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: ENST00000331683
Querying Taster for transcript #2: ENST00000374309
MT speed 0 s - this script 4.299614 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPAG16	polymorphism_automatic	1.50260344800035e-06	simple_aae		affected		Q267H	single base exchange	rs2042791		show file
SPAG16	polymorphism_automatic	6.11820021301224e-06	simple_aae		affected		Q361H	single base exchange	rs2042791		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999998497396552 (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)

chr2:214727221A>CN/A show variant in all transcripts IGV

HGNC symbol

SPAG16

Ensembl transcript ID

ENST00000374309

Genbank transcript ID

N/A

UniProt peptide

Q8N0X2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.801A>C
cDNA.801A>C
g.578109A>C

AA changes

Q267H Score: 24 explain score(s)

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

267

frameshift

known variant

Reference ID: rs2042791

database	homozygous (C/C)	heterozygous	allele carriers
1000G	404	1116	1520
ExAC	9560	13647	23207

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.308	0.997
	-0.6	0.857
(flanking)	3.949	0.98

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	578107	wt: 0.6557 / mu: 0.7158 (marginal change - not scored)	wt: CCTCGCGCAGTGTCTCCATGCAACCCCACAAAGACATCCTA mu: CCTCGCGCAGTGTCTCCATGCACCCCCACAAAGACATCCTA	atgc\|AACC
Acc increased	578117	wt: 0.35 / mu: 0.57	wt: TGTCTCCATGCAACCCCACAAAGACATCCTAGTCTCCTGTG mu: TGTCTCCATGCACCCCCACAAAGACATCCTAGTCTCCTGTG	acaa\|AGAC
Acc marginally increased	578105	wt: 0.5697 / mu: 0.6103 (marginal change - not scored)	wt: CTCCTCGCGCAGTGTCTCCATGCAACCCCACAAAGACATCC mu: CTCCTCGCGCAGTGTCTCCATGCACCCCCACAAAGACATCC	ccat\|GCAA
Acc increased	578103	wt: 0.32 / mu: 0.36	wt: TTCTCCTCGCGCAGTGTCTCCATGCAACCCCACAAAGACAT mu: TTCTCCTCGCGCAGTGTCTCCATGCACCCCCACAAAGACAT	ctcc\|ATGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

267

mutated

not conserved

267

Ptroglodytes

not conserved

ENSPTRG00000012885

361

Mmulatta

not conserved

ENSMMUG00000000382

361

Fcatus

no alignment

ENSFCAG00000015155

n/a

Mmusculus

not conserved

ENSMUSG00000053153

369

Ggallus

not conserved

ENSGALG00000023831

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000075239

347

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
152	267	COILED	Potential.	lost
350	389	REPEAT	WD 1.	might get lost (downstream of altered splice site)
392	431	REPEAT	WD 2.	might get lost (downstream of altered splice site)
434	473	REPEAT	WD 3.	might get lost (downstream of altered splice site)
476	515	REPEAT	WD 4.	might get lost (downstream of altered splice site)
518	557	REPEAT	WD 5.	might get lost (downstream of altered splice site)
560	600	REPEAT	WD 6.	might get lost (downstream of altered splice site)
601	630	REPEAT	WD 7.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1614 / 1614

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

538 / 538

position of stopcodon in wt / mu cDNA

1614 / 1614

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

1 / 1

chromosome

strand

last intron/exon boundary

1439

theoretical NMD boundary in CDS

1388

length of CDS

1614

coding sequence (CDS) position

801

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

801

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

578109

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

214727221

original gDNA sequence snippet

TCGCGCAGTGTCTCCATGCAACCCCACAAAGACATCCTAGT

altered gDNA sequence snippet

TCGCGCAGTGTCTCCATGCACCCCCACAAAGACATCCTAGT

original cDNA sequence snippet

GTGAGCTGTGTCTCCATGCAACCCCACAAAGACATCCTAGT

altered cDNA sequence snippet

GTGAGCTGTGTCTCCATGCACCCCCACAAAGACATCCTAGT

wildtype AA sequence

MTMNMKRYQM TILASQKVKK IWQKQFRWPK NRLQILKFWY ELIQKGVTEL RTVGNVPDVY
TQIMLLENEN KNLKKDLKHY KQAADKARED LLKIQKERDF HRMHHKRIVQ EKNKLINDLK
GLKLHYASYE PTIRVLHEKH HTLLKEKMLT SLERDKVVGQ ISGLQETLKK LQRGHSYHGP
QIKVDHSREK ENAPEGPTQK GLREAREQNK CKTKMKGNTK DSEFPIDMQP NPNLNVSKES
LSPAKFDYKL KNIFRLHELP VSCVSMQPHK DILVSCGEDR LWKVLGLPKC NVLLTGFGHT
DWLSDCCFHP SGDKLATSSG DTTVKLWDLC KGDCILTFEG HSRAVWSCTW HSCGNFVASS
SLDKTSKIWD VNSERCRCTL YGHTDSVNSI EFFPFSNTLL TSSADKTLSI WDARTGICEQ
SLYGHMHSIN DAIFDPRGHM IASCDACGVT KLWDFRKLLP IVSIDIGPSP GNEVNFDSSG
RVLAQASGNG VIHLLDLKSG EIHKLMGHEN EAHTVVFSHD GEILFSGGSD GTVRTWS*

mutated AA sequence

MTMNMKRYQM TILASQKVKK IWQKQFRWPK NRLQILKFWY ELIQKGVTEL RTVGNVPDVY
TQIMLLENEN KNLKKDLKHY KQAADKARED LLKIQKERDF HRMHHKRIVQ EKNKLINDLK
GLKLHYASYE PTIRVLHEKH HTLLKEKMLT SLERDKVVGQ ISGLQETLKK LQRGHSYHGP
QIKVDHSREK ENAPEGPTQK GLREAREQNK CKTKMKGNTK DSEFPIDMQP NPNLNVSKES
LSPAKFDYKL KNIFRLHELP VSCVSMHPHK DILVSCGEDR LWKVLGLPKC NVLLTGFGHT
DWLSDCCFHP SGDKLATSSG DTTVKLWDLC KGDCILTFEG HSRAVWSCTW HSCGNFVASS
SLDKTSKIWD VNSERCRCTL YGHTDSVNSI EFFPFSNTLL TSSADKTLSI WDARTGICEQ
SLYGHMHSIN DAIFDPRGHM IASCDACGVT KLWDFRKLLP IVSIDIGPSP GNEVNFDSSG
RVLAQASGNG VIHLLDLKSG EIHKLMGHEN EAHTVVFSHD GEILFSGGSD GTVRTWS*

speed

1.45 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: 0.999993881799787 (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)

chr2:214727221A>CN/A show variant in all transcripts IGV

HGNC symbol

SPAG16

Ensembl transcript ID

ENST00000331683

Genbank transcript ID

NM_024532

UniProt peptide

Q8N0X2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1083A>C
cDNA.1178A>C
g.578109A>C

AA changes

Q361H Score: 24 explain score(s)

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

361

frameshift

known variant

Reference ID: rs2042791

database	homozygous (C/C)	heterozygous	allele carriers
1000G	404	1116	1520
ExAC	9560	13647	23207

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.308	0.997
	-0.6	0.857
(flanking)	3.949	0.98

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	578107	wt: 0.6557 / mu: 0.7158 (marginal change - not scored)	wt: CCTCGCGCAGTGTCTCCATGCAACCCCACAAAGACATCCTA mu: CCTCGCGCAGTGTCTCCATGCACCCCCACAAAGACATCCTA	atgc\|AACC
Acc increased	578117	wt: 0.35 / mu: 0.57	wt: TGTCTCCATGCAACCCCACAAAGACATCCTAGTCTCCTGTG mu: TGTCTCCATGCACCCCCACAAAGACATCCTAGTCTCCTGTG	acaa\|AGAC
Acc marginally increased	578105	wt: 0.5697 / mu: 0.6103 (marginal change - not scored)	wt: CTCCTCGCGCAGTGTCTCCATGCAACCCCACAAAGACATCC mu: CTCCTCGCGCAGTGTCTCCATGCACCCCCACAAAGACATCC	ccat\|GCAA
Acc increased	578103	wt: 0.32 / mu: 0.36	wt: TTCTCCTCGCGCAGTGTCTCCATGCAACCCCACAAAGACAT mu: TTCTCCTCGCGCAGTGTCTCCATGCACCCCCACAAAGACAT	ctcc\|ATGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

361

mutated

not conserved

361

Ptroglodytes

not conserved

ENSPTRG00000012885

361

Mmulatta

not conserved

ENSMMUG00000000382

361

Fcatus

no alignment

ENSFCAG00000015155

n/a

Mmusculus

not conserved

ENSMUSG00000053153

369

Ggallus

not conserved

ENSGALG00000023831

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000075239

347

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
350	389	REPEAT	WD 1.	lost
392	431	REPEAT	WD 2.	might get lost (downstream of altered splice site)
434	473	REPEAT	WD 3.	might get lost (downstream of altered splice site)
476	515	REPEAT	WD 4.	might get lost (downstream of altered splice site)
518	557	REPEAT	WD 5.	might get lost (downstream of altered splice site)
560	600	REPEAT	WD 6.	might get lost (downstream of altered splice site)
601	630	REPEAT	WD 7.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1896 / 1896

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

632 / 632

position of stopcodon in wt / mu cDNA

1991 / 1991

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

96 / 96

chromosome

strand

last intron/exon boundary

1816

theoretical NMD boundary in CDS

1670

length of CDS

1896

coding sequence (CDS) position

1083

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

1178

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

578109

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

214727221

original gDNA sequence snippet

TCGCGCAGTGTCTCCATGCAACCCCACAAAGACATCCTAGT

altered gDNA sequence snippet

TCGCGCAGTGTCTCCATGCACCCCCACAAAGACATCCTAGT

original cDNA sequence snippet

GTGAGCTGTGTCTCCATGCAACCCCACAAAGACATCCTAGT

altered cDNA sequence snippet

GTGAGCTGTGTCTCCATGCACCCCCACAAAGACATCCTAGT

wildtype AA sequence

MAAQRGMPSS AVRVLEEALG MGLTAAGDAR DTADAVAAEG AYYLEQVTIT EASEDDYEYE
EIPDDNFSIP EGEEDLAKAI QMAQEQATDT EILERKTVLP SKHAVPEVIE DFLCNFLIKM
GMTRTLDCFQ SEWYELIQKG VTELRTVGNV PDVYTQIMLL ENENKNLKKD LKHYKQAADK
AREDLLKIQK ERDFHRMHHK RIVQEKNKLI NDLKGLKLHY ASYEPTIRVL HEKHHTLLKE
KMLTSLERDK VVGQISGLQE TLKKLQRGHS YHGPQIKVDH SREKENAPEG PTQKGLREAR
EQNKCKTKMK GNTKDSEFPI DMQPNPNLNV SKESLSPAKF DYKLKNIFRL HELPVSCVSM
QPHKDILVSC GEDRLWKVLG LPKCNVLLTG FGHTDWLSDC CFHPSGDKLA TSSGDTTVKL
WDLCKGDCIL TFEGHSRAVW SCTWHSCGNF VASSSLDKTS KIWDVNSERC RCTLYGHTDS
VNSIEFFPFS NTLLTSSADK TLSIWDARTG ICEQSLYGHM HSINDAIFDP RGHMIASCDA
CGVTKLWDFR KLLPIVSIDI GPSPGNEVNF DSSGRVLAQA SGNGVIHLLD LKSGEIHKLM
GHENEAHTVV FSHDGEILFS GGSDGTVRTW S*

mutated AA sequence

MAAQRGMPSS AVRVLEEALG MGLTAAGDAR DTADAVAAEG AYYLEQVTIT EASEDDYEYE
EIPDDNFSIP EGEEDLAKAI QMAQEQATDT EILERKTVLP SKHAVPEVIE DFLCNFLIKM
GMTRTLDCFQ SEWYELIQKG VTELRTVGNV PDVYTQIMLL ENENKNLKKD LKHYKQAADK
AREDLLKIQK ERDFHRMHHK RIVQEKNKLI NDLKGLKLHY ASYEPTIRVL HEKHHTLLKE
KMLTSLERDK VVGQISGLQE TLKKLQRGHS YHGPQIKVDH SREKENAPEG PTQKGLREAR
EQNKCKTKMK GNTKDSEFPI DMQPNPNLNV SKESLSPAKF DYKLKNIFRL HELPVSCVSM
HPHKDILVSC GEDRLWKVLG LPKCNVLLTG FGHTDWLSDC CFHPSGDKLA TSSGDTTVKL
WDLCKGDCIL TFEGHSRAVW SCTWHSCGNF VASSSLDKTS KIWDVNSERC RCTLYGHTDS
VNSIEFFPFS NTLLTSSADK TLSIWDARTG ICEQSLYGHM HSINDAIFDP RGHMIASCDA
CGVTKLWDFR KLLPIVSIDI GPSPGNEVNF DSSGRVLAQA SGNGVIHLLD LKSGEIHKLM
GHENEAHTVV FSHDGEILFS GGSDGTVRTW S*

speed

0.84 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems