mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999952853343 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM993117)
known disease mutation: rs17124 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:33139540G>AN/A show variant in all transcripts IGV

HGNC symbol

COL11A2

Ensembl transcript ID

ENST00000357486

Genbank transcript ID

N/A

UniProt peptide

P13942

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3037C>T
cDNA.3265C>T
g.20737C>T

AA changes

R1013C Score: 180 explain score(s)

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

1013

frameshift

known variant

Reference ID: rs121912947
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17124 (pathogenic for Deafness, autosomal dominant 13|not provided|Rare genetic deafness) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993117)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993117)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993117)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.795	1
	1.028	1
(flanking)	0.369	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
Acc marginally increased	20733	wt: 0.6427 / mu: 0.6680 (marginal change - not scored)	wt: GGGGGACCCATTGGTCCGCCAGGGCGCCCAGGCCCGCAGGG mu: GGGGGACCCATTGGTCCGCCAGGGTGCCCAGGCCCGCAGGG	gcca\|GGGC
Donor marginally increased	20742	wt: 0.6115 / mu: 0.6703 (marginal change - not scored)	wt: CGCCCAGGCCCGCAG mu: TGCCCAGGCCCGCAG	CCCA\|ggcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1013

mutated

not conserved

1013

Ptroglodytes

all identical

ENSPTRG00000018033

996

Mmulatta

all identical

ENSMMUG00000003850

1033

Fcatus

all identical

ENSFCAG00000004005

661

Mmusculus

all identical

ENSMUSG00000024330

987

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000005534

1101

Drerio

all identical

ENSDARG00000012422

1280

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012724

1264

protein features

start (aa)	end (aa)	feature	details
487	1500	REGION	Triple-helical region.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5148 / 5148

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

1716 / 1716

position of stopcodon in wt / mu cDNA

5376 / 5376

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

229 / 229

chromosome

strand

-1

last intron/exon boundary

5236

theoretical NMD boundary in CDS

4957

length of CDS

5148

coding sequence (CDS) position

3037

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

3265

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

20737

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

33139540

original gDNA sequence snippet

GACCCATTGGTCCGCCAGGGCGCCCAGGCCCGCAGGGTCCC

altered gDNA sequence snippet

GACCCATTGGTCCGCCAGGGTGCCCAGGCCCGCAGGGTCCC

original cDNA sequence snippet

GACCCATTGGTCCGCCAGGGCGCCCAGGCCCGCAGGGTCCC

altered cDNA sequence snippet

GACCCATTGGTCCGCCAGGGTGCCCAGGCCCGCAGGGTCCC

wildtype AA sequence

MERCSRCHRL LLLLPLVLGL SAAPGWAGAP PVDVLRALRF PSLPDGVRRA KGICPADVAY
RVARPAQLSA PTRQLFPGGF PKDFSLLTVV RTRPGLQAPL LTLYSAQGVR QLGLELGRPV
RFLYEDQTGR PQPPSQPVFR GLSLADGKWH RVAVAVKGQS VTLIVDCKKR VTRPLPRSAR
PVLDTHGVII FGARILDEEV FEGDVQELAI VPGVQAAYES CEQKELECEG GQRERPQNQQ
PHRAQRSPQQ QPSRLHRPQN QEPQSQPTES LYYDYEPPYY DVMTTGTTPD YQEQTDLQVP
PTADRFQAEE YGEGGTDPPE GPYDYTYGYG DDYREETELG PALSAETAHS GAAAHGPRGL
KGEKGEPAVL EPGMLVEGPP GPEGPAGLIG PPGIQGNPGP VGDPGERGPP GRAGLPGSDG
APGPPGTSLM LPFRFGSGGG DKGPVVAAQE AQAQAILQQA RLALRGPPGP MGYTGRPGPL
GQPGSPGLKG ESGDLGPQGP RGPQGLTGPP GKAGRRGRAG ADGARGMPGD PGVKGDRGFD
GLPGLPGEKG HRGDTGAQGL PGPPGEDGER GDDGEIGPRG LPGESGPRGL LGPKGPPGIP
GPPGVRGMDG PQGPKGSLGP QGEPGPPGQQ GTPGTQGLPG PQGAIGPHGE KGPQGKPGLP
GMPGSDGPPG HPGKEGPPGT KGNQGPSGPQ GPLGYPGPRG VKGVDGIRGL KGHKGEKGED
GFPGFKGDIG VKGDRGEVGV PGSRGEDGPE GPKGRTGPTG DPGPPGLMGE KGKLGVPGLP
GYPGRQGPKG SLGFPGFPGA SGEKGARGLS GKSGPRGERG PTGPRGQRGP RGATGKSGAK
GTSGGDGPHG PPGERGLPGP QGPNGFPGPK GPPGPPGKDG LPGHPGQRGE VGFQGKTGPP
GPPGVVGPQG AAGETGPMGE RGHPGPPGPP GEQGLPGTAG KEGTKGDPGP PGAPGKDGPA
GLRGFPGERG LPGTAGGPGL KGNEGPSGPP GPAGSPGERG AAGSGGPIGP PGRPGPQGPP
GAAGEKGVPG EKGPIGPTGR DGVQGPVGLP GPAGPPGVAG EDGDKGEVGD PGQKGTKGNK
GEHGPPGPPG PIGPVGQPGA AGADGEPGAR GPQGHFGAKG DEGTRGFNGP PGPIGLQGLP
GPSGEKGETG DVGPMGPPGP PGPRGPAGPN GADGPQGPPG GVGNLGPPGE KGEPGESGSP
GIQGEPGVKG PRGERGEKGE SGQPGEPGPP GPKGPTGDDG PKGNPGPVGF PGDPGPPGEG
GPRGQDGAKG DRGEDGEPGQ PGSPGPTGEN GPPGPLGKRG PAGSPGSEGR QGGKGAKGDP
GAIGAPGKTG PVGPAGPAGK PGPDGLRGLP GSVGQQGRPG ATGQAGPPGP VGPPGLPGLR
GDAGAKGEKG HPGLIGLIGP PGEQGEKGDR GLPGPQGSPG QKGEMGIPGA SGPIGPGGPP
GLPGPAGPKG AKGATGPGGP KGEKGVQGPP GHPGPPGEVI QPLPIQMPKK TRRSVDGSRL
MQEDEAIPTG GAPGSPGGLE EIFGSLDSLR EEIEQMRRPT GTQDSPARTC QDLKLCHPEL
PDGEYWVDPN QGCARDAFRV FCNFTAGGET CVTPRDDVTQ FSYVDSEGSP VGVVQLTFLR
LLSVSAHQDV SYPCSGAARD GPLRLRGANE DELSPETSPY VKEFRDGCQT QQGRTVLEVR
TPVLEQLPVL DASFSDLGAP PRRGGVLLGP VCFMG*

mutated AA sequence

MERCSRCHRL LLLLPLVLGL SAAPGWAGAP PVDVLRALRF PSLPDGVRRA KGICPADVAY
RVARPAQLSA PTRQLFPGGF PKDFSLLTVV RTRPGLQAPL LTLYSAQGVR QLGLELGRPV
RFLYEDQTGR PQPPSQPVFR GLSLADGKWH RVAVAVKGQS VTLIVDCKKR VTRPLPRSAR
PVLDTHGVII FGARILDEEV FEGDVQELAI VPGVQAAYES CEQKELECEG GQRERPQNQQ
PHRAQRSPQQ QPSRLHRPQN QEPQSQPTES LYYDYEPPYY DVMTTGTTPD YQEQTDLQVP
PTADRFQAEE YGEGGTDPPE GPYDYTYGYG DDYREETELG PALSAETAHS GAAAHGPRGL
KGEKGEPAVL EPGMLVEGPP GPEGPAGLIG PPGIQGNPGP VGDPGERGPP GRAGLPGSDG
APGPPGTSLM LPFRFGSGGG DKGPVVAAQE AQAQAILQQA RLALRGPPGP MGYTGRPGPL
GQPGSPGLKG ESGDLGPQGP RGPQGLTGPP GKAGRRGRAG ADGARGMPGD PGVKGDRGFD
GLPGLPGEKG HRGDTGAQGL PGPPGEDGER GDDGEIGPRG LPGESGPRGL LGPKGPPGIP
GPPGVRGMDG PQGPKGSLGP QGEPGPPGQQ GTPGTQGLPG PQGAIGPHGE KGPQGKPGLP
GMPGSDGPPG HPGKEGPPGT KGNQGPSGPQ GPLGYPGPRG VKGVDGIRGL KGHKGEKGED
GFPGFKGDIG VKGDRGEVGV PGSRGEDGPE GPKGRTGPTG DPGPPGLMGE KGKLGVPGLP
GYPGRQGPKG SLGFPGFPGA SGEKGARGLS GKSGPRGERG PTGPRGQRGP RGATGKSGAK
GTSGGDGPHG PPGERGLPGP QGPNGFPGPK GPPGPPGKDG LPGHPGQRGE VGFQGKTGPP
GPPGVVGPQG AAGETGPMGE RGHPGPPGPP GEQGLPGTAG KEGTKGDPGP PGAPGKDGPA
GLRGFPGERG LPGTAGGPGL KGNEGPSGPP GPAGSPGERG AAGSGGPIGP PGCPGPQGPP
GAAGEKGVPG EKGPIGPTGR DGVQGPVGLP GPAGPPGVAG EDGDKGEVGD PGQKGTKGNK
GEHGPPGPPG PIGPVGQPGA AGADGEPGAR GPQGHFGAKG DEGTRGFNGP PGPIGLQGLP
GPSGEKGETG DVGPMGPPGP PGPRGPAGPN GADGPQGPPG GVGNLGPPGE KGEPGESGSP
GIQGEPGVKG PRGERGEKGE SGQPGEPGPP GPKGPTGDDG PKGNPGPVGF PGDPGPPGEG
GPRGQDGAKG DRGEDGEPGQ PGSPGPTGEN GPPGPLGKRG PAGSPGSEGR QGGKGAKGDP
GAIGAPGKTG PVGPAGPAGK PGPDGLRGLP GSVGQQGRPG ATGQAGPPGP VGPPGLPGLR
GDAGAKGEKG HPGLIGLIGP PGEQGEKGDR GLPGPQGSPG QKGEMGIPGA SGPIGPGGPP
GLPGPAGPKG AKGATGPGGP KGEKGVQGPP GHPGPPGEVI QPLPIQMPKK TRRSVDGSRL
MQEDEAIPTG GAPGSPGGLE EIFGSLDSLR EEIEQMRRPT GTQDSPARTC QDLKLCHPEL
PDGEYWVDPN QGCARDAFRV FCNFTAGGET CVTPRDDVTQ FSYVDSEGSP VGVVQLTFLR
LLSVSAHQDV SYPCSGAARD GPLRLRGANE DELSPETSPY VKEFRDGCQT QQGRTVLEVR
TPVLEQLPVL DASFSDLGAP PRRGGVLLGP VCFMG*

speed

0.82 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