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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000409478
Querying Taster for transcript #2: ENST00000264160
Querying Taster for transcript #3: ENST00000410054
Querying Taster for transcript #4: ENST00000409606
Querying Taster for transcript #5: ENST00000329971
MT speed 0 s - this script 4.955385 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
R3HDM1	polymorphism_automatic	0.037511672193198	simple_aae		affected		M226V	single base exchange	rs961360		show file
R3HDM1	polymorphism_automatic	0.037511672193198	simple_aae		affected		M226V	single base exchange	rs961360		show file
R3HDM1	polymorphism_automatic	0.989414784458298	simple_aae		affected		M270V	single base exchange	rs961360		show file
R3HDM1	polymorphism_automatic	0.989414784458298	simple_aae		affected		M270V	single base exchange	rs961360		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.962488327806802 (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)

chr2:136393658A>GN/A show variant in all transcripts IGV

HGNC symbol

R3HDM1

Ensembl transcript ID

ENST00000409478

Genbank transcript ID

N/A

UniProt peptide

Q15032

alteration type

single base exchange

alteration region

CDS

DNA changes

c.676A>G
cDNA.1058A>G
g.104634A>G

AA changes

M226V Score: 21 explain score(s)

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

226

frameshift

known variant

Reference ID: rs961360

database	homozygous (G/G)	heterozygous	allele carriers
1000G	266	1017	1283
ExAC	4392	20294	24686

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.735	1
	3.113	1
(flanking)	3.449	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	104633	sequence motif lost	-	wt: gtag\|ATGA mu: gtag.GTGA
Acc increased	104630	wt: 0.45 / mu: 0.57	wt: TAAAAATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAA mu: TAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAA	tctg\|TAGA
Acc gained	104626	0.33	mu: TGCCTAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTT	cttt\|TCTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

226

mutated

all conserved

226

Ptroglodytes

not conserved

ENSPTRG00000012494

270

IFSQ

Mmulatta

not conserved

ENSMMUG00000009844

214

Fcatus

no alignment

ENSFCAG00000019217

n/a

Mmusculus

not conserved

ENSMUSG00000056211

270

Ggallus

all identical

ENSGALG00000012246

270

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000063141

211

Dmelanogaster

not conserved

FBgn0004875

543

Celegans

no alignment

ZK121.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
168	231	DOMAIN	R3H.	lost
251	301	DOMAIN	SUZ.	might get lost (downstream of altered splice site)
337	337	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
381	381	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
541	541	CONFLICT	Q -> QQ (in Ref. 2; BAA04878).	might get lost (downstream of altered splice site)
589	608	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
822	826	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
973	973	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2916 / 2916

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

972 / 972

position of stopcodon in wt / mu cDNA

3298 / 3298

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

383 / 383

chromosome

strand

last intron/exon boundary

2943

theoretical NMD boundary in CDS

2510

length of CDS

2916

coding sequence (CDS) position

676

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

1058

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

104634

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

136393658

original gDNA sequence snippet

AATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAAAGAT

altered gDNA sequence snippet

AATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAAAGAT

original cDNA sequence snippet

TTGACAAAGATGATAACCAGATGAGAATACGTTTGAAAGAT

altered cDNA sequence snippet

TTGACAAAGATGATAACCAGGTGAGAATACGTTTGAAAGAT

wildtype AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQEKI
QIQLTQSFEK EEKPSKDEAE KEKASDKLPR KMLSRDSSQE YTDSTGIDLH EFLVNTLKNN
PRDRMMLLKL EQEILDFIGN NESPRKKFPP MTSYHRMLLH RVAAYFGLDH NVDQSGKSVI
VNKTSNTRIP DQKFNEHIKD DKGEDFQKRY ILKRDNSSFD KDDNQMRIRL KDDRRSKSIE
EREEEYQRAR DRIFSQDSLC SQENYIIDKR LQDEDASSTQ QRRQIFRVNK DASGRSTNSH
QSSTENELKY SEPRPWSSTD SDSSLRNLKP AVTKASSFSG ISVLTRGDSS GSSKSIGRLS
KTGQPFINPD GSPVVYNPPM TQQPVRSQVP GPPQPPLPAP PQQPAANHIF SQQDNLGSQF
SHMSLARQPS ADGSDPHAAM FQSTVVLQSP QQSGYIMTAA PPPHPPPPPP PPPPPPPLPP
GQPVPTAGYP ASGHPVSQPV LQQQGYIQQP SPQMPACYCA PGHYHSSQPQ YRPVPSVHYN
SHLNQPLPQP AQQTGYQVIP NQQQNYQGIV GVQQPQSQSL VSGQPNSIGN QIQGVVIPYT
SVPTYQVSLP QGSQGIPHQT YQQPVMFPNQ SNQGSMPTTG MPVYYSVIPP GQQNNLSSSV
GYLQHPGSEQ VQFPRTTSPC SSQQLQGHQC TAGPPPPPGG GMVMMQLSVP NNPQSCAHSP
PQWKQNKYYC DHQRGQKCVE FSSVDNIVQH SPQLSSPIIS PAQSPAPAQL STLKTVRPSG
PPLSIMPQFS RPFVPGQGDS RYPLLGQPLQ YNPPAVLHGH IPNQQGQPGS RHGNRGRRQA
KKAASTDLGA GETVVGKVLE ITELPDGITR MEAEKLFGEL FKIGAKIRWL RDPQSQPRRH
PLCCGSGDNT ANPERSKPSD LASTYTVLAT FPSISAAQNA LKKQINSVNK FKLRTSKKHY
DFHILERASS Q*

mutated AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQEKI
QIQLTQSFEK EEKPSKDEAE KEKASDKLPR KMLSRDSSQE YTDSTGIDLH EFLVNTLKNN
PRDRMMLLKL EQEILDFIGN NESPRKKFPP MTSYHRMLLH RVAAYFGLDH NVDQSGKSVI
VNKTSNTRIP DQKFNEHIKD DKGEDFQKRY ILKRDNSSFD KDDNQVRIRL KDDRRSKSIE
EREEEYQRAR DRIFSQDSLC SQENYIIDKR LQDEDASSTQ QRRQIFRVNK DASGRSTNSH
QSSTENELKY SEPRPWSSTD SDSSLRNLKP AVTKASSFSG ISVLTRGDSS GSSKSIGRLS
KTGQPFINPD GSPVVYNPPM TQQPVRSQVP GPPQPPLPAP PQQPAANHIF SQQDNLGSQF
SHMSLARQPS ADGSDPHAAM FQSTVVLQSP QQSGYIMTAA PPPHPPPPPP PPPPPPPLPP
GQPVPTAGYP ASGHPVSQPV LQQQGYIQQP SPQMPACYCA PGHYHSSQPQ YRPVPSVHYN
SHLNQPLPQP AQQTGYQVIP NQQQNYQGIV GVQQPQSQSL VSGQPNSIGN QIQGVVIPYT
SVPTYQVSLP QGSQGIPHQT YQQPVMFPNQ SNQGSMPTTG MPVYYSVIPP GQQNNLSSSV
GYLQHPGSEQ VQFPRTTSPC SSQQLQGHQC TAGPPPPPGG GMVMMQLSVP NNPQSCAHSP
PQWKQNKYYC DHQRGQKCVE FSSVDNIVQH SPQLSSPIIS PAQSPAPAQL STLKTVRPSG
PPLSIMPQFS RPFVPGQGDS RYPLLGQPLQ YNPPAVLHGH IPNQQGQPGS RHGNRGRRQA
KKAASTDLGA GETVVGKVLE ITELPDGITR MEAEKLFGEL FKIGAKIRWL RDPQSQPRRH
PLCCGSGDNT ANPERSKPSD LASTYTVLAT FPSISAAQNA LKKQINSVNK FKLRTSKKHY
DFHILERASS Q*

speed

1.28 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: 0.962488327806802 (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)

chr2:136393658A>GN/A show variant in all transcripts IGV

HGNC symbol

R3HDM1

Ensembl transcript ID

ENST00000329971

Genbank transcript ID

N/A

UniProt peptide

Q15032

alteration type

single base exchange

alteration region

CDS

DNA changes

c.676A>G
cDNA.1046A>G
g.104634A>G

AA changes

M226V Score: 21 explain score(s)

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

226

frameshift

known variant

Reference ID: rs961360

database	homozygous (G/G)	heterozygous	allele carriers
1000G	266	1017	1283
ExAC	4392	20294	24686

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.735	1
	3.113	1
(flanking)	3.449	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	104633	sequence motif lost	-	wt: gtag\|ATGA mu: gtag.GTGA
Acc increased	104630	wt: 0.45 / mu: 0.57	wt: TAAAAATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAA mu: TAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAA	tctg\|TAGA
Acc gained	104626	0.33	mu: TGCCTAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTT	cttt\|TCTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

226

mutated

all conserved

226

Ptroglodytes

not conserved

ENSPTRG00000012494

270

IFSQ

Mmulatta

not conserved

ENSMMUG00000009844

214

Fcatus

no alignment

ENSFCAG00000019217

n/a

Mmusculus

not conserved

ENSMUSG00000056211

270

Ggallus

all identical

ENSGALG00000012246

270

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000063141

211

Dmelanogaster

not conserved

FBgn0004875

543

Celegans

no alignment

ZK121.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
168	231	DOMAIN	R3H.	lost
251	301	DOMAIN	SUZ.	might get lost (downstream of altered splice site)
337	337	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
381	381	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
541	541	CONFLICT	Q -> QQ (in Ref. 2; BAA04878).	might get lost (downstream of altered splice site)
589	608	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
822	826	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
973	973	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2913 / 2913

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

971 / 971

position of stopcodon in wt / mu cDNA

3283 / 3283

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

371 / 371

chromosome

strand

last intron/exon boundary

2928

theoretical NMD boundary in CDS

2507

length of CDS

2913

coding sequence (CDS) position

676

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

1046

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

104634

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

136393658

original gDNA sequence snippet

AATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAAAGAT

altered gDNA sequence snippet

AATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAAAGAT

original cDNA sequence snippet

TTGACAAAGATGATAACCAGATGAGAATACGTTTGAAAGAT

altered cDNA sequence snippet

TTGACAAAGATGATAACCAGGTGAGAATACGTTTGAAAGAT

wildtype AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQEKI
QIQLTQSFEK EEKPSKDEAE KEKASDKLPR KMLSRDSSQE YTDSTGIDLH EFLVNTLKNN
PRDRMMLLKL EQEILDFIGN NESPRKKFPP MTSYHRMLLH RVAAYFGLDH NVDQSGKSVI
VNKTSNTRIP DQKFNEHIKD DKGEDFQKRY ILKRDNSSFD KDDNQMRIRL KDDRRSKSIE
EREEEYQRAR DRIFSQDSLC SQENYIIDKR LQDEDASSTQ QRRQIFRVNK DASGRSTNSH
QSSTENELKY SEPRPWSSTD SDSSLRNLKP AVTKASSFSG ISVLTRGDSS GSSKSIGRLS
KTGQPFINPD GSPVVYNPPM TQQPVRSQVP GPPQPPLPAP PQQPAANHIF SQDNLGSQFS
HMSLARQPSA DGSDPHAAMF QSTVVLQSPQ QSGYIMTAAP PPHPPPPPPP PPPPPPLPPG
QPVPTAGYPA SGHPVSQPVL QQQGYIQQPS PQMPACYCAP GHYHSSQPQY RPVPSVHYNS
HLNQPLPQPA QQTGYQVIPN QQQNYQGIVG VQQPQSQSLV SGQPNSIGNQ IQGVVIPYTS
VPTYQVSLPQ GSQGIPHQTY QQPVMFPNQS NQGSMPTTGM PVYYSVIPPG QQNNLSSSVG
YLQHPGSEQV QFPRTTSPCS SQQLQGHQCT AGPPPPPGGG MVMMQLSVPN NPQSCAHSPP
QWKQNKYYCD HQRGQKCVEF SSVDNIVQHS PQLSSPIISP AQSPAPAQLS TLKTVRPSGP
PLSIMPQFSR PFVPGQGDSR YPLLGQPLQY NPPAVLHGHI PNQQGQPGSR HGNRGRRQAK
KAASTDLGAG ETVVGKVLEI TELPDGITRM EAEKLFGELF KIGAKIRWLR DPQSQPRRHP
LCCGSGDNTA NPERSKPSDL ASTYTVLATF PSISAAQNAL KKQINSVNKF KLRTSKKHYD
FHILERASSQ *

mutated AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQEKI
QIQLTQSFEK EEKPSKDEAE KEKASDKLPR KMLSRDSSQE YTDSTGIDLH EFLVNTLKNN
PRDRMMLLKL EQEILDFIGN NESPRKKFPP MTSYHRMLLH RVAAYFGLDH NVDQSGKSVI
VNKTSNTRIP DQKFNEHIKD DKGEDFQKRY ILKRDNSSFD KDDNQVRIRL KDDRRSKSIE
EREEEYQRAR DRIFSQDSLC SQENYIIDKR LQDEDASSTQ QRRQIFRVNK DASGRSTNSH
QSSTENELKY SEPRPWSSTD SDSSLRNLKP AVTKASSFSG ISVLTRGDSS GSSKSIGRLS
KTGQPFINPD GSPVVYNPPM TQQPVRSQVP GPPQPPLPAP PQQPAANHIF SQDNLGSQFS
HMSLARQPSA DGSDPHAAMF QSTVVLQSPQ QSGYIMTAAP PPHPPPPPPP PPPPPPLPPG
QPVPTAGYPA SGHPVSQPVL QQQGYIQQPS PQMPACYCAP GHYHSSQPQY RPVPSVHYNS
HLNQPLPQPA QQTGYQVIPN QQQNYQGIVG VQQPQSQSLV SGQPNSIGNQ IQGVVIPYTS
VPTYQVSLPQ GSQGIPHQTY QQPVMFPNQS NQGSMPTTGM PVYYSVIPPG QQNNLSSSVG
YLQHPGSEQV QFPRTTSPCS SQQLQGHQCT AGPPPPPGGG MVMMQLSVPN NPQSCAHSPP
QWKQNKYYCD HQRGQKCVEF SSVDNIVQHS PQLSSPIISP AQSPAPAQLS TLKTVRPSGP
PLSIMPQFSR PFVPGQGDSR YPLLGQPLQY NPPAVLHGHI PNQQGQPGSR HGNRGRRQAK
KAASTDLGAG ETVVGKVLEI TELPDGITRM EAEKLFGELF KIGAKIRWLR DPQSQPRRHP
LCCGSGDNTA NPERSKPSDL ASTYTVLATF PSISAAQNAL KKQINSVNKF KLRTSKKHYD
FHILERASSQ *

speed

1.36 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0105852155417023 (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)

chr2:136393658A>GN/A show variant in all transcripts IGV

HGNC symbol

R3HDM1

Ensembl transcript ID

ENST00000264160

Genbank transcript ID

NM_015361

UniProt peptide

Q15032

alteration type

single base exchange

alteration region

CDS

DNA changes

c.808A>G
cDNA.1178A>G
g.104634A>G

AA changes

M270V Score: 21 explain score(s)

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

270

frameshift

known variant

Reference ID: rs961360

database	homozygous (G/G)	heterozygous	allele carriers
1000G	266	1017	1283
ExAC	4392	20294	24686

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.735	1
	3.113	1
(flanking)	3.449	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	104633	sequence motif lost	-	wt: gtag\|ATGA mu: gtag.GTGA
Acc increased	104630	wt: 0.45 / mu: 0.57	wt: TAAAAATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAA mu: TAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAA	tctg\|TAGA
Acc gained	104626	0.33	mu: TGCCTAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTT	cttt\|TCTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

270

mutated

all conserved

270

Ptroglodytes

all identical

ENSPTRG00000012494

270

Mmulatta

not conserved

ENSMMUG00000009844

168

Fcatus

no alignment

ENSFCAG00000019217

n/a

Mmusculus

all identical

ENSMUSG00000056211

270

Ggallus

all identical

ENSGALG00000012246

270

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000063141

211

Dmelanogaster

not conserved

FBgn0004875

543

Celegans

not conserved

ZK121.2

263

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
251	301	DOMAIN	SUZ.	lost
337	337	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
381	381	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
541	541	CONFLICT	Q -> QQ (in Ref. 2; BAA04878).	might get lost (downstream of altered splice site)
589	608	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
822	826	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
973	973	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3300 / 3300

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

1100 / 1100

position of stopcodon in wt / mu cDNA

3670 / 3670

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

371 / 371

chromosome

strand

last intron/exon boundary

3315

theoretical NMD boundary in CDS

2894

length of CDS

3300

coding sequence (CDS) position

808

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

1178

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

104634

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

136393658

original gDNA sequence snippet

AATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAAAGAT

altered gDNA sequence snippet

AATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAAAGAT

original cDNA sequence snippet

TTGACAAAGATGATAACCAGATGAGAATACGTTTGAAAGAT

altered cDNA sequence snippet

TTGACAAAGATGATAACCAGGTGAGAATACGTTTGAAAGAT

wildtype AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQRPL
QSFGQTGKRS KSSSKLKLVR SLAVCEESPP PPAPEISQEN QEKIQIQLTQ SFEKEEKPSK
DEAEKEKASD KLPRKMLSRD SSQEYTDSTG IDLHEFLVNT LKNNPRDRMM LLKLEQEILD
FIGNNESPRK KFPPMTSYHR MLLHRVAAYF GLDHNVDQSG KSVIVNKTSN TRIPDQKFNE
HIKDDKGEDF QKRYILKRDN SSFDKDDNQM RIRLKDDRRS KSIEEREEEY QRARDRIFSQ
DSLCSQENYI IDKRLQDEDA SSTQQRRQIF RVNKDASGRS TNSHQSSTEN ELKYSEPRPW
SSTDSDSSLR NLKPAVTKAS SFSGISVLTR GDSSGSSKSI GRLSKTGSES SGSVGSSTGS
LSHIQQPLPG TALSQSSHGA PVVYPTVSTH SSLSFDGGLN GQVASPSTSF FLLPLEAAGI
PPGSILINPQ TGQPFINPDG SPVVYNPPMT QQPVRSQVPG PPQPPLPAPP QQPAANHIFS
QDNLGSQFSH MSLARQPSAD GSDPHAAMFQ STVVLQSPQQ SGYIMTAAPP PHPPPPPPPP
PPPPPLPPGQ PVPTAGYPAS GHPVSQPVLQ QQGYIQQPSP QMPACYCAPG HYHSSQPQYR
PVPSVHYNSH LNQPLPQPAQ QTGYQVIPNQ QQNYQGIVGV QQPQSQSLVS GQPNSIGNQI
QGVVIPYTSV PTYQVSLPQG SQGIPHQTYQ QPVMFPNQSN QGSMPTTGMP VYYSVIPPGQ
QNNLSSSVGY LQHPGSEQVQ FPRTTSPCSS QQLQGHQCTA GPPPPPGGGM VMMQLSVPNN
PQSCAHSPPQ WKQNKYYCDH QRGQKCVEFS SVDNIVQHSP QLSSPIISPA QSPAPAQLST
LKTVRPSGPP LSIMPQFSRP FVPGQGDSRY PLLGQPLQYN PPAVLHGHIP NQQGQPGSRH
GNRGRRQAKK AASTDLGAGE TVVGKVLEIT ELPDGITRME AEKLFGELFK IGAKIRWLRD
PQSQPRRHPL CCGSGDNTAN PERSKPSDLA STYTVLATFP SISAAQNALK KQINSVNKFK
LRTSKKHYDF HILERASSQ*

mutated AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQRPL
QSFGQTGKRS KSSSKLKLVR SLAVCEESPP PPAPEISQEN QEKIQIQLTQ SFEKEEKPSK
DEAEKEKASD KLPRKMLSRD SSQEYTDSTG IDLHEFLVNT LKNNPRDRMM LLKLEQEILD
FIGNNESPRK KFPPMTSYHR MLLHRVAAYF GLDHNVDQSG KSVIVNKTSN TRIPDQKFNE
HIKDDKGEDF QKRYILKRDN SSFDKDDNQV RIRLKDDRRS KSIEEREEEY QRARDRIFSQ
DSLCSQENYI IDKRLQDEDA SSTQQRRQIF RVNKDASGRS TNSHQSSTEN ELKYSEPRPW
SSTDSDSSLR NLKPAVTKAS SFSGISVLTR GDSSGSSKSI GRLSKTGSES SGSVGSSTGS
LSHIQQPLPG TALSQSSHGA PVVYPTVSTH SSLSFDGGLN GQVASPSTSF FLLPLEAAGI
PPGSILINPQ TGQPFINPDG SPVVYNPPMT QQPVRSQVPG PPQPPLPAPP QQPAANHIFS
QDNLGSQFSH MSLARQPSAD GSDPHAAMFQ STVVLQSPQQ SGYIMTAAPP PHPPPPPPPP
PPPPPLPPGQ PVPTAGYPAS GHPVSQPVLQ QQGYIQQPSP QMPACYCAPG HYHSSQPQYR
PVPSVHYNSH LNQPLPQPAQ QTGYQVIPNQ QQNYQGIVGV QQPQSQSLVS GQPNSIGNQI
QGVVIPYTSV PTYQVSLPQG SQGIPHQTYQ QPVMFPNQSN QGSMPTTGMP VYYSVIPPGQ
QNNLSSSVGY LQHPGSEQVQ FPRTTSPCSS QQLQGHQCTA GPPPPPGGGM VMMQLSVPNN
PQSCAHSPPQ WKQNKYYCDH QRGQKCVEFS SVDNIVQHSP QLSSPIISPA QSPAPAQLST
LKTVRPSGPP LSIMPQFSRP FVPGQGDSRY PLLGQPLQYN PPAVLHGHIP NQQGQPGSRH
GNRGRRQAKK AASTDLGAGE TVVGKVLEIT ELPDGITRME AEKLFGELFK IGAKIRWLRD
PQSQPRRHPL CCGSGDNTAN PERSKPSDLA STYTVLATFP SISAAQNALK KQINSVNKFK
LRTSKKHYDF HILERASSQ*

speed

1.40 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0105852155417023 (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)

chr2:136393658A>GN/A show variant in all transcripts IGV

HGNC symbol

R3HDM1

Ensembl transcript ID

ENST00000409606

Genbank transcript ID

N/A

UniProt peptide

Q15032

alteration type

single base exchange

alteration region

CDS

DNA changes

c.808A>G
cDNA.1127A>G
g.104634A>G

AA changes

M270V Score: 21 explain score(s)

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

270

frameshift

known variant

Reference ID: rs961360

database	homozygous (G/G)	heterozygous	allele carriers
1000G	266	1017	1283
ExAC	4392	20294	24686

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.735	1
	3.113	1
(flanking)	3.449	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	104633	sequence motif lost	-	wt: gtag\|ATGA mu: gtag.GTGA
Acc increased	104630	wt: 0.45 / mu: 0.57	wt: TAAAAATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAA mu: TAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAA	tctg\|TAGA
Acc gained	104626	0.33	mu: TGCCTAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTT	cttt\|TCTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

270

mutated

all conserved

270

Ptroglodytes

all identical

ENSPTRG00000012494

270

Mmulatta

not conserved

ENSMMUG00000009844

168

Fcatus

no alignment

ENSFCAG00000019217

n/a

Mmusculus

all identical

ENSMUSG00000056211

270

Ggallus

all identical

ENSGALG00000012246

270

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000063141

211

Dmelanogaster

not conserved

FBgn0004875

543

Celegans

not conserved

ZK121.2

263

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
251	301	DOMAIN	SUZ.	lost
337	337	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
381	381	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
541	541	CONFLICT	Q -> QQ (in Ref. 2; BAA04878).	might get lost (downstream of altered splice site)
589	608	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
822	826	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
973	973	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3303 / 3303

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

1101 / 1101

position of stopcodon in wt / mu cDNA

3622 / 3622

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

320 / 320

chromosome

strand

last intron/exon boundary

3267

theoretical NMD boundary in CDS

2897

length of CDS

3303

coding sequence (CDS) position

808

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

1127

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

104634

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

136393658

original gDNA sequence snippet

AATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAAAGAT

altered gDNA sequence snippet

AATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAAAGAT

original cDNA sequence snippet

TTGACAAAGATGATAACCAGATGAGAATACGTTTGAAAGAT

altered cDNA sequence snippet

TTGACAAAGATGATAACCAGGTGAGAATACGTTTGAAAGAT

wildtype AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQRPL
QSFGQTGKRS KSSSKLKLVR SLAVCEESPP PPAPEISQEN QEKIQIQLTQ SFEKEEKPSK
DEAEKEKASD KLPRKMLSRD SSQEYTDSTG IDLHEFLVNT LKNNPRDRMM LLKLEQEILD
FIGNNESPRK KFPPMTSYHR MLLHRVAAYF GLDHNVDQSG KSVIVNKTSN TRIPDQKFNE
HIKDDKGEDF QKRYILKRDN SSFDKDDNQM RIRLKDDRRS KSIEEREEEY QRARDRIFSQ
DSLCSQENYI IDKRLQDEDA SSTQQRRQIF RVNKDASGRS TNSHQSSTEN ELKYSEPRPW
SSTDSDSSLR NLKPAVTKAS SFSGISVLTR GDSSGSSKSI GRLSKTGSES SGSVGSSTGS
LSHIQQPLPG TALSQSSHGA PVVYPTVSTH SSLSFDGGLN GQVASPSTSF FLLPLEAAGI
PPGSILINPQ TGQPFINPDG SPVVYNPPMT QQPVRSQVPG PPQPPLPAPP QQPAANHIFS
QQDNLGSQFS HMSLARQPSA DGSDPHAAMF QSTVVLQSPQ QSGYIMTAAP PPHPPPPPPP
PPPPPPLPPG QPVPTAGYPA SGHPVSQPVL QQQGYIQQPS PQMPACYCAP GHYHSSQPQY
RPVPSVHYNS HLNQPLPQPA QQTGYQVIPN QQQNYQGIVG VQQPQSQSLV SGQPNSIGNQ
IQGVVIPYTS VPTYQVSLPQ GSQGIPHQTY QQPVMFPNQS NQGSMPTTGM PVYYSVIPPG
QQNNLSSSVG YLQHPGSEQV QFPRTTSPCS SQQLQGHQCT AGPPPPPGGG MVMMQLSVPN
NPQSCAHSPP QWKQNKYYCD HQRGQKCVEF SSVDNIVQHS PQLSSPIISP AQSPAPAQLS
TLKTVRPSGP PLSIMPQFSR PFVPGQGDSR YPLLGQPLQY NPPAVLHGHI PNQQGQPGSR
HGNRGRRQAK KAASTDLGAG ETVVGKVLEI TELPDGITRM EAEKLFGELF KIGAKIRWLR
DPQSQPRRHP LCCGSGDNTA NPERSKPSDL ASTYTVLATF PSISAAQNAL KKQINSVNKF
KLRTSKKHYD FHILERASSQ *

mutated AA sequence

MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQRPL
QSFGQTGKRS KSSSKLKLVR SLAVCEESPP PPAPEISQEN QEKIQIQLTQ SFEKEEKPSK
DEAEKEKASD KLPRKMLSRD SSQEYTDSTG IDLHEFLVNT LKNNPRDRMM LLKLEQEILD
FIGNNESPRK KFPPMTSYHR MLLHRVAAYF GLDHNVDQSG KSVIVNKTSN TRIPDQKFNE
HIKDDKGEDF QKRYILKRDN SSFDKDDNQV RIRLKDDRRS KSIEEREEEY QRARDRIFSQ
DSLCSQENYI IDKRLQDEDA SSTQQRRQIF RVNKDASGRS TNSHQSSTEN ELKYSEPRPW
SSTDSDSSLR NLKPAVTKAS SFSGISVLTR GDSSGSSKSI GRLSKTGSES SGSVGSSTGS
LSHIQQPLPG TALSQSSHGA PVVYPTVSTH SSLSFDGGLN GQVASPSTSF FLLPLEAAGI
PPGSILINPQ TGQPFINPDG SPVVYNPPMT QQPVRSQVPG PPQPPLPAPP QQPAANHIFS
QQDNLGSQFS HMSLARQPSA DGSDPHAAMF QSTVVLQSPQ QSGYIMTAAP PPHPPPPPPP
PPPPPPLPPG QPVPTAGYPA SGHPVSQPVL QQQGYIQQPS PQMPACYCAP GHYHSSQPQY
RPVPSVHYNS HLNQPLPQPA QQTGYQVIPN QQQNYQGIVG VQQPQSQSLV SGQPNSIGNQ
IQGVVIPYTS VPTYQVSLPQ GSQGIPHQTY QQPVMFPNQS NQGSMPTTGM PVYYSVIPPG
QQNNLSSSVG YLQHPGSEQV QFPRTTSPCS SQQLQGHQCT AGPPPPPGGG MVMMQLSVPN
NPQSCAHSPP QWKQNKYYCD HQRGQKCVEF SSVDNIVQHS PQLSSPIISP AQSPAPAQLS
TLKTVRPSGP PLSIMPQFSR PFVPGQGDSR YPLLGQPLQY NPPAVLHGHI PNQQGQPGSR
HGNRGRRQAK KAASTDLGAG ETVVGKVLEI TELPDGITRM EAEKLFGELF KIGAKIRWLR
DPQSQPRRHP LCCGSGDNTA NPERSKPSDL ASTYTVLATF PSISAAQNAL KKQINSVNKF
KLRTSKKHYD FHILERASSQ *

speed

1.32 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