MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000326581
Querying Taster for transcript #2: ENST00000514652
MT speed 0 s - this script 2.872727 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C4orf17	polymorphism_automatic	2.39808173319034e-14	simple_aae		affected		S85P	single base exchange	rs13119384		show file
C4orf17	polymorphism_automatic	2.39808173319034e-14	simple_aae		affected		S85P	single base exchange	rs13119384		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999976 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:100443782T>CN/A show variant in all transcripts IGV

HGNC symbol

C4orf17

Ensembl transcript ID

ENST00000326581

Genbank transcript ID

NM_032149

UniProt peptide

Q53FE4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.253T>C
cDNA.615T>C
g.11622T>C

AA changes

S85P Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs13119384

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1001	879	1880
ExAC	13069	6629	19698

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.877	0
	0.467	0.012
(flanking)	1.617	0.025

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	11624	wt: 0.2862 / mu: 0.2863 (marginal change - not scored)	wt: GCCAATTGCAGTTACCCCTCCAGCACTGCAGTCCAGGAGAG mu: GCCAATTGCAGTTACCCCCCCAGCACTGCAGTCCAGGAGAG	ctcc\|AGCA
Acc increased	11614	wt: 0.24 / mu: 0.30	wt: GATACCATTTGCCAATTGCAGTTACCCCTCCAGCACTGCAG mu: GATACCATTTGCCAATTGCAGTTACCCCCCCAGCACTGCAG	gcag\|TTAC

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

not conserved

ENSPTRG00000016306

Mmulatta

not conserved

ENSMMUG00000009089

Fcatus

not conserved

ENSFCAG00000004690

Mmusculus

not conserved

ENSMUSG00000012042

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
289	289	CONFLICT	K -> R (in Ref. 2; CAG38573).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1080 / 1080

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

360 / 360

position of stopcodon in wt / mu cDNA

1442 / 1442

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

363 / 363

chromosome

strand

last intron/exon boundary

1243

theoretical NMD boundary in CDS

830

length of CDS

1080

coding sequence (CDS) position

253

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

615

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

11622

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

100443782

original gDNA sequence snippet

TTGCCAATTGCAGTTACCCCTCCAGCACTGCAGTCCAGGAG

altered gDNA sequence snippet

TTGCCAATTGCAGTTACCCCCCCAGCACTGCAGTCCAGGAG

original cDNA sequence snippet

TTGCCAATTGCAGTTACCCCTCCAGCACTGCAGTCCAGGAG

altered cDNA sequence snippet

TTGCCAATTGCAGTTACCCCCCCAGCACTGCAGTCCAGGAG

wildtype AA sequence

MNLNPPTSAL QIEGKGSHIM ARNVSCFLVR HTPHPRRVCH IKGLNNIPIC TVNDDENAFG
TLWGVGQSNY LEKNRIPFAN CSYPSSTAVQ ESPVRGMSPA PNGAKVPPRP HSEPSRKIKE
CFKTSSENPL VIKKEEIKAK RPPSPPKACS TPGSCSSGMT STKNDVKANT ICIPNYLDQE
IKILAKLCSI LHTDSLAEVL QWLLHATSKE KEWVSALIHS ELAEINLLTH HRRNTSMEPA
AETGKPPTVK SPPTVKLPPN FTAKSKVLTR DTEGDQPTRV SSQGSEENKE VPKEAEHKPP
LLIRRNNMKI PVAEYFSKPN SPPRPNTQES GSAKPVSARS IQEYNLCPQR ACYPSTHRR*

mutated AA sequence

MNLNPPTSAL QIEGKGSHIM ARNVSCFLVR HTPHPRRVCH IKGLNNIPIC TVNDDENAFG
TLWGVGQSNY LEKNRIPFAN CSYPPSTAVQ ESPVRGMSPA PNGAKVPPRP HSEPSRKIKE
CFKTSSENPL VIKKEEIKAK RPPSPPKACS TPGSCSSGMT STKNDVKANT ICIPNYLDQE
IKILAKLCSI LHTDSLAEVL QWLLHATSKE KEWVSALIHS ELAEINLLTH HRRNTSMEPA
AETGKPPTVK SPPTVKLPPN FTAKSKVLTR DTEGDQPTRV SSQGSEENKE VPKEAEHKPP
LLIRRNNMKI PVAEYFSKPN SPPRPNTQES GSAKPVSARS IQEYNLCPQR ACYPSTHRR*

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: 0.999999999999976 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:100443782T>CN/A show variant in all transcripts IGV

HGNC symbol

C4orf17

Ensembl transcript ID

ENST00000514652

Genbank transcript ID

N/A

UniProt peptide

Q53FE4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.253T>C
cDNA.607T>C
g.11622T>C

AA changes

S85P Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs13119384

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1001	879	1880
ExAC	13069	6629	19698

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.877	0
	0.467	0.012
(flanking)	1.617	0.025

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	11624	wt: 0.2862 / mu: 0.2863 (marginal change - not scored)	wt: GCCAATTGCAGTTACCCCTCCAGCACTGCAGTCCAGGAGAG mu: GCCAATTGCAGTTACCCCCCCAGCACTGCAGTCCAGGAGAG	ctcc\|AGCA
Acc increased	11614	wt: 0.24 / mu: 0.30	wt: GATACCATTTGCCAATTGCAGTTACCCCTCCAGCACTGCAG mu: GATACCATTTGCCAATTGCAGTTACCCCCCCAGCACTGCAG	gcag\|TTAC

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

not conserved

ENSPTRG00000016306

Mmulatta

not conserved

ENSMMUG00000009089

Fcatus

not conserved

ENSFCAG00000004690

Mmusculus

not conserved

ENSMUSG00000012042

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
289	289	CONFLICT	K -> R (in Ref. 2; CAG38573).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

885 / 885

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

295 / 295

position of stopcodon in wt / mu cDNA

1239 / 1239

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

last intron/exon boundary

1191

theoretical NMD boundary in CDS

786

length of CDS

885

coding sequence (CDS) position

253

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

607

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

11622

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

100443782

original gDNA sequence snippet

TTGCCAATTGCAGTTACCCCTCCAGCACTGCAGTCCAGGAG

altered gDNA sequence snippet

TTGCCAATTGCAGTTACCCCCCCAGCACTGCAGTCCAGGAG

original cDNA sequence snippet

TTGCCAATTGCAGTTACCCCTCCAGCACTGCAGTCCAGGAG

altered cDNA sequence snippet

TTGCCAATTGCAGTTACCCCCCCAGCACTGCAGTCCAGGAG

wildtype AA sequence

mutated AA sequence

speed

0.44 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems