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: ENST00000607273
MT speed 0 s - this script 4.31199 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

PRIM2

disease causing

0.996194374753508

simple_aae

n/a

62398997

show file

Taster files

mutation t@sting

documentation

Alteration 6:57398201T>C_1_ENST00000607273

Prediction	disease causing	Model: simple_aae, prob: 0.996194374753508 (explain)
Summary	amino acid sequence changed heterozygous in TGP or ExAC	hyperlink

analysed issue

analysis result

name of alteration

6:57398201T>C_1_ENST00000607273

alteration (phys. location)

chr6:57398201T>C show variant in all transcripts IGV

HGNC symbol

PRIM2

ExAC LOF metrics

LOF: 0.00, misssense: -0.86, synonymous: -0.47

Ensembl transcript ID

ENST00000607273

Genbank transcript ID

NM_000947

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.904T>C
g.218599T>C

AA changes

C302R Score: 180
explain score(s)

frameshift

length of protein

normal

known variant

Reference ID: rs62398997

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	8	32767	32775

regulatory features

name	class
H3K36me3	Histone	Histone 3 Lysine 36 Tri-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)	-0.181	0.967
	2.722	1
(flanking)	6.235	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

302

mutated

not conserved

302

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000001150

302

Fcatus

not conserved

ENSFCAG00000029312

304

Mmusculus

not conserved

ENSMUSG00000026134

302

Ggallus

not conserved

ENSGALG00000016278

302

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000052721

307

Dmelanogaster

not conserved

FBgn0259676

314

Celegans

not conserved

WBGene00004181

321

Xtropicalis

not conserved

ENSXETG00000004450

310

protein features

N/A

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1041 / 1041

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

347 / 347

position of stopcodon in wt / mu cDNA

1128 / 1128

poly(A) signal

N/A

position of start ATG in wt / mu cDNA

88 / 88

chromosome

strand

last intron/exon boundary

1386

theoretical NMD boundary in CDS

1248

length of CDS

1041

coding sequence (CDS) position

904

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

991

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

218599

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

57398201

original gDNA sequence snippet

TGCGGGAAAATCACCATCTTTGTCATGGAGGCCGAATGCAG

altered gDNA sequence snippet

TGCGGGAAAATCACCATCTTCGTCATGGAGGCCGAATGCAG

original cDNA sequence snippet

TGCGGGAAAATCACCATCTTTGTCATGGAGGCCGAATGCAG

altered cDNA sequence snippet

TGCGGGAAAATCACCATCTTCGTCATGGAGGCCGAATGCAG

wildtype AA sequence

MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV KLLKSVENLG
VSYVKGTEQY QSKLESELRK LKFSYRENLE DEYEPRRRDH ISHFILRLAY CQSEELRRWF
IQQEMDLLRF RFSILPKDKI QDFLKDSQLQ FEAISDEEKT LREQEIVASS PSLSGLKLGF
ESIYKIPFAD ALDLFRGRKV YLEDGFAYVP LKDIVAIILN EFRAKLSKAL ALTARSLPAV
QSDERLQPLL NHLSHSYTSQ DYSTQGNVGK ISLDQIDLLS TKSFPLYMHQ LHKALRENHH
LCHGGRMQYV LFLKGIGLTL EQTLQFWKQE FIKGKMDPDK FDKGYS*

mutated AA sequence

version

genome build 37 / Ensembl release 85

speed

0.24 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Alteration 6:57398201T>C_1_ENST00000607273

Prediction

disease causing

for research use only

Problems