mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 1 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs17129 (probable pathogenic)
known disease mutation at this position (HGMD CM053813)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:33145920G>TN/A show variant in all transcripts IGV

HGNC symbol

COL11A2

Ensembl transcript ID

ENST00000395197

Genbank transcript ID

N/A

UniProt peptide

P13942

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1681C>A
cDNA.1909C>A
g.14357C>A

AA changes

P561T Score: 38 explain score(s)

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

561

frameshift

known variant

Reference ID: rs121912952

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	15	15

known as potential disease variant: rs17129 (probable pathogenic for Deafness, autosomal recessive 53|not specified|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM053813)

known disease mutation at this position, please check HGMD for details (HGMD ID CM053813)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053813)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.602	1
	2.031	1
(flanking)	0.431	0.999

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 decreased	14368	wt: 0.71 / mu: 0.32	wt: CCTGGTATTCCTGGACCCCCTGTAAGTGACTCCCTGACTTC mu: CCTGGTATTACTGGACCCCCTGTAAGTGACTCCCTGACTTC	ccct\|GTAA
Acc increased	14360	wt: 0.31 / mu: 0.53	wt: AAGGCCCACCTGGTATTCCTGGACCCCCTGTAAGTGACTCC mu: AAGGCCCACCTGGTATTACTGGACCCCCTGTAAGTGACTCC	cctg\|GACC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

561

mutated

not conserved

561

Ptroglodytes

all identical

ENSPTRG00000018033

583

Mmulatta

all identical

ENSMMUG00000003850

620

Fcatus

not conserved

ENSFCAG00000004005

248

Mmusculus

all identical

ENSMUSG00000024330

574

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000005534

688

Drerio

all identical

ENSDARG00000012422

867

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012724

851

protein features

start (aa)	end (aa)	feature	details
487	1500	REGION	Triple-helical region.	lost
546	590	DOMAIN	Collagen-like 3.	lost
578	579	CONFLICT	AQ -> PR (in Ref. 6; AAA35498).	might get lost (downstream of altered splice site)
704	705	CONFLICT	NQ -> KP (in Ref. 6; AAA35498).	might get lost (downstream of altered splice site)
720	720	CONFLICT	R -> Q (in Ref. 6; AAA35498).	might get lost (downstream of altered splice site)
726	726	CONFLICT	D -> N (in Ref. 6; AAA35498).	might get lost (downstream of altered splice site)
805	862	DOMAIN	Collagen-like 4.	might get lost (downstream of altered splice site)
843	846	CONFLICT	TGPR -> HGST (in Ref. 7; AAA52034).	might get lost (downstream of altered splice site)
863	899	DOMAIN	Collagen-like 5.	might get lost (downstream of altered splice site)
882	884	CONFLICT	QGP -> SGS (in Ref. 7; AAA52034).	might get lost (downstream of altered splice site)
1031	1032	CONFLICT	PP -> RQ (in Ref. 1; AAC50213/AAC50214/ AAC50215 and 7; AAA52034).	might get lost (downstream of altered splice site)
1091	1091	CONFLICT	D -> V (in Ref. 7; AAA52034).	might get lost (downstream of altered splice site)
1099	1156	DOMAIN	Collagen-like 6.	might get lost (downstream of altered splice site)
1124	1124	CONFLICT	A -> R (in Ref. 7; AAA52034).	might get lost (downstream of altered splice site)
1127	1133	CONFLICT	EPGARGP -> GAGGLGT (in Ref. 7; AAA52034).	might get lost (downstream of altered splice site)
1157	1172	DOMAIN	Collagen-like 7.	might get lost (downstream of altered splice site)
1253	1253	CONFLICT	P -> A (in Ref. 1; AAC50213/AAC50214/ AAC50215 and 7; AAA52034).	might get lost (downstream of altered splice site)
1257	1257	CONFLICT	T -> Q (in Ref. 1; AAC50213/AAC50214/ AAC50215 and 7; AAA52034).	might get lost (downstream of altered splice site)
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

5031 / 5031

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

1677 / 1677

position of stopcodon in wt / mu cDNA

5259 / 5259

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

5119

theoretical NMD boundary in CDS

4840

length of CDS

5031

coding sequence (CDS) position

1681

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

1909

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

14357

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

33145920

original gDNA sequence snippet

CCAAAGGCCCACCTGGTATTCCTGGACCCCCTGTAAGTGAC

altered gDNA sequence snippet

CCAAAGGCCCACCTGGTATTACTGGACCCCCTGTAAGTGAC

original cDNA sequence snippet

CCAAAGGCCCACCTGGTATTCCTGGACCCCCTGGCGTCCGA

altered cDNA sequence snippet

CCAAAGGCCCACCTGGTATTACTGGACCCCCTGGCGTCCGA

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 YQDPTPGEEE
EILESSLLPP LEEAAHGPRG LKGEKGEPAV LEPGMLVEGP PGPEGPAGLI GPPGIQGNPG
PVGDPGERGP PGRAGLPGSD GAPGPPGTSL MLPFRFGSGG GDKGPVVAAQ EAQAQAILQQ
ARLALRGPPG PMGYTGRPGP LGQPGSPGLK GESGDLGPQG PRGPQGLTGP PGKAGRRGRA
GADGARGMPG DPGVKGDRGF DGLPGLPGEK GHRGDTGAQG LPGPPGEDGE RGDDGEIGPR
GLPGESGPRG LLGPKGPPGI PGPPGVRGMD GPQGPKGSLG PQGEPGPPGQ QGTPGTQGLP
GPQGAIGPHG EKGPQGKPGL PGMPGSDGPP GHPGKEGPPG TKGNQGPSGP QGPLGYPGPR
GVKGVDGIRG LKGHKGEKGE DGFPGFKGDI GVKGDRGEVG VPGSRGEDGP EGPKGRTGPT
GDPGPPGLMG EKGKLGVPGL PGYPGRQGPK GSLGFPGFPG ASGEKGARGL SGKSGPRGER
GPTGPRGQRG PRGATGKSGA KGTSGGDGPH GPPGERGLPG PQGPNGFPGP KGPPGPPGKD
GLPGHPGQRG EVGFQGKTGP PGPPGVVGPQ GAAGETGPMG ERGHPGPPGP PGEQGLPGTA
GKEGTKGDPG PPGAPGKDGP AGLRGFPGER GLPGTAGGPG LKGNEGPSGP PGPAGSPGER
GAAGSGGPIG PPGRPGPQGP PGAAGEKGVP GEKGPIGPTG RDGVQGPVGL PGPAGPPGVA
GEDGDKGEVG DPGQKGTKGN KGEHGPPGPP GPIGPVGQPG AAGADGEPGA RGPQGHFGAK
GDEGTRGFNG PPGPIGLQGL PGPSGEKGET GDVGPMGPPG PPGPRGPAGP NGADGPQGPP
GGVGNLGPPG EKGEPGESGS PGIQGEPGVK GPRGERGEKG ESGQPGEPGP PGPKGPTGDD
GPKGNPGPVG FPGDPGPPGE GGPRGQDGAK GDRGEDGEPG QPGSPGPTGE NGPPGPLGKR
GPAGSPGSEG RQGGKGAKGD PGAIGAPGKT GPVGPAGPAG KPGPDGLRGL PGSVGQQGRP
GATGQAGPPG PVGPPGLPGL RGDAGAKGEK GHPGLIGLIG PPGEQGEKGD RGLPGPQGSP
GQKGEMGIPG ASGPIGPGGP PGLPGPAGPK GAKGATGPGG PKGEKGVQGP PGHPGPPGEV
IQPLPIQMPK KTRRSVDGSR LMQEDEAIPT GGAPGSPGGL EEIFGSLDSL REEIEQMRRP
TGTQDSPART CQDLKLCHPE LPDGEYWVDP NQGCARDAFR VFCNFTAGGE TCVTPRDDVT
QFSYVDSEGS PVGVVQLTFL RLLSVSAHQD VSYPCSGAAR DGPLRLRGAN EDELSPETSP
YVKEFRDGCQ TQQGRTVLEV RTPVLEQLPV LDASFSDLGA PPRRGGVLLG PVCFMG*

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 YQDPTPGEEE
EILESSLLPP LEEAAHGPRG LKGEKGEPAV LEPGMLVEGP PGPEGPAGLI GPPGIQGNPG
PVGDPGERGP PGRAGLPGSD GAPGPPGTSL MLPFRFGSGG GDKGPVVAAQ EAQAQAILQQ
ARLALRGPPG PMGYTGRPGP LGQPGSPGLK GESGDLGPQG PRGPQGLTGP PGKAGRRGRA
GADGARGMPG DPGVKGDRGF DGLPGLPGEK GHRGDTGAQG LPGPPGEDGE RGDDGEIGPR
GLPGESGPRG LLGPKGPPGI TGPPGVRGMD GPQGPKGSLG PQGEPGPPGQ QGTPGTQGLP
GPQGAIGPHG EKGPQGKPGL PGMPGSDGPP GHPGKEGPPG TKGNQGPSGP QGPLGYPGPR
GVKGVDGIRG LKGHKGEKGE DGFPGFKGDI GVKGDRGEVG VPGSRGEDGP EGPKGRTGPT
GDPGPPGLMG EKGKLGVPGL PGYPGRQGPK GSLGFPGFPG ASGEKGARGL SGKSGPRGER
GPTGPRGQRG PRGATGKSGA KGTSGGDGPH GPPGERGLPG PQGPNGFPGP KGPPGPPGKD
GLPGHPGQRG EVGFQGKTGP PGPPGVVGPQ GAAGETGPMG ERGHPGPPGP PGEQGLPGTA
GKEGTKGDPG PPGAPGKDGP AGLRGFPGER GLPGTAGGPG LKGNEGPSGP PGPAGSPGER
GAAGSGGPIG PPGRPGPQGP PGAAGEKGVP GEKGPIGPTG RDGVQGPVGL PGPAGPPGVA
GEDGDKGEVG DPGQKGTKGN KGEHGPPGPP GPIGPVGQPG AAGADGEPGA RGPQGHFGAK
GDEGTRGFNG PPGPIGLQGL PGPSGEKGET GDVGPMGPPG PPGPRGPAGP NGADGPQGPP
GGVGNLGPPG EKGEPGESGS PGIQGEPGVK GPRGERGEKG ESGQPGEPGP PGPKGPTGDD
GPKGNPGPVG FPGDPGPPGE GGPRGQDGAK GDRGEDGEPG QPGSPGPTGE NGPPGPLGKR
GPAGSPGSEG RQGGKGAKGD PGAIGAPGKT GPVGPAGPAG KPGPDGLRGL PGSVGQQGRP
GATGQAGPPG PVGPPGLPGL RGDAGAKGEK GHPGLIGLIG PPGEQGEKGD RGLPGPQGSP
GQKGEMGIPG ASGPIGPGGP PGLPGPAGPK GAKGATGPGG PKGEKGVQGP PGHPGPPGEV
IQPLPIQMPK KTRRSVDGSR LMQEDEAIPT GGAPGSPGGL EEIFGSLDSL REEIEQMRRP
TGTQDSPART CQDLKLCHPE LPDGEYWVDP NQGCARDAFR VFCNFTAGGE TCVTPRDDVT
QFSYVDSEGS PVGVVQLTFL RLLSVSAHQD VSYPCSGAAR DGPLRLRGAN EDELSPETSP
YVKEFRDGCQ TQQGRTVLEV RTPVLEQLPV LDASFSDLGA PPRRGGVLLG PVCFMG*

speed

1.13 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