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: ENST00000296604
Querying Taster for transcript #2: ENST00000502994
Querying Taster for transcript #3: ENST00000515759
MT speed 0 s - this script 3.017348 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RANBP3L	polymorphism_automatic	1.31515123340531e-05	simple_aae		affected		T70R	single base exchange	rs1035480		show file
RANBP3L	polymorphism_automatic	1.31515123340531e-05	simple_aae		affected		T70R	single base exchange	rs1035480		show file
RANBP3L	polymorphism_automatic	3.07044233059939e-05	simple_aae		affected		T70R	single base exchange	rs1035480		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999986848487666 (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)

chr5:36269551G>CN/A show variant in all transcripts IGV

HGNC symbol

RANBP3L

Ensembl transcript ID

ENST00000296604

Genbank transcript ID

NM_145000

UniProt peptide

Q86VV4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.209C>G
cDNA.695C>G
g.32666C>G

AA changes

T70R Score: 71 explain score(s)

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

frameshift

known variant

Reference ID: rs1035480

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1679	681	2360
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.474	1
	1.63	1
(flanking)	2.474	1

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 gained	32665	0.61	mu: TTCCAAGAAAGCGTG	CCAA\|gaaa
Donor gained	32660	0.37	mu: TGGTTTTCCAAGAAA	GTTT\|tcca

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

ENSPTRG00000016799

Mmulatta

not conserved

ENSMMUG00000018820

Fcatus

no alignment

ENSFCAG00000001019

n/a

Mmusculus

not conserved

ENSMUSG00000048424

Ggallus

not conserved

ENSGALG00000021304

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0039110

n/a

Celegans

no alignment

R12C12.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
276	417	DOMAIN	RanBD1.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1398 / 1398

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

466 / 466

position of stopcodon in wt / mu cDNA

1884 / 1884

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

487 / 487

chromosome

strand

-1

last intron/exon boundary

1841

theoretical NMD boundary in CDS

1304

length of CDS

1398

coding sequence (CDS) position

209

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

695

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

32666

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

36269551

original gDNA sequence snippet

AGAATGTAATGGTTTTCCAACAAAGCGTGTACGGTCTTCAT

altered gDNA sequence snippet

AGAATGTAATGGTTTTCCAAGAAAGCGTGTACGGTCTTCAT

original cDNA sequence snippet

AGAATGTAATGGTTTTCCAACAAAGCGTGTACGGTCTTCAT

altered cDNA sequence snippet

AGAATGTAATGGTTTTCCAAGAAAGCGTGTACGGTCTTCAT

wildtype AA sequence

MTTIPRKGSS HLPGSLHTCK LKLQEDRRQQ EKSVIAQPIF VFEKGEQTFK RPAEDTLYEA
AEPECNGFPT KRVRSSSFTF HITDSQSQGV RKNNVFMTSA LVQSSVDIKS AEQGPVKHSK
HVIRPAILQL PQARSCAKVR KTFGHKALES CKTKEKTNNK ISEGNSYLLS ENLSRARISV
QLSTNQDFLG ATSVGCQPNE DKCSFKSCSS NFVFGENMVE RVLGTQKLTQ PQLENDSYAK
EKPFKSIPKF PVNFLSSRTD SIKNTSLIES AAAFSSQPSR KCLLEKIDVI TGEETEHNVL
KINCKLFIFN KTTQSWIERG RGTLRLNDTA STDCGTLQSR LIMRNQGSLR LILNSKLWAQ
MKIQRANHKN VRITATDLED YSIKIFLIQA SAQDTAYLYA AIHHRLVALQ SFNKQRDVNQ
AESLSETAQQ LNCESCDENE DDFIQVTKNG SDPSSWTHRQ SVACS*

mutated AA sequence

MTTIPRKGSS HLPGSLHTCK LKLQEDRRQQ EKSVIAQPIF VFEKGEQTFK RPAEDTLYEA
AEPECNGFPR KRVRSSSFTF HITDSQSQGV RKNNVFMTSA LVQSSVDIKS AEQGPVKHSK
HVIRPAILQL PQARSCAKVR KTFGHKALES CKTKEKTNNK ISEGNSYLLS ENLSRARISV
QLSTNQDFLG ATSVGCQPNE DKCSFKSCSS NFVFGENMVE RVLGTQKLTQ PQLENDSYAK
EKPFKSIPKF PVNFLSSRTD SIKNTSLIES AAAFSSQPSR KCLLEKIDVI TGEETEHNVL
KINCKLFIFN KTTQSWIERG RGTLRLNDTA STDCGTLQSR LIMRNQGSLR LILNSKLWAQ
MKIQRANHKN VRITATDLED YSIKIFLIQA SAQDTAYLYA AIHHRLVALQ SFNKQRDVNQ
AESLSETAQQ LNCESCDENE DDFIQVTKNG SDPSSWTHRQ SVACS*

speed

0.54 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: 0.999986848487666 (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)

chr5:36269551G>CN/A show variant in all transcripts IGV

HGNC symbol

RANBP3L

Ensembl transcript ID

ENST00000502994

Genbank transcript ID

NM_001161429

UniProt peptide

Q86VV4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.209C>G
cDNA.693C>G
g.32666C>G

AA changes

T70R Score: 71 explain score(s)

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

frameshift

known variant

Reference ID: rs1035480

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1679	681	2360
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.474	1
	1.63	1
(flanking)	2.474	1

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 gained	32665	0.61	mu: TTCCAAGAAAGCGTG	CCAA\|gaaa
Donor gained	32660	0.37	mu: TGGTTTTCCAAGAAA	GTTT\|tcca

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

ENSPTRG00000016799

Mmulatta

not conserved

ENSMMUG00000018820

Fcatus

no alignment

ENSFCAG00000001019

n/a

Mmusculus

not conserved

ENSMUSG00000048424

Ggallus

not conserved

ENSGALG00000021304

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0039110

n/a

Celegans

no alignment

R12C12.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
276	417	DOMAIN	RanBD1.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1473 / 1473

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

491 / 491

position of stopcodon in wt / mu cDNA

1957 / 1957

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

485 / 485

chromosome

strand

-1

last intron/exon boundary

1914

theoretical NMD boundary in CDS

1379

length of CDS

1473

coding sequence (CDS) position

209

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

693

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

32666

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

36269551

original gDNA sequence snippet

AGAATGTAATGGTTTTCCAACAAAGCGTGTACGGTCTTCAT

altered gDNA sequence snippet

AGAATGTAATGGTTTTCCAAGAAAGCGTGTACGGTCTTCAT

original cDNA sequence snippet

AGAATGTAATGGTTTTCCAACAAAGCGTGTACGGTCTTCAT

altered cDNA sequence snippet

AGAATGTAATGGTTTTCCAAGAAAGCGTGTACGGTCTTCAT

wildtype AA sequence

MTTIPRKGSS HLPGSLHTCK LKLQEDRRQQ EKSVIAQPIF VFEKGEQTFK RPAEDTLYEA
AEPECNGFPT KRVRSSSFTF HITDSQSQGV STLSQKQMRC SSVTNLPTFP HSGPVRKNNV
FMTSALVQSS VDIKSAEQGP VKHSKHVIRP AILQLPQARS CAKVRKTFGH KALESCKTKE
KTNNKISEGN SYLLSENLSR ARISVQLSTN QDFLGATSVG CQPNEDKCSF KSCSSNFVFG
ENMVERVLGT QKLTQPQLEN DSYAKEKPFK SIPKFPVNFL SSRTDSIKNT SLIESAAAFS
SQPSRKCLLE KIDVITGEET EHNVLKINCK LFIFNKTTQS WIERGRGTLR LNDTASTDCG
TLQSRLIMRN QGSLRLILNS KLWAQMKIQR ANHKNVRITA TDLEDYSIKI FLIQASAQDT
AYLYAAIHHR LVALQSFNKQ RDVNQAESLS ETAQQLNCES CDENEDDFIQ VTKNGSDPSS
WTHRQSVACS *

mutated AA sequence

MTTIPRKGSS HLPGSLHTCK LKLQEDRRQQ EKSVIAQPIF VFEKGEQTFK RPAEDTLYEA
AEPECNGFPR KRVRSSSFTF HITDSQSQGV STLSQKQMRC SSVTNLPTFP HSGPVRKNNV
FMTSALVQSS VDIKSAEQGP VKHSKHVIRP AILQLPQARS CAKVRKTFGH KALESCKTKE
KTNNKISEGN SYLLSENLSR ARISVQLSTN QDFLGATSVG CQPNEDKCSF KSCSSNFVFG
ENMVERVLGT QKLTQPQLEN DSYAKEKPFK SIPKFPVNFL SSRTDSIKNT SLIESAAAFS
SQPSRKCLLE KIDVITGEET EHNVLKINCK LFIFNKTTQS WIERGRGTLR LNDTASTDCG
TLQSRLIMRN QGSLRLILNS KLWAQMKIQR ANHKNVRITA TDLEDYSIKI FLIQASAQDT
AYLYAAIHHR LVALQSFNKQ RDVNQAESLS ETAQQLNCES CDENEDDFIQ VTKNGSDPSS
WTHRQSVACS *

speed

0.52 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999969295576694 (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)

chr5:36269551G>CN/A show variant in all transcripts IGV

HGNC symbol

RANBP3L

Ensembl transcript ID

ENST00000515759

Genbank transcript ID

N/A

UniProt peptide

Q86VV4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.209C>G
cDNA.693C>G
g.32666C>G

AA changes

T70R Score: 71 explain score(s)

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

frameshift

known variant

Reference ID: rs1035480

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1679	681	2360
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.474	1
	1.63	1
(flanking)	2.474	1

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 gained	32665	0.61	mu: TTCCAAGAAAGCGTG	CCAA\|gaaa
Donor gained	32660	0.37	mu: TGGTTTTCCAAGAAA	GTTT\|tcca

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

ENSPTRG00000016799

Mmulatta

not conserved

ENSMMUG00000018820

Fcatus

no alignment

ENSFCAG00000001019

n/a

Mmusculus

not conserved

ENSMUSG00000048424

Ggallus

not conserved

ENSGALG00000021304

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0039110

n/a

Celegans

not conserved

R12C12.2

183

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
276	417	DOMAIN	RanBD1.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

966 / 966

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

322 / 322

position of stopcodon in wt / mu cDNA

1450 / 1450

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

485 / 485

chromosome

strand

-1

last intron/exon boundary

1257

theoretical NMD boundary in CDS

722

length of CDS

966

coding sequence (CDS) position

209

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

693

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

32666

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

36269551

original gDNA sequence snippet

AGAATGTAATGGTTTTCCAACAAAGCGTGTACGGTCTTCAT

altered gDNA sequence snippet

AGAATGTAATGGTTTTCCAAGAAAGCGTGTACGGTCTTCAT

original cDNA sequence snippet

AGAATGTAATGGTTTTCCAACAAAGCGTGTACGGTCTTCAT

altered cDNA sequence snippet

AGAATGTAATGGTTTTCCAAGAAAGCGTGTACGGTCTTCAT

wildtype AA sequence

mutated AA sequence

speed

0.43 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