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

ENST00000341947

Genbank transcript ID

NM_080680

UniProt peptide

P13942

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3100C>T
cDNA.3328C>T
g.20737C>T

AA changes

R1034C Score: 180 explain score(s)

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

1034

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

1034

mutated

not conserved

1034

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

5211 / 5211

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

1737 / 1737

position of stopcodon in wt / mu cDNA

5439 / 5439

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

5299

theoretical NMD boundary in CDS

5020

length of CDS

5211

coding sequence (CDS) position

3100

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

3328

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 YQDPTPGEEE
EILESSLLPP LEEEQTDLQV PPTADRFQAE EYGEGGTDPP EGPYDYTYGY GDDYREETEL
GPALSAETAH SGAAAHGPRG 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 LEEEQTDLQV PPTADRFQAE EYGEGGTDPP EGPYDYTYGY GDDYREETEL
GPALSAETAH SGAAAHGPRG 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 PPGCPGPQGP 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

1.01 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