intron

DNA changes

g.48225G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs625223

database	homozygous (G/G)	heterozygous	allele carriers
1000G	814	1091	1905
ExAC	11090	10587	21677

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	0.71
	0.769	0.549
(flanking)	-0.598	0.182

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 increased	48220	wt: 0.22 / mu: 0.76	wt: TCCTGAACCAGATCC mu: TCCTGAACCACATCC	CTGA\|acca
Donor increased	48226	wt: 0.57 / mu: 0.82	wt: ACCAGATCCAGGCAA mu: ACCACATCCAGGCAA	CAGA\|tcca

distance from splice site

46420

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
29	63	REPEAT	Nebulin 1.	might get lost (downstream of altered splice site)
53	60	CONFLICT	RYKEEFKK -> VIKKSLKS (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
64	99	REPEAT	Nebulin 2.	might get lost (downstream of altered splice site)
75	75	CONFLICT	N -> T (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
100	136	REPEAT	Nebulin 3.	might get lost (downstream of altered splice site)
129	138	CONFLICT	KHDAAKGFSD -> NMMLPRILS (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
137	172	REPEAT	Nebulin 4.	might get lost (downstream of altered splice site)
173	205	REPEAT	Nebulin 5.	might get lost (downstream of altered splice site)
206	241	REPEAT	Nebulin 6.	might get lost (downstream of altered splice site)
242	278	REPEAT	Nebulin 7.	might get lost (downstream of altered splice site)
279	313	REPEAT	Nebulin 8.	might get lost (downstream of altered splice site)
314	348	REPEAT	Nebulin 9.	might get lost (downstream of altered splice site)
349	385	REPEAT	Nebulin 10.	might get lost (downstream of altered splice site)
386	422	REPEAT	Nebulin 11.	might get lost (downstream of altered splice site)
423	459	REPEAT	Nebulin 12.	might get lost (downstream of altered splice site)
439	445	CONFLICT	RASEMAS -> QPLKWQG (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
460	496	REPEAT	Nebulin 13.	might get lost (downstream of altered splice site)
497	533	REPEAT	Nebulin 14.	might get lost (downstream of altered splice site)
534	569	REPEAT	Nebulin 15.	might get lost (downstream of altered splice site)
570	599	REPEAT	Nebulin 16.	might get lost (downstream of altered splice site)
600	635	REPEAT	Nebulin 17.	might get lost (downstream of altered splice site)
636	666	REPEAT	Nebulin 18.	might get lost (downstream of altered splice site)
667	693	REPEAT	Nebulin 19.	might get lost (downstream of altered splice site)
694	728	REPEAT	Nebulin 20.	might get lost (downstream of altered splice site)
706	726	CONFLICT	RAKENQKNISNVYYRGQLGRA -> PKETRKTSACLLQSSA GES (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
729	759	REPEAT	Nebulin 21.	might get lost (downstream of altered splice site)
732	732	CONFLICT	T -> I (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
740	740	CONFLICT	K -> E (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
743	743	CONFLICT	E -> G (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
760	794	REPEAT	Nebulin 22.	might get lost (downstream of altered splice site)
795	830	REPEAT	Nebulin 23.	might get lost (downstream of altered splice site)
836	953	REGION	Linker.	might get lost (downstream of altered splice site)
902	904	CONFLICT	EIY -> RDL (in Ref. 2; AAF24858).	might get lost (downstream of altered splice site)
954	1014	DOMAIN	SH3.	might get lost (downstream of altered splice site)
959	963	STRAND		might get lost (downstream of altered splice site)
980	986	STRAND		might get lost (downstream of altered splice site)
988	996	STRAND		might get lost (downstream of altered splice site)
997	1000	TURN		might get lost (downstream of altered splice site)
1001	1006	STRAND		might get lost (downstream of altered splice site)
1007	1009	HELIX		might get lost (downstream of altered splice site)
1010	1012	STRAND		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

355 / 355

chromosome

strand

-1

last intron/exon boundary

991

theoretical NMD boundary in CDS

586

length of CDS

813

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)

48225

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

21414892

original gDNA sequence snippet

TCCAGGCAGCTCCTGAACCAGATCCAGGCAACTGGGCCAAG

altered gDNA sequence snippet

TCCAGGCAGCTCCTGAACCACATCCAGGCAACTGGGCCAAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MNPQCARCGK VVYPTEKVNC LDKYWHKGCF HCEVCKMALN MNNYKGYEKK PYCNAHYPKQ
SFTTVADTPE NLRLKQQSEL QSQVKYKRDF EESKGRGFSI VTDTPELQRL KRTQEQISNV
KYHEDFEKTK GRGFTPVVDD PVTERVRKNT QVVSDAAYKG VHPHIVEMDR RPGIIVAPVL
PGAYQQSHSQ GYGYMHQTSV SSMRSMQHSP NLRTYRAMYD YSAQDEDEVS FRDGDYIVNV
QPIDDGWMYG TVQRTGRTGM LPANYIEFVN *

mutated AA sequence

N/A

speed

0.65 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems