mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999792516987 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980386)
known disease mutation: rs17123 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:33134513C>TN/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.4259G>A
cDNA.4487G>A
g.25764G>A

AA changes

G1420E Score: 98 explain score(s)

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

1420

frameshift

known variant

Reference ID: rs121912946
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17123 (pathogenic for Otospondylomegaepiphyseal dysplasia, autosomal dominant) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980386)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980386)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980386)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.059	1
	4.778	1
(flanking)	4.778	0.998

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	25764	wt: 0.5682 / mu: 0.6376 (marginal change - not scored)	wt: TGGGCCTCAGGGCTCCCCTGGGCAGAAGGGTGAGATGGTGA mu: TGGGCCTCAGGGCTCCCCTGAGCAGAAGGGTGAGATGGTGA	ctgg\|GCAG
Donor marginally increased	25767	wt: 0.8507 / mu: 0.9089 (marginal change - not scored)	wt: TGGGCAGAAGGGTGA mu: TGAGCAGAAGGGTGA	GGCA\|gaag
Donor increased	25765	wt: 0.84 / mu: 0.96	wt: CCTGGGCAGAAGGGT mu: CCTGAGCAGAAGGGT	TGGG\|caga
Donor gained	25762	0.42	mu: TCCCCTGAGCAGAAG	CCCT\|gagc
Donor gained	25759	0.51	mu: GGCTCCCCTGAGCAG	CTCC\|cctg
Donor gained	25764	0.79	mu: CCCTGAGCAGAAGGG	CTGA\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1420

mutated

not conserved

1420

Ptroglodytes

all identical

ENSPTRG00000018033

1403

Mmulatta

all identical

ENSMMUG00000003850

1447

Fcatus

all identical

ENSFCAG00000004005

1068

Mmusculus

all identical

ENSMUSG00000024330

1394

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000005534

1508

Drerio

all identical

ENSDARG00000012422

1687

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000012724

1671

protein features

start (aa)	end (aa)	feature	details
487	1500	REGION	Triple-helical region.	lost
1441	1499	DOMAIN	Collagen-like 8.	might get lost (downstream of altered splice site)
1501	1736	PROPEP	C-terminal propeptide. /FTId=PRO_0000005841.	might get lost (downstream of altered splice site)
1541	1735	DOMAIN	Fibrillar collagen NC1.	might get lost (downstream of altered splice site)
1552	1552	CONFLICT	E -> R (in Ref. 7; AAA52034).	might get lost (downstream of altered splice site)
1571	1571	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1571	1571	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1577	1577	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1577	1577	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1594	1594	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1594	1594	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1603	1603	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1603	1603	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1604	1604	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1612	1612	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1655	1655	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1689	1689	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1733	1733	DISULFID	By similarity.	might get lost (downstream of altered splice site)

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

4259

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

4487

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

25764

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

33134513

original gDNA sequence snippet

TGGGCCTCAGGGCTCCCCTGGGCAGAAGGGTGAGATGGTGA

altered gDNA sequence snippet

TGGGCCTCAGGGCTCCCCTGAGCAGAAGGGTGAGATGGTGA

original cDNA sequence snippet

TGGGCCTCAGGGCTCCCCTGGGCAGAAGGGTGAGATGGGTA

altered cDNA sequence snippet

TGGGCCTCAGGGCTCCCCTGAGCAGAAGGGTGAGATGGGTA

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 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 GLPGPQGSPE 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

1.02 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