MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000402775
Querying Taster for transcript #2: ENST00000307486
Querying Taster for transcript #3: ENST00000388934
MT speed 0 s - this script 4.22635 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MAB21L4	polymorphism_automatic	3.16719983572966e-11	simple_aae		affected		I220V	single base exchange	rs11899555		show file
MAB21L4	polymorphism_automatic	3.16719983572966e-11	simple_aae		affected		I239V	single base exchange	rs11899555		show file
MAB21L4	polymorphism_automatic	3.16719983572966e-11	simple_aae		affected		I388V	single base exchange	rs11899555		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999968328 (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)

chr2:241827798T>CN/A show variant in all transcripts IGV

HGNC symbol

MAB21L4

Ensembl transcript ID

ENST00000402775

Genbank transcript ID

NM_024861

UniProt peptide

Q08AI8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.658A>G
cDNA.754A>G
g.8509A>G

AA changes

I220V Score: 29 explain score(s)

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

220

frameshift

known variant

Reference ID: rs11899555

database	homozygous (C/C)	heterozygous	allele carriers
1000G	228	736	964
ExAC	592	5004	5596

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.779	0.001
	-0.773	0
(flanking)	0.663	0.045

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 increased	8508	wt: 0.81 / mu: 0.92	wt: GGCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGC mu: GGCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGC	gcgc\|ATCG
Acc marginally increased	8505	wt: 0.4438 / mu: 0.4841 (marginal change - not scored)	wt: CTGGGCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAA mu: CTGGGCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAA	gccg\|CGCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

220

mutated

all conserved

220

Ptroglodytes

all identical

ENSPTRG00000013114

388

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000010449

381

Mmusculus

all identical

ENSMUSG00000034159

393

Ggallus

not conserved

ENSGALG00000006044

391

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
317	317	CONFLICT	L -> P (in Ref. 1; BAB15445).	might get lost (downstream of altered splice site)
383	383	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

840 / 840

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

280 / 280

position of stopcodon in wt / mu cDNA

936 / 936

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

97 / 97

chromosome

strand

-1

last intron/exon boundary

844

theoretical NMD boundary in CDS

697

length of CDS

840

coding sequence (CDS) position

658

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

754

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

8509

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

241827798

original gDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGCG

altered gDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGCG

original cDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGCG

altered cDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGCG

wildtype AA sequence

MDTGSLNAAS LREEQLHLSL LVSSGWRTIS FHVVPVVRRK LGAPALEGVQ QMPGFPEGSL
RRILSQGVDL VPASAQLWRT STDYLLTRLL GELGSLQGHR LDSLSILDRV NHESWRDSGQ
TDGLTFGHLK MVLLWASVLF LAPEDWAELQ GAVYRLLVVL LCCLATRKLP HFLHPQRNLL
QGSGLDLGAI YQRVEGFASQ PEAALRIHAT HLGRSPPPRI GSGLKALLQL PASDPTYWAT
AYFDVLLDKF QVFNIQDKDR ISAMQSIFQK TRTLGGEES*

mutated AA sequence

MDTGSLNAAS LREEQLHLSL LVSSGWRTIS FHVVPVVRRK LGAPALEGVQ QMPGFPEGSL
RRILSQGVDL VPASAQLWRT STDYLLTRLL GELGSLQGHR LDSLSILDRV NHESWRDSGQ
TDGLTFGHLK MVLLWASVLF LAPEDWAELQ GAVYRLLVVL LCCLATRKLP HFLHPQRNLL
QGSGLDLGAI YQRVEGFASQ PEAALRIHAT HLGRSPPPRV GSGLKALLQL PASDPTYWAT
AYFDVLLDKF QVFNIQDKDR ISAMQSIFQK TRTLGGEES*

speed

0.59 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: 0.999999999968328 (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)

chr2:241827798T>CN/A show variant in all transcripts IGV

HGNC symbol

MAB21L4

Ensembl transcript ID

ENST00000307486

Genbank transcript ID

N/A

UniProt peptide

Q08AI8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.715A>G
cDNA.814A>G
g.8509A>G

AA changes

I239V Score: 29 explain score(s)

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

239

frameshift

known variant

Reference ID: rs11899555

database	homozygous (C/C)	heterozygous	allele carriers
1000G	228	736	964
ExAC	592	5004	5596

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.779	0.001
	-0.773	0
(flanking)	0.663	0.045

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 increased	8508	wt: 0.81 / mu: 0.92	wt: GGCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGC mu: GGCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGC	gcgc\|ATCG
Acc marginally increased	8505	wt: 0.4438 / mu: 0.4841 (marginal change - not scored)	wt: CTGGGCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAA mu: CTGGGCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAA	gccg\|CGCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

239

mutated

all conserved

239

Ptroglodytes

all identical

ENSPTRG00000013114

388

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000010449

381

Mmusculus

all identical

ENSMUSG00000034159

393

Ggallus

not conserved

ENSGALG00000006044

391

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
317	317	CONFLICT	L -> P (in Ref. 1; BAB15445).	might get lost (downstream of altered splice site)
383	383	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

897 / 897

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

299 / 299

position of stopcodon in wt / mu cDNA

996 / 996

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

100 / 100

chromosome

strand

-1

last intron/exon boundary

904

theoretical NMD boundary in CDS

754

length of CDS

897

coding sequence (CDS) position

715

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

814

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

8509

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

241827798

original gDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGCG

altered gDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGCG

original cDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGCG

altered cDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGCG

wildtype AA sequence

MDTGVWGWGA AACRWGPAER AAGSLNAASL REEQLHLSLL VSSGWRTISF HVVPVVRRKL
GAPALEGVQQ MPGFPEGSLR RILSQGVDLV PASAQLWRTS TDYLLTRLLG ELGSLQGHRL
DSLSILDRVN HESWRDSGQT DGLTFGHLKM VLLWASVLFL APEDWAELQG AVYRLLVVLL
CCLATRKLPH FLHPQRNLLQ GSGLDLGAIY QRVEGFASQP EAALRIHATH LGRSPPPRIG
SGLKALLQLP ASDPTYWATA YFDVLLDKFQ VFNIQDKDRI SAMQSIFQKT RTLGGEES*

mutated AA sequence

MDTGVWGWGA AACRWGPAER AAGSLNAASL REEQLHLSLL VSSGWRTISF HVVPVVRRKL
GAPALEGVQQ MPGFPEGSLR RILSQGVDLV PASAQLWRTS TDYLLTRLLG ELGSLQGHRL
DSLSILDRVN HESWRDSGQT DGLTFGHLKM VLLWASVLFL APEDWAELQG AVYRLLVVLL
CCLATRKLPH FLHPQRNLLQ GSGLDLGAIY QRVEGFASQP EAALRIHATH LGRSPPPRVG
SGLKALLQLP ASDPTYWATA YFDVLLDKFQ VFNIQDKDRI SAMQSIFQKT RTLGGEES*

speed

1.37 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999968328 (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)

chr2:241827798T>CN/A show variant in all transcripts IGV

HGNC symbol

MAB21L4

Ensembl transcript ID

ENST00000388934

Genbank transcript ID

NM_001085437

UniProt peptide

Q08AI8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1162A>G
cDNA.1321A>G
g.8509A>G

AA changes

I388V Score: 29 explain score(s)

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

388

frameshift

known variant

Reference ID: rs11899555

database	homozygous (C/C)	heterozygous	allele carriers
1000G	228	736	964
ExAC	592	5004	5596

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.779	0.001
	-0.773	0
(flanking)	0.663	0.045

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 increased	8508	wt: 0.81 / mu: 0.92	wt: GGCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGC mu: GGCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGC	gcgc\|ATCG
Acc marginally increased	8505	wt: 0.4438 / mu: 0.4841 (marginal change - not scored)	wt: CTGGGCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAA mu: CTGGGCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAA	gccg\|CGCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

388

mutated

all conserved

388

Ptroglodytes

all identical

ENSPTRG00000013114

388

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000010449

381

Mmusculus

all identical

ENSMUSG00000034159

393

Ggallus

not conserved

ENSGALG00000006044

391

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

1344 / 1344

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

448 / 448

position of stopcodon in wt / mu cDNA

1503 / 1503

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

160 / 160

chromosome

strand

-1

last intron/exon boundary

1411

theoretical NMD boundary in CDS

1201

length of CDS

1344

coding sequence (CDS) position

1162

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

1321

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

8509

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

241827798

original gDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGCG

altered gDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGCG

original cDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCATCGGCTCCGGGCTCAAGGCG

altered cDNA sequence snippet

GCCGCAGCCCCCCGCCGCGCGTCGGCTCCGGGCTCAAGGCG

wildtype AA sequence

MPAPALPTSA MAVQVPLWHH YLQAIRSREA PRAQDFQRAE NVLLTVLERV HALDPRFIVD
YSRGLEAFQF ALRSSEDPMD MEVPLWVDAE ALLIEEPEAT QPEDGLELCH LGVPREGAGL
ERWTTEDTFT ASSEGDAKCR GHIVPSKVLC VLKDLLVAAI VHCKHHSLIA PGSLNAASLR
EEQLHLSLLV SSGWRTISFH VVPVVRRKLG APALEGVQQM PGFPEGSLRR ILSQGVDLVP
ASAQLWRTST DYLLTRLLGE LGSLQGHRLD SLSILDRVNH ESWRDSGQTD GLTFGHLKMV
LLWASVLFLA PEDWAELQGA VYRLLVVLLC CLATRKLPHF LHPQRNLLQG SGLDLGAIYQ
RVEGFASQPE AALRIHATHL GRSPPPRIGS GLKALLQLPA SDPTYWATAY FDVLLDKFQV
FNIQDKDRIS AMQSIFQKTR TLGGEES*

mutated AA sequence

MPAPALPTSA MAVQVPLWHH YLQAIRSREA PRAQDFQRAE NVLLTVLERV HALDPRFIVD
YSRGLEAFQF ALRSSEDPMD MEVPLWVDAE ALLIEEPEAT QPEDGLELCH LGVPREGAGL
ERWTTEDTFT ASSEGDAKCR GHIVPSKVLC VLKDLLVAAI VHCKHHSLIA PGSLNAASLR
EEQLHLSLLV SSGWRTISFH VVPVVRRKLG APALEGVQQM PGFPEGSLRR ILSQGVDLVP
ASAQLWRTST DYLLTRLLGE LGSLQGHRLD SLSILDRVNH ESWRDSGQTD GLTFGHLKMV
LLWASVLFLA PEDWAELQGA VYRLLVVLLC CLATRKLPHF LHPQRNLLQG SGLDLGAIYQ
RVEGFASQPE AALRIHATHL GRSPPPRVGS GLKALLQLPA SDPTYWATAY FDVLLDKFQV
FNIQDKDRIS AMQSIFQKTR TLGGEES*

speed

0.87 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems