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 CM960721)
known disease mutation: rs2084 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:13010285C>TN/A show variant in all transcripts IGV

HGNC symbol

SYCE2

Ensembl transcript ID

ENST00000293695

Genbank transcript ID

NM_001105578

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.19806G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434368
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2084 (pathogenic for Glutaric aciduria, type 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.629	1
	5.605	1
(flanking)	-0.565	0.864

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 marginally increased	19798	wt: 0.9889 / mu: 0.9906 (marginal change - not scored)	wt: GTGAATGTCATGTGT mu: GTGAATGTCATGTAT	GAAT\|gtca

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

20 / 20

chromosome

strand

-1

last intron/exon boundary

632

theoretical NMD boundary in CDS

562

length of CDS

657

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)

19806

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

13010285

original gDNA sequence snippet

TCAGGGCGTGAATGTCATGTGTACCTGGACAAGATTAATAC

altered gDNA sequence snippet

TCAGGGCGTGAATGTCATGTATACCTGGACAAGATTAATAC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MERQGVDVPH VKCKDQEPQP LGESKEHPRW EENCEEEAGG GPASASCQLT VLEGKSGLYF
SSLDSSIDIL QKRAQELIEN INKSRQKDHA LMTNFRNSLK TKVSDLTEKL EERIYQIYND
HNKIIQEKLQ EFTQKMAKIS HLETELKQVC HSVETVYKDL CLQPEQSLRL RWGPDHSRGK
SPPRPGNSQP PDVFVSSVAE TTSQATASEV QTNRDGEC*

mutated AA sequence

N/A

speed

0.34 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