MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #2: ENST00000433625
Querying Taster for transcript #3: ENST00000182527
MT speed 0 s - this script 5.117232 s

Results

genesymbol

pred

model

pred_problem

f_splice

f_known_DM

f_pot_DM

AA_changes

alt_type

snp_id

features_at_a_glance

file

TRAM2

disease causing

0.999999999985428

simple_aae

n/a

776994347

show file

EFHC1

disease causing

without_aae

n/a

776994347

show file

Taster files

mutation t@sting

documentation

Alteration 6:52370454C>G_2_ENST00000182527

Prediction	disease causing	Model: simple_aae, prob: 0.999999999985428 (explain)
Summary	amino acid sequence changed heterozygous in TGP or ExAC protein features (might be) affected	hyperlink

analysed issue

analysis result

name of alteration

6:52370454C>G_2_ENST00000182527

alteration (phys. location)

chr6:52370454C>G show variant in all transcripts IGV

HGNC symbol

TRAM2

ExAC LOF metrics

LOF: 0.99, misssense: 1.78, synonymous: 0.68

Ensembl transcript ID

ENST00000182527

Genbank transcript ID

NM_012288

UniProt peptide

Q15035

alteration type

single base exchange

alteration region

CDS

DNA changes

c.818G>C
g.71260G>C

AA changes

R273P Score: 103
explain score(s)

frameshift

length of protein

normal

known variant

Reference ID: rs776994347

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	522	522

regulatory features

name	class
H3K27ac	Histone	Histone 3 Lysine 27 Acetylation
H3K36me3	Histone	Histone 3 Lysine 36 Tri-Methylation
H3K4me1	Histone	Histone 3 Lysine 4 Mono-Methylation

multicell regulatory features

N/A

external features from FANTOM5 and/or VISTA

N/A

miRNA binding site(s)

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.282	0
	6.06	1
(flanking)	6.06	1

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

N/A

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

273

mutated

not conserved

273

Ptroglodytes

all identical

ENSPTRG00000040958

273

Mmulatta

all identical

ENSMMUG00000013718

273

Fcatus

all identical

ENSFCAG00000002975

236

Mmusculus

all identical

ENSMUSG00000041779

273

Ggallus

all identical

ENSGALG00000016673

269

Trubripes

all identical

ENSTRUG00000007487

273

Drerio

all identical

ENSDARG00000030092

273

Dmelanogaster

not conserved

FBgn0040340

287

Celegans

all conserved

WBGene00007696

289

Xtropicalis

all identical

ENSXETG00000000663

272

protein features

start (aa)	end (aa)	feature	details
112	321	DOMAIN	TLC.	lost

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1113 / 1113

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

371 / 371

position of stopcodon in wt / mu cDNA

1113 / 1113

poly(A) signal

N/A

position of start ATG in wt / mu cDNA

1 / 1

chromosome

strand

-1

last intron/exon boundary

1039

theoretical NMD boundary in CDS

988

length of CDS

1113

coding sequence (CDS) position

818

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

818

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

71260

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

52370454

original gDNA sequence snippet

CATTGGCTTTGGACTGGCTCGCATGGAAAACCAGGCATTTG

altered gDNA sequence snippet

CATTGGCTTTGGACTGGCTCCCATGGAAAACCAGGCATTTG

original cDNA sequence snippet

CATTGGCTTTGGACTGGCTCGCATGGAAAACCAGGCATTTG

altered cDNA sequence snippet

CATTGGCTTTGGACTGGCTCCCATGGAAAACCAGGCATTTG

wildtype AA sequence

MAFRRRTKSY PLFSQEFVIH NHADIGFCLV LCVLIGLMFE VTAKTAFLFI LPQYNISVPT
ADSETVHYHY GPKDLVTILF YIFITIILHA VVQEYILDKI SKRLHLSKVK HSKFNESGQL
VVFHFTSVIW CFYVVVTEGY LTNPRSLWED YPHVHLPFQV KFFYLCQLAY WLHALPELYF
QKVRKEEIPR QLQYICLYLV HIAGAYLLNL SRLGLILLLL QYSTEFLFHT ARLFYFADEN
NEKLFSAWAA VFGVTRLFIL TLAVLAIGFG LARMENQAFD PEKGNFNTLF CRLCVLLLVC
AAQAWLMWRF IHSQLRHWRE YWNEQSAKRR VPATPRLPAR LIKRESGYHE NGVVKAENGT
SPRTKKLKSP *

mutated AA sequence

MAFRRRTKSY PLFSQEFVIH NHADIGFCLV LCVLIGLMFE VTAKTAFLFI LPQYNISVPT
ADSETVHYHY GPKDLVTILF YIFITIILHA VVQEYILDKI SKRLHLSKVK HSKFNESGQL
VVFHFTSVIW CFYVVVTEGY LTNPRSLWED YPHVHLPFQV KFFYLCQLAY WLHALPELYF
QKVRKEEIPR QLQYICLYLV HIAGAYLLNL SRLGLILLLL QYSTEFLFHT ARLFYFADEN
NEKLFSAWAA VFGVTRLFIL TLAVLAIGFG LAPMENQAFD PEKGNFNTLF CRLCVLLLVC
AAQAWLMWRF IHSQLRHWRE YWNEQSAKRR VPATPRLPAR LIKRESGYHE NGVVKAENGT
SPRTKKLKSP *

version

genome build 37 / Ensembl release 85

speed

0.39 s

for research use only

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

Alteration 6:52370454C>G_1_ENST00000433625

Prediction	disease causing	Model: without_aae, prob: 1 (explain)
Summary	heterozygous in TGP or ExAC	hyperlink

analysed issue

analysis result

name of alteration

6:52370454C>G_1_ENST00000433625

alteration (phys. location)

chr6:52370454C>G show variant in all transcripts IGV

HGNC symbol

EFHC1

ExAC LOF metrics

LOF: 0.00, misssense: -0.80, synonymous: 1.23

Ensembl transcript ID

ENST00000433625

Genbank transcript ID

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

c.1578+15306C>G
g.85349C>G

AA changes

N/A

frameshift

length of protein

N/A

known variant

Reference ID: rs776994347

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	522	522

regulatory features

name	class
H3K27ac	Histone	Histone 3 Lysine 27 Acetylation
H3K36me3	Histone	Histone 3 Lysine 36 Tri-Methylation
H3K4me1	Histone	Histone 3 Lysine 4 Mono-Methylation

multicell regulatory features

N/A

external features from FANTOM5 and/or VISTA

N/A

miRNA binding site(s)

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.282	0
	6.06	1
(flanking)	6.06	1

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

N/A

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

N/A

position of start ATG in wt / mu cDNA

232 / 232

chromosome

strand

last intron/exon boundary

1809

theoretical NMD boundary in CDS

1527

length of CDS

1653

coding sequence (CDS) position

N/A

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

N/A

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

85349

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

52370454

original gDNA sequence snippet

CAAATGCCTGGTTTTCCATGCGAGCCAGTCCAAAGCCAATG

altered gDNA sequence snippet

CAAATGCCTGGTTTTCCATGGGAGCCAGTCCAAAGCCAATG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSWPVLKFDA YFQEDVPMST EEQYRIRQVN IYYYLEDDSM SVIEPVVENS GILQGKLIKR
QRLAKNDRGD HYHWKDLNRG INITIYGKTF RVVDCDQFTQ VFLESQGIEL NPPEKMALDP
YTELRKQPLR KYVTPSDFDQ LKQFLTFDKQ VLRFYAIWDD TDSMYGECRT YIIHYYLMDD
TVEIREVHER NDGRDPFPLL MNRQRVPKVL VENAKNFPQC VLEISDQEVL EWYTAKDFIV
GKSLTILGRT FFIYDCDPFT RRYYKEKFGI TDLPRIDVSK REPPPVKQEL PPYNGFGLVE
DSAQNCFALI PKAPKKDVIK MLVNDNKVLR YLAVLESPIP EDKDRRFVFS YFLATDMISI
FEPPVRNSGI IGGKYLGRTK VVKPYSTVDN PVYYGPSDFF IGAVIEVFGH RFIILDTDEY
VLKYMESNAA QYSPEALASI QNHVRKREAP APEAESKQTE KDPGVQELEA LIDTIQKQLK
DHSCKDNIRE AFQIYDKEAS GYVDRDMFFK ICESLNVPVD DSLVKEVTCK RLLLPAFTFP
SPVWIPLCGL *

mutated AA sequence

N/A

version

genome build 37 / Ensembl release 85

speed

0.03 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Alteration 6:52370454C>G_2_ENST00000182527

Prediction

disease causing

for research use only

mutation t@sting

Alteration 6:52370454C>G_1_ENST00000433625

Prediction

disease causing

for research use only

Problems