mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM057325)
known disease mutation: rs1818 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:25458221T>AN/A show variant in all transcripts IGV

HGNC symbol

CENPJ

Ensembl transcript ID

ENST00000545981

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.3761A>T
g.38798A>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434311

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs1818 (pathogenic for Primary autosomal recessive microcephaly 6) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)

known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)
known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.045	1
	4.508	1
(flanking)	5.446	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	38797.5	sequence motif lost	-	wt: aaca\|GAAA mu: aaca.GTAA
Donor marginally increased	38796	wt: 0.9905 / mu: 0.9920 (marginal change - not scored)	wt: TAAACAGAAAAACAT mu: TAAACAGTAAAACAT	AACA\|gaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

143 / 143

chromosome

strand

-1

last intron/exon boundary

3882

theoretical NMD boundary in CDS

3689

length of CDS

3261

coding sequence (CDS) position

N/A

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

3761

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

38798

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

25458221

original gDNA sequence snippet

TGTAACAACTTTTTAAACAGAAAAACATTACCCAGATGGAA

altered gDNA sequence snippet

TGTAACAACTTTTTAAACAGTAAAACATTACCCAGATGGAA

original cDNA sequence snippet

TTTCTCAAGTGGACAAATAGAAAAACATTACCCAGATGGAA

altered cDNA sequence snippet

TTTCTCAAGTGGACAAATAGTAAAACATTACCCAGATGGAA

wildtype AA sequence

MFLMPTSSEL NSGQNFLTQW MTNPSRAGVI LNRGFPILEA DKEKRAAVDI STSFPIKGTH
FSDSFSFINE EDSLLEEQKL ESNNPYKPQS DKSETHTAFP CIKKGPQVAA CHSAPGHQEE
NKNDFIPDLA SEFKEGAYKD PLFKKLEQLK EVQQKKQEQL KRQQLEQLQR LMEEQEKLLT
MVSGQCTLPG LSLLPDDQSQ KHRSPGNTTT GERATCCFPS YVYPDPTQEE TYPSNILSHE
QSNFCRTAHG DFVLTSKRAS PNLFSEAQYQ EAPVEKNNLK EENRNHPTGE SILCWEKVTE
QIQEANDKNL QKHDDSSEVA NIEERPIKAA IGERKQTFED YLEEQIQLEE QELKQKQLKE
AEGPLPIKAK PKQPFLKRGE GLARFTNAKS KFQKGKESKL VTNQSTSEDQ PLFKMDRQQL
QRKTALKNKE LCADNPILKK DSKARTKSGS VTLSQKPKML KCSNRKSLSP SGLKIQTGKK
CDGQFRDQIK FENKVTSNNK ENVTECPKPC DTGCTGWNKT QGKDRLPLST GPASRLAAKS
PIRETMKESE SSLDVSLQKK LETWEREKEK ENLELDEFLF LEQAADEISF SSNSSFVLKI
LERDQQICKG HRMSSTPVKA VPQKTNPADP ISHCNRSEDL DHTAREKESE CEVAPKQLHS
LSSADELREQ PCKIRKAVQK STSENQTEWN ARDDEGVPNS DSSTDSEEQL DVTIKPSTED
RERGISSRED SPQVCDDKGP FKDTRTQEDK RRDVDLDLSD KDYSSDESIM ESIKHKVSEP
SRSSSLSLSK MDFDDERTWT DLEENLCNHD VVLGNESTYG TPQTCYPNNE IGILDKTIKR
KIAPVKRGED LSKSRRSRSP PTSELMMKFF PSLKPKPKSD SHLGNELKLN ISQDQPPGDN
ARSQVLREKI IELETEIEKF KAENASLAKL RIERESALEK LRKEIADFEQ QKAKELARIE
EFKKEEMRKL QKERKVFEKY TTAARTFPDK KEREEIQTLK QQIADLREDL KRKETKWSST
HSRLRSQIQM LVRENTDLRE EIKVMERFRL DAWKRAEAIE SSLEVEKKDK LAAIHLEDPS
LHLLVI*

mutated AA sequence

N/A

speed

0.11 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