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: ENST00000257248
Querying Taster for transcript #2: ENST00000541311
MT speed 0 s - this script 3.18448 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CBLIF	disease_causing	0.726784450664774	simple_aae				S46L	single base exchange	rs121434322		show file
CBLIF	disease_causing	0.726784450664774	simple_aae				S21L	single base exchange	rs121434322		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.726784450664774 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs1746 (probable pathogenic)
known disease mutation at this position (HGMD CM051061)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:59611471G>AN/A show variant in all transcripts IGV

HGNC symbol

CBLIF

Ensembl transcript ID

ENST00000257248

Genbank transcript ID

NM_005142

UniProt peptide

P27352

alteration type

single base exchange

alteration region

CDS

DNA changes

c.137C>T
cDNA.185C>T
g.1504C>T

AA changes

S46L Score: 145 explain score(s)

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

frameshift

known variant

Reference ID: rs121434322

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	14	14

known as potential disease variant: rs1746 (probable pathogenic for Intrinsic factor deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051061)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051061)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051061)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.505	0.007
	3.206	0.657
(flanking)	2.697	0.665

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

splice sites

no abrogation of potential splice sites

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

all identical

ENSPTRG00000003701

Mmulatta

all identical

ENSMMUG00000013523

Fcatus

all identical

ENSFCAG00000007542

Mmusculus

all identical

ENSMUSG00000024682

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000025742

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1254 / 1254

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

418 / 418

position of stopcodon in wt / mu cDNA

1302 / 1302

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

49 / 49

chromosome

strand

-1

last intron/exon boundary

1241

theoretical NMD boundary in CDS

1142

length of CDS

1254

coding sequence (CDS) position

137

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

185

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

1504

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

59611471

original gDNA sequence snippet

ACAAGTACTCATGGAGAACTCGGTGACTTCATCAGCCTACC

altered gDNA sequence snippet

ACAAGTACTCATGGAGAACTTGGTGACTTCATCAGCCTACC

original cDNA sequence snippet

ACAAGTACTCATGGAGAACTCGGTGACTTCATCAGCCTACC

altered cDNA sequence snippet

ACAAGTACTCATGGAGAACTTGGTGACTTCATCAGCCTACC

wildtype AA sequence

MAWFALYLLS LLWATAGTST QTQSSCSVPS AQEPLVNGIQ VLMENSVTSS AYPNPSILIA
MNLAGAYNLK AQKLLTYQLM SSDNNDLTIG QLGLTIMALT SSCRDPGDKV SILQRQMENW
APSSPNAEAS AFYGPSLAIL ALCQKNSEAT LPIAVRFAKT LLANSSPFNV DTGAMATLAL
TCMYNKIPVG SEEGYRSLFG QVLKDIVEKI SMKIKDNGII GDIYSTGLAM QALSVTPEPS
KKEWNCKKTT DMILNEIKQG KFHNPMSIAQ ILPSLKGKTY LDVPQVTCSP DHEVQPTLPS
NPGPGPTSAS NITVIYTINN QLRGVELLFN ETINVSVKSG SVLLVVLEEA QRKNPMFKFE
TTMTSWGLVV SSINNIAENV NHKTYWQFLS GVTPLNEGVA DYIPFNHEHI TANFTQY*

mutated AA sequence

MAWFALYLLS LLWATAGTST QTQSSCSVPS AQEPLVNGIQ VLMENLVTSS AYPNPSILIA
MNLAGAYNLK AQKLLTYQLM SSDNNDLTIG QLGLTIMALT SSCRDPGDKV SILQRQMENW
APSSPNAEAS AFYGPSLAIL ALCQKNSEAT LPIAVRFAKT LLANSSPFNV DTGAMATLAL
TCMYNKIPVG SEEGYRSLFG QVLKDIVEKI SMKIKDNGII GDIYSTGLAM QALSVTPEPS
KKEWNCKKTT DMILNEIKQG KFHNPMSIAQ ILPSLKGKTY LDVPQVTCSP DHEVQPTLPS
NPGPGPTSAS NITVIYTINN QLRGVELLFN ETINVSVKSG SVLLVVLEEA QRKNPMFKFE
TTMTSWGLVV SSINNIAENV NHKTYWQFLS GVTPLNEGVA DYIPFNHEHI TANFTQY*

speed

0.37 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

disease causing

Model: simple_aae, prob: 0.726784450664774 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs1746 (probable pathogenic)
known disease mutation at this position (HGMD CM051061)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:59611471G>AN/A show variant in all transcripts IGV

HGNC symbol

CBLIF

Ensembl transcript ID

ENST00000541311

Genbank transcript ID

N/A

UniProt peptide

P27352

alteration type

single base exchange

alteration region

CDS

DNA changes

c.62C>T
cDNA.297C>T
g.1504C>T

AA changes

S21L Score: 145 explain score(s)

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

frameshift

known variant

Reference ID: rs121434322

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	14	14

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.505	0.007
	3.206	0.657
(flanking)	2.697	0.665

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

splice sites

no abrogation of potential splice sites

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

all identical

ENSPTRG00000003701

Mmulatta

all identical

ENSMMUG00000013523

Fcatus

all identical

ENSFCAG00000007542

Mmusculus

all identical

ENSMUSG00000024682

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000025742

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1179 / 1179

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

393 / 393

position of stopcodon in wt / mu cDNA

1414 / 1414

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

236 / 236

chromosome

strand

-1

last intron/exon boundary

1353

theoretical NMD boundary in CDS

1067

length of CDS

1179

coding sequence (CDS) position

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

297

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

1504

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

59611471

original gDNA sequence snippet

ACAAGTACTCATGGAGAACTCGGTGACTTCATCAGCCTACC

altered gDNA sequence snippet

ACAAGTACTCATGGAGAACTTGGTGACTTCATCAGCCTACC

original cDNA sequence snippet

ACAAGTACTCATGGAGAACTCGGTGACTTCATCAGCCTACC

altered cDNA sequence snippet

ACAAGTACTCATGGAGAACTTGGTGACTTCATCAGCCTACC

wildtype AA sequence

MAVPSAQEPL VNGIQVLMEN SVTSSAYPNP SILIAMNLAG AYNLKAQKLL TYQLMSSDNN
DLTIGQLGLT IMALTSSCRD PGDKVSILQR QMENWAPSSP NAEASAFYGP SLAILALCQK
NSEATLPIAV RFAKTLLANS SPFNVDTGAM ATLALTCMYN KIPVGSEEGY RSLFGQVLKD
IVEKISMKIK DNGIIGDIYS TGLAMQALSV TPEPSKKEWN CKKTTDMILN EIKQGKFHNP
MSIAQILPSL KGKTYLDVPQ VTCSPDHEVQ PTLPSNPGPG PTSASNITVI YTINNQLRGV
ELLFNETINV SVKSGSVLLV VLEEAQRKNP MFKFETTMTS WGLVVSSINN IAENVNHKTY
WQFLSGVTPL NEGVADYIPF NHEHITANFT QY*

mutated AA sequence

MAVPSAQEPL VNGIQVLMEN LVTSSAYPNP SILIAMNLAG AYNLKAQKLL TYQLMSSDNN
DLTIGQLGLT IMALTSSCRD PGDKVSILQR QMENWAPSSP NAEASAFYGP SLAILALCQK
NSEATLPIAV RFAKTLLANS SPFNVDTGAM ATLALTCMYN KIPVGSEEGY RSLFGQVLKD
IVEKISMKIK DNGIIGDIYS TGLAMQALSV TPEPSKKEWN CKKTTDMILN EIKQGKFHNP
MSIAQILPSL KGKTYLDVPQ VTCSPDHEVQ PTLPSNPGPG PTSASNITVI YTINNQLRGV
ELLFNETINV SVKSGSVLLV VLEEAQRKNP MFKFETTMTS WGLVVSSINN IAENVNHKTY
WQFLSGVTPL NEGVADYIPF NHEHITANFT QY*

speed

0.88 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems