mutation t@sting

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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 CM067659)
known disease mutation: rs17414 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:110839528C>TN/A show variant in all transcripts IGV

HGNC symbol

COL4A1

Ensembl transcript ID

ENST00000397198

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.119969G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121912857
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17414 (pathogenic for Brain small vessel disease 1 with or without ocular anomalies) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM067659)

known disease mutation at this position, please check HGMD for details (HGMD ID CM067659)
known disease mutation at this position, please check HGMD for details (HGMD ID CM067659)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.172	0.967
	5.335	1
(flanking)	5.335	1

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	119966	wt: 0.8582 / mu: 0.8718 (marginal change - not scored)	wt: TTCTCCTGGAAGAGA mu: TTCTCCTGAAAGAGA	CTCC\|tgga
Donor marginally increased	119971	wt: 0.9970 / mu: 0.9984 (marginal change - not scored)	wt: CTGGAAGAGATGGCC mu: CTGAAAGAGATGGCC	GGAA\|gaga

distance from splice site

5077

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

123 / 123

chromosome

strand

-1

last intron/exon boundary

3998

theoretical NMD boundary in CDS

3825

length of CDS

3957

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)

119969

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

110839528

original gDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGGAAGAGATGGCCATCCGGGTC

altered gDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGAAAGAGATGGCCATCCGGGTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGPRLSVWLL LLPAALLLHE EHSRAAAKGG CAGSGCGKCD CHGVKGQKGE RGLPGLQGVI
GFPGMQGPEG PQGPPGQKGD TGEPGLPGTK GTRGPPGASG YPGNPGLPGI PGQDGPPGPP
GIPGCNGTKG ERGPLGPPGL PGFAGNPGPP GLPGMKGDPG EILGHVPGML LKGERGFPGI
PGTPGPPGLP GLQGPVGPPG FTGPPGPPGP PGPPGEKGQM GLSFQGPKGD KGDQGVSGPP
GVPGQAQVQE KGDFATKGEK GQKGEPGFQG MPGVGEKGEP GKPGPRGKPG KDGDKGEKGS
PGFPGEPGYP GLIGRQGPQG EKGEAGPPGP PGIVIGTGPL GEKGERGYPG TPGPRGEPGP
KGFPGLPGQP GPPGLPVPGQ AGAPGFPGER GEKGDRGFPG TSLPGPSGRD GLPGPPGSPG
PPGQPGYTNG IVECQPGPPG DQGPPGIPGQ PGFIGEIGEK GQKGESCLIC DIDGYRGPPG
PQGPPGEIGF PGQPGAKGLP GITGQSGLPG LPGQQGAPGI PGFPGSKGEM GVMGTPGQPG
SPGPVGAPGL PGEKGDHGFP GSSGPRGDPG LKGDKGDVGL PGKPGSMDKV DMGSMKGQKG
DQGEKGQIGP IGEKGSRGDP GTPGVPGKDG QAGQPGQPGP KGDPGISGTP GAPGLPGPKG
SVGGMGLPGT PGEKGVPGIP GPQGSPGLPG DKGAKGEKGQ AGPPGIGIPG LRGEKGDQGI
AGFPGSPGEK GEKGSIGIPG MPGSPGLKGS PGSVGYPGSP GLPGEKGDKG LPGLDGIPGV
KGEAGLPGTP GPTGPAGQKG EPGSDGIPGS AGEKGEPGLP GRGFPGFPGA KGDKGSKGEV
GFPGLAGSPG IPGSKGEQGF MGPPGPQGQP GLPGSPGHAT EGPKGDRGPQ GQPGLPGLPG
PMGPPGLPGI DGVKGDKGNP GWPGAPGVPG PKGDPGFQGM PGIGGSPGIT GSKGDMGPPG
VPGFQGPKGL PGLQGIKGDQ GDQGVPGAKG LPGPPGPPGP YDIIKGEPGL PGPEGPPGLK
GLQGLPGPKG QQGVTGLVGI PGPPGIPGFD GAPGQKGEMG PAGPTGPRGF PGPPGPDGLP
GSMGPPGTPS VDHGFLVTRH SQTIDDPQCP SGTKILYHGY SLLYVQGNER AHGQDLGTAG
SCLRKFSTMP FLFCNINNVC NFASRNDYSY WLSTPEPMPM SMAPITGENI RPFISRCAVC
EAPAMVMAVH SQTIQIPPCP SGWSSLWIGY SFVMHTSAGA EGSGQALASP GSCLEEFRSA
PFIECHGRGT CNYYANAYSF WLATIERSEM FKKPTPSTLK AGELRTHVSR CQVCMRRT*

mutated AA sequence

N/A

speed

1.01 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