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: ENST00000320876
Querying Taster for transcript #2: ENST00000261598
MT speed 1.58 s - this script 3.549149 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SMCHD1	polymorphism_automatic	1.0991207943789e-14	simple_aae				V708I	single base exchange	rs2276092		show file
SMCHD1	polymorphism_automatic	1.0991207943789e-14	simple_aae				V708I	single base exchange	rs2276092		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999989 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:2707619G>AN/A show variant in all transcripts IGV

HGNC symbol

SMCHD1

Ensembl transcript ID

ENST00000320876

Genbank transcript ID

NM_015295

UniProt peptide

A6NHR9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2122G>A
cDNA.2460G>A
g.51883G>A

AA changes

V708I Score: 29 explain score(s)

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

708

frameshift

known variant

Reference ID: rs2276092

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1211	1035	2246
ExAC	29306	-25845	3461

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.277	0.016
	0.05	0.006
(flanking)	0.984	0.007

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	51881	wt: 0.9276 / mu: 0.9836 (marginal change - not scored)	wt: TAATGAGGTTAGGCC mu: TAATGAGATTAGGCC	ATGA\|ggtt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

708

mutated

all conserved

708

Ptroglodytes

all conserved

ENSPTRG00000009831

708

Mmulatta

all conserved

ENSMMUG00000005461

156

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000024054

708

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

6018 / 6018

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

2006 / 2006

position of stopcodon in wt / mu cDNA

6356 / 6356

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

339 / 339

chromosome

strand

last intron/exon boundary

6332

theoretical NMD boundary in CDS

5943

length of CDS

6018

coding sequence (CDS) position

2122

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

2460

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

51883

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

2707619

original gDNA sequence snippet

ATGAATTATTGCCTAATGAGGTTAGGCCTGCTGGAACCCCT

altered gDNA sequence snippet

ATGAATTATTGCCTAATGAGATTAGGCCTGCTGGAACCCCT

original cDNA sequence snippet

ATGAATTATTGCCTAATGAGGTTAGGCCTGCTGGAACCCCT

altered cDNA sequence snippet

ATGAATTATTGCCTAATGAGATTAGGCCTGCTGGAACCCCT

wildtype AA sequence

MAAADGGGPG GASVGTEEDG GGVGHRTVYL FDRREKESEL GDRPLQVGER SDYAGFRACV
CQTLGISPEE KFVITTTSRK EITCDNFDET VKDGVTLYLL QSVNQLLLTA TKERIDFLPH
YDTLVKSGMY EYYASEGQNP LPFALAELID NSLSATSRNI GVRRIQIKLL FDETQGKPAV
AVIDNGRGMT SKQLNNWAVY RLSKFTRQGD FESDHSGYVR PVPVPRSLNS DISYFGVGGK
QAVFFVGQSA RMISKPADSQ DVHELVLSKE DFEKKEKNKE AIYSGYIRNR KPSDSVHITN
DDERFLHHLI IEEKEKDSFT AVVITGVQPE HIQYLKNYFH LWTRQLAHIY HYYIHGPKGN
EIRTSKEVEP FNNIDIEISM FEKGKVPKIV NLREIQDDMQ TLYVNTAADS FEFKAHVEGD
GVVEGIIRYH PFLYDRETYP DDPCFPSKLK DEDDEDDCFI LEKAARGKRP IFECFWNGRL
IPYTSVEDFD WCTPPKKRGL APIECYNRIS GALFTNDKFQ VSTNKLTFMD LELKLKDKNT
LFTRILNGQE QRMKIDREFA LWLKDCHEKY DKQIKFTLFK GVITRPDLPS KKQGPWATYA
AIEWDGKIYK AGQLVKTIKT LPLFYGSIVR FFLYGDHDGE VYATGGEVQI AMEPQALYDE
VRTVPIAKLD RTVAEKAVKK YVEDEMARLP DRLSVTWPEG DELLPNEVRP AGTPIGALRI
EILNKKGEAM QKLPGTSHGG SKKLLVELKV ILHSSSGNKE IISHISQHGG KWPYWFKKME
NIQKLGNYTL KLQVVLNESN ADTYAGRPLP SKAIKFSVKE GKPEKFSFGL LDLPFRVGVP
FNIPLEFQDE FGHTSQLVTD IQPVLEASGL SLHYEEITKG PNCVIRGVTA KGPVNSCQGK
NYNLKVTLPG LKEDSQILKI RLLPGHPRRL KVKPDSEILV IENGTAFPFQ VEVLDESDNI
TAQPKLIVHC KFSGAPNLPV YVVDCSSSGT SILTGSAIQV QNIKKDQTLK ARIEIPSCKD
VAPVEKTIKL LPSSHVARLQ IFSVEGQKAI QIKHQDEVNW IAGDIMHNLI FQMYDEGERE
INITSALAEK IKVNWTPEIN KEHLLQGLLP DVQVPTSVKD MRYCQVSFQD DHVSLESAFT
VRPLPDEPKH LKCEMKGGKT VQMGQELQGE VVIIITDQYG NQIQAFSPSS LSSLSIAGVG
LDSSNLKTTF QENTQSISVR GIKFIPGPPG NKDLCFTWRE FSDFIRVQLI SGPPAKLLLI
DWPELKESIP VINGRDLQNP IIVQLCDQWD NPAPVQHVKI SLTKASNLKL MPSNQQHKTD
EKGRANLGVF SVFAPRGEHT LQVKAIYNKS IIEGPIIKLM ILPDPEKPVR LNVKYDKDAS
FLAGGLFTDF MISVISEDDS IIKNINPARI SMKMWKLSTS GNRPPANAET FSCNKIKDND
KEDGCFYFRD KVIPNKVGTY CIQFGFMMDK TNILNSEQVI VEVLPNQPVK LVPKIKPPTP
AVSNVRSVAS RTLVRDLHLS ITDDYDNHTG IDLVGTIIAT IKGSNEEDTD TPLFIGKVRT
LEFPFVNGSA EIMSLVLAES SPGRDSTEYF IVFEPRLPLL SRTLEPYILP FMFYNDVKKQ
QQMAALTKEK DQLSQSIVMY KSLFEASQQL LNEMKCQVEE ARLKEAQLRN ELKIHNIDIP
TTQQVPHIEA LLKRKLSEQE ELKKKPRRSC TLPNYTKGSG DVLGKIAHLA QIEDDRAAMV
ISWHLASDMD CVVTLTTDAA RRIYDETQGR QQVLPLDSIY KKTLPDWKRS LPHFRNGKLY
FKPIGDPVFA RDLLTFPDNV EHCETVFGML LGDTIILDNL DAANHYRKEV VKITHCPTLL
TRDGDRIRSN GKFGGLQNKA PPMDKLRGMV FGAPVPKQCL ILGEQIDLLQ QYRSAVCKLD
SVNKDLNSQL EYLRTPDMRK KKQELDEHEK NLKLIEEKLG MTPIRKCNDS LRHSPKVETT
DCPVPPKRMR REATRQNRII TKTDV*

mutated AA sequence

MAAADGGGPG GASVGTEEDG GGVGHRTVYL FDRREKESEL GDRPLQVGER SDYAGFRACV
CQTLGISPEE KFVITTTSRK EITCDNFDET VKDGVTLYLL QSVNQLLLTA TKERIDFLPH
YDTLVKSGMY EYYASEGQNP LPFALAELID NSLSATSRNI GVRRIQIKLL FDETQGKPAV
AVIDNGRGMT SKQLNNWAVY RLSKFTRQGD FESDHSGYVR PVPVPRSLNS DISYFGVGGK
QAVFFVGQSA RMISKPADSQ DVHELVLSKE DFEKKEKNKE AIYSGYIRNR KPSDSVHITN
DDERFLHHLI IEEKEKDSFT AVVITGVQPE HIQYLKNYFH LWTRQLAHIY HYYIHGPKGN
EIRTSKEVEP FNNIDIEISM FEKGKVPKIV NLREIQDDMQ TLYVNTAADS FEFKAHVEGD
GVVEGIIRYH PFLYDRETYP DDPCFPSKLK DEDDEDDCFI LEKAARGKRP IFECFWNGRL
IPYTSVEDFD WCTPPKKRGL APIECYNRIS GALFTNDKFQ VSTNKLTFMD LELKLKDKNT
LFTRILNGQE QRMKIDREFA LWLKDCHEKY DKQIKFTLFK GVITRPDLPS KKQGPWATYA
AIEWDGKIYK AGQLVKTIKT LPLFYGSIVR FFLYGDHDGE VYATGGEVQI AMEPQALYDE
VRTVPIAKLD RTVAEKAVKK YVEDEMARLP DRLSVTWPEG DELLPNEIRP AGTPIGALRI
EILNKKGEAM QKLPGTSHGG SKKLLVELKV ILHSSSGNKE IISHISQHGG KWPYWFKKME
NIQKLGNYTL KLQVVLNESN ADTYAGRPLP SKAIKFSVKE GKPEKFSFGL LDLPFRVGVP
FNIPLEFQDE FGHTSQLVTD IQPVLEASGL SLHYEEITKG PNCVIRGVTA KGPVNSCQGK
NYNLKVTLPG LKEDSQILKI RLLPGHPRRL KVKPDSEILV IENGTAFPFQ VEVLDESDNI
TAQPKLIVHC KFSGAPNLPV YVVDCSSSGT SILTGSAIQV QNIKKDQTLK ARIEIPSCKD
VAPVEKTIKL LPSSHVARLQ IFSVEGQKAI QIKHQDEVNW IAGDIMHNLI FQMYDEGERE
INITSALAEK IKVNWTPEIN KEHLLQGLLP DVQVPTSVKD MRYCQVSFQD DHVSLESAFT
VRPLPDEPKH LKCEMKGGKT VQMGQELQGE VVIIITDQYG NQIQAFSPSS LSSLSIAGVG
LDSSNLKTTF QENTQSISVR GIKFIPGPPG NKDLCFTWRE FSDFIRVQLI SGPPAKLLLI
DWPELKESIP VINGRDLQNP IIVQLCDQWD NPAPVQHVKI SLTKASNLKL MPSNQQHKTD
EKGRANLGVF SVFAPRGEHT LQVKAIYNKS IIEGPIIKLM ILPDPEKPVR LNVKYDKDAS
FLAGGLFTDF MISVISEDDS IIKNINPARI SMKMWKLSTS GNRPPANAET FSCNKIKDND
KEDGCFYFRD KVIPNKVGTY CIQFGFMMDK TNILNSEQVI VEVLPNQPVK LVPKIKPPTP
AVSNVRSVAS RTLVRDLHLS ITDDYDNHTG IDLVGTIIAT IKGSNEEDTD TPLFIGKVRT
LEFPFVNGSA EIMSLVLAES SPGRDSTEYF IVFEPRLPLL SRTLEPYILP FMFYNDVKKQ
QQMAALTKEK DQLSQSIVMY KSLFEASQQL LNEMKCQVEE ARLKEAQLRN ELKIHNIDIP
TTQQVPHIEA LLKRKLSEQE ELKKKPRRSC TLPNYTKGSG DVLGKIAHLA QIEDDRAAMV
ISWHLASDMD CVVTLTTDAA RRIYDETQGR QQVLPLDSIY KKTLPDWKRS LPHFRNGKLY
FKPIGDPVFA RDLLTFPDNV EHCETVFGML LGDTIILDNL DAANHYRKEV VKITHCPTLL
TRDGDRIRSN GKFGGLQNKA PPMDKLRGMV FGAPVPKQCL ILGEQIDLLQ QYRSAVCKLD
SVNKDLNSQL EYLRTPDMRK KKQELDEHEK NLKLIEEKLG MTPIRKCNDS LRHSPKVETT
DCPVPPKRMR REATRQNRII TKTDV*

speed

0.60 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: 0.999999999999989 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:2707619G>AN/A show variant in all transcripts IGV

HGNC symbol

SMCHD1

Ensembl transcript ID

ENST00000261598

Genbank transcript ID

N/A

UniProt peptide

A6NHR9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2122G>A
cDNA.2311G>A
g.51883G>A

AA changes

V708I Score: 29 explain score(s)

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

708

frameshift

known variant

Reference ID: rs2276092

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1211	1035	2246
ExAC	29306	-25845	3461

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.277	0.016
	0.05	0.006
(flanking)	0.984	0.007

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	51881	wt: 0.9276 / mu: 0.9836 (marginal change - not scored)	wt: TAATGAGGTTAGGCC mu: TAATGAGATTAGGCC	ATGA\|ggtt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

708

mutated

all conserved

708

Ptroglodytes

all conserved

ENSPTRG00000009831

708

Mmulatta

all conserved

ENSMMUG00000005461

156

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000024054

708

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

5754 / 5754

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

1918 / 1918

position of stopcodon in wt / mu cDNA

5943 / 5943

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

190 / 190

chromosome

strand

last intron/exon boundary

5909

theoretical NMD boundary in CDS

5669

length of CDS

5754

coding sequence (CDS) position

2122

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

2311

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

51883

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

2707619

original gDNA sequence snippet

ATGAATTATTGCCTAATGAGGTTAGGCCTGCTGGAACCCCT

altered gDNA sequence snippet

ATGAATTATTGCCTAATGAGATTAGGCCTGCTGGAACCCCT

original cDNA sequence snippet

ATGAATTATTGCCTAATGAGGTTAGGCCTGCTGGAACCCCT

altered cDNA sequence snippet

ATGAATTATTGCCTAATGAGATTAGGCCTGCTGGAACCCCT

wildtype AA sequence

mutated AA sequence

MAAADGGGPG GASVGTEEDG GGVGHRTVYL FDRREKESEL GDRPLQVGER SDYAGFRACV
CQTLGISPEE KFVITTTSRK EITCDNFDET VKDGVTLYLL QSVNQLLLTA TKERIDFLPH
YDTLVKSGMY EYYASEGQNP LPFALAELID NSLSATSRNI GVRRIQIKLL FDETQGKPAV
AVIDNGRGMT SKQLNNWAVY RLSKFTRQGD FESDHSGYVR PVPVPRSLNS DISYFGVGGK
QAVFFVGQSA RMISKPADSQ DVHELVLSKE DFEKKEKNKE AIYSGYIRNR KPSDSVHITN
DDERFLHHLI IEEKEKDSFT AVVITGVQPE HIQYLKNYFH LWTRQLAHIY HYYIHGPKGN
EIRTSKEVEP FNNIDIEISM FEKGKVPKIV NLREIQDDMQ TLYVNTAADS FEFKAHVEGD
GVVEGIIRYH PFLYDRETYP DDPCFPSKLK DEDDEDDCFI LEKAARGKRP IFECFWNGRL
IPYTSVEDFD WCTPPKKRGL APIECYNRIS GALFTNDKFQ VSTNKLTFMD LELKLKDKNT
LFTRILNGQE QRMKIDREFA LWLKDCHEKY DKQIKFTLFK GVITRPDLPS KKQGPWATYA
AIEWDGKIYK AGQLVKTIKT LPLFYGSIVR FFLYGDHDGE VYATGGEVQI AMEPQALYDE
VRTVPIAKLD RTVAEKAVKK YVEDEMARLP DRLSVTWPEG DELLPNEIRP AGTPIGALRI
EILNKKGEAM QKLPGTSHGG SKKLLVELKV ILHSSSGNKE IISHISQHGG KWPYWFKKME
NIQKLGNYTL KLQVVLNESN ADTYAGRPLP SKAIKFSVKE GKPEKFSFGL LDLPFRVGVP
FNIPLEFQDE FGHTSQLVTD IQPVLEASGL SLHYEEITKG PNCVIRGVTA KGPVNSCQGK
NYNLKVTLPG LKEDSQILKI RLLPGHPRRL KVKPDSEILV IENGTAFPFQ VEVLDESDNI
TAQPKLIVHC KFSGAPNLPV YVVDCSSSGT SILTGSAIQV QNIKKDQTLK ARIEIPSCKD
VAPVEKTIKL LPSSHVARLQ IFSVEGQKAI QIKHQDEVNW IAGDIMHNLI FQMYDEGERE
INITSALAEK IKVNWTPEIN KEHLLQGLLP DVQVPTSVKD MRYCQVSFQD DHVSLESAFT
VRPLPDEPKH LKCEMKGGKT VQMGQELQGE VVIIITDQYG NQIQAFSPSS LSSLSIAGVG
LDSSNLKTTF QENTQSISVR GIKFIPGPPG NKDLCFTWRE FSDFIRVQLI SGPPAKLLLI
DWPELKESIP VINGRDLQNP IIVQLCDQWD NPAPVQHVKI SLTKASNLKL MPSNQQHKTD
EKGRANLGVF SVFAPRGEHT LQVKAIYNKS IIEGPIIKLM ILPDPEKPVR LNVKYDKDAS
FLAGGLFTDF MISVISEDDS IIKNINPARI SMKMWKLSTS GNRPPANAET FSCNKIKDND
KEDGCFYFRD KVIPNKVGTY CIQFGFMMDK TNILNSEQVI VEVLPNQPVK LVPKIKPPTP
AVSNVRSVAS RTLVRDLHLS ITDDYDNHTG IDLVGTIIAT IKGSNEEDTD TPLFIGKVRT
LEFPFVNGSA EIMSLVLAES SPGRDSTEYF IVFEPRLPLL SRTLEPYILP FMFYNDVKKQ
QQMAALTKEK DQLSQSIVMY KSLFEASQQL LNEMKCQVEE ARLKEAQLRN ELKIHNIDIP
TTQQVPHIEA LLKRKLSEQE ELKKKPRRSC TLPNYTKGSG DVLGKIAHLA QIEDDRAAMV
ISWHLASDMD CVVTLTTDAA RRIYDETQGR QQVLPLDSIY KKTLPDWKRS LPHFRNGKLY
FKPIGDPVFA RDLLTFPDNV EHCETVFGML LGDTIILDNL DAANHYRKEV VKITHCPTLL
TRDGDRIRSN GKFGGLQNKA PPMDKLRGMV FGAPVPKQCL ILGEQIVHAC VPSYSGG*

speed

0.98 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems