mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:238244963A>GN/A show variant in all transcripts IGV

HGNC symbol

COL6A3

Ensembl transcript ID

ENST00000472056

Genbank transcript ID

NM_057166

UniProt peptide

P12111

alteration type

single base exchange

alteration region

CDS

DNA changes

c.6959T>C
cDNA.7185T>C
g.78056T>C

AA changes

M2320T Score: 81 explain score(s)

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

2320

frameshift

known variant

Reference ID: rs6728818

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1070	1048	2118
ExAC	25150	-17533	7617

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.877	0
	0.156	0
(flanking)	-1.454	0

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	78048	wt: 0.8509 / mu: 0.8900 (marginal change - not scored)	wt: GTGGCCACAAAGATG mu: GTGGCCACAAAGACG	GGCC\|acaa
Donor marginally increased	78053	wt: 0.2851 / mu: 0.3345 (marginal change - not scored)	wt: CACAAAGATGGCCAC mu: CACAAAGACGGCCAC	CAAA\|gatg
Donor marginally increased	78051	wt: 0.8907 / mu: 0.9485 (marginal change - not scored)	wt: GCCACAAAGATGGCC mu: GCCACAAAGACGGCC	CACA\|aaga
Donor gained	78057	0.52	mu: AAGACGGCCACTGTT	GACG\|gcca

distance from splice site

186

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2320

mutated

not conserved

2320

Ptroglodytes

not conserved

ENSPTRG00000013074

2927

Mmulatta

not conserved

ENSMMUG00000014049

2714

Fcatus

no alignment

ENSFCAG00000012720

n/a

Mmusculus

not conserved

ENSMUSG00000048126

2408

AKPAVPAQPAAAQ

PASANK

KPVATNTATATAR

Ggallus

not conserved

ENSGALG00000003923

2906

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000077139

3502

Dmelanogaster

no homologue

Celegans

no alignment

C18H7.1

n/a

Xtropicalis

no alignment

ENSXETG00000031229

n/a

protein features

start (aa)	end (aa)	feature	details
2039	2375	REGION	Triple-helical region.	lost
2314	2373	DOMAIN	Collagen-like 5.	lost
2322	2322	MOD_RES	5-hydroxylysine.	might get lost (downstream of altered splice site)
2322	2322	CARBOHYD	O-linked (Gal...).	might get lost (downstream of altered splice site)
2331	2331	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
2337	2337	MOD_RES	5-hydroxylysine.	might get lost (downstream of altered splice site)
2337	2337	CARBOHYD	O-linked (Gal...).	might get lost (downstream of altered splice site)
2357	2357	CONFLICT	D -> R (in Ref. 1; CAA36267 and 6; M20778).	might get lost (downstream of altered splice site)
2367	2367	CONFLICT	K -> R (in Ref. 1; CAA36267 and 6; M20778).	might get lost (downstream of altered splice site)
2370	2372	MOTIF	Cell attachment site.	might get lost (downstream of altered splice site)
2376	3177	REGION	Nonhelical region.	might get lost (downstream of altered splice site)
2402	2581	DOMAIN	VWFA 11.	might get lost (downstream of altered splice site)
2441	2441	CONFLICT	R -> T (in Ref. 1; CAA36267).	might get lost (downstream of altered splice site)
2558	2558	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
2619	2815	DOMAIN	VWFA 12.	might get lost (downstream of altered splice site)
2677	2677	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
2861	2861	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
2863	2898	COMPBIAS	Thr-rich.	might get lost (downstream of altered splice site)
2908	2983	COMPBIAS	Ala-rich.	might get lost (downstream of altered splice site)
2956	2956	CONFLICT	Missing (in Ref. 1; CAA36267).	might get lost (downstream of altered splice site)
2988	3076	DOMAIN	Fibronectin type-III.	might get lost (downstream of altered splice site)
2992	2992	CONFLICT	S -> L (in Ref. 1; CAA36267).	might get lost (downstream of altered splice site)
3037	3037	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
3110	3113	HELIX		might get lost (downstream of altered splice site)
3112	3112	DISULFID	By similarity.	might get lost (downstream of altered splice site)
3112	3162	DOMAIN	BPTI/Kunitz inhibitor.	might get lost (downstream of altered splice site)
3120	3122	STRAND		might get lost (downstream of altered splice site)
3121	3121	DISULFID	By similarity.	might get lost (downstream of altered splice site)
3122	3123	SITE	Reactive bond.	might get lost (downstream of altered splice site)
3125	3131	STRAND		might get lost (downstream of altered splice site)
3132	3135	TURN		might get lost (downstream of altered splice site)
3136	3142	STRAND		might get lost (downstream of altered splice site)
3137	3137	DISULFID	By similarity.	might get lost (downstream of altered splice site)
3144	3146	STRAND		might get lost (downstream of altered splice site)
3145	3145	DISULFID	By similarity.	might get lost (downstream of altered splice site)
3152	3154	STRAND		might get lost (downstream of altered splice site)
3155	3162	HELIX		might get lost (downstream of altered splice site)
3158	3158	DISULFID	By similarity.	might get lost (downstream of altered splice site)
3162	3162	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

7713 / 7713

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

2571 / 2571

position of stopcodon in wt / mu cDNA

7939 / 7939

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

227 / 227

chromosome

strand

-1

last intron/exon boundary

7899

theoretical NMD boundary in CDS

7622

length of CDS

7713

coding sequence (CDS) position

6959

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

7185

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

78056

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

238244963

original gDNA sequence snippet

CAAGCCTGTGGCCACAAAGATGGCCACTGTTAGACCCCCAG

altered gDNA sequence snippet

CAAGCCTGTGGCCACAAAGACGGCCACTGTTAGACCCCCAG

original cDNA sequence snippet

CAAGCCTGTGGCCACAAAGATGGCCACTGTTAGACCCCCAG

altered cDNA sequence snippet

CAAGCCTGTGGCCACAAAGACGGCCACTGTTAGACCCCCAG

wildtype AA sequence

MRKHRHLPLV AVFCLFLSGF PTTHAQQQQA VIEVNKRDIV FLVDGSSALG LANFNAIRDF
IAKVIQRLEI GQDLIQVAVA QYADTVRPEF YFNTHPTKRE VITAVRKMKP LDGSALYTGS
ALDFVRNNLF TSSAGYRAAE GIPKLLVLIT GGKSLDEISQ PAQELKRSSI MAFAIGNKGA
DQAELEEIAF DSSLVFIPAE FRAAPLQGML PGLLAPLRTL SGTPEESKRD ILFLFDGSAN
LVGQFPVVRD FLYKIIDELN VKPEGTRIAV AQYSDDVKVE SRFDEHQSKP EILNLVKRMK
IKTGKALNLG YALDYAQRYI FVKSAGSRIE DGVLQFLVLL VAGRSSDRVD GPASNLKQSG
VVPFIFQAKN ADPAELEQIV LSPAFILAAE SLPKIGDLHP QIVNLLKSVH NGAPAPVSGE
KDVVFLLDGS EGVRSGFPLL KEFVQRVVES LDVGQDRVRV AVVQYSDRTR PEFYLNSYMN
KQDVVNAVRQ LTLLGGPTPN TGAALEFVLR NILVSSAGSR ITEGVPQLLI VLTADRSGDD
VRNPSVVVKR GGAVPIGIGI GNADITEMQT ISFIPDFAVA IPTFRQLGTV QQVISERVTQ
LTREELSRLQ PVLQPLPSPG VGGKRDVVFL IDGSQSAGPE FQYVRTLIER LVDYLDVGFD
TTRVAVIQFS DDPKVEFLLN AHSSKDEVQN AVQRLRPKGG RQINVGNALE YVSRNIFKRP
LGSRIEEGVP QFLVLISSGK SDDEVDDPAV ELKQFGVAPF TIARNADQEE LVKISLSPEY
VFSVSTFREL PSLEQKLLTP ITTLTSEQIQ KLLASTRYPP PAVESDAADI VFLIDSSEGV
RPDGFAHIRD FVSRIVRRLN IGPSKVRVGV VQFSNDVFPE FYLKTYRSQA PVLDAIRRLR
LRGGSPLNTG KALEFVARNL FVKSAGSRIE DGVPQHLVLV LGGKSQDDVS RFAQVIRSSG
IVSLGVGDRN IDRTELQTIT NDPRLVFTVR EFRELPNIEE RIMNSFGPSA ATPAPPGVDT
PPPSRPEKKK ADIVFLLDGS INFRRDSFQE VLRFVSEIVD TVYEDGDSIQ VGLVQYNSDP
TDEFFLKDFS TKRQIIDAIN KVVYKGGRHA NTKVGLEHLR VNHFVPEAGS RLDQRVPQIA
FVITGGKSVE DAQDVSLALT QRGVKVFAVG VRNIDSEEVG KIASNSATAF RVGNVQELSE
LSEQVLETLH DAMHETLCPG VTDAAKACNL DVILGFDGSR DQNVFVAQKG FESKVDAILN
RISQMHRVSC SGGRSPTVRV SVVANTPSGP VEAFDFDEYQ PEMLEKFRNM RSQHPYVLTE
DTLKVYLNKF RQSSPDSVKV VIHFTDGADG DLADLHRASE NLRQEGVRAL ILVGLERVVN
LERLMHLEFG RGFMYDRPLR LNLLDLDYEL AEQLDNIAEK ACCGVPCKCS GQRGDRGPIG
SIGPKGIPGE DGYRGYPGDE GGPGERGPPG VNGTQGFQGC PGQRGVKGSR GFPGEKGEVG
EIGLDGLDGE DGDKGLPGSS GEKGNPGRRG DKGPRGEKGE RGDVGIRGDP GNPGQDSQER
GPKGETGDLG PMGVPGRDGV PGGPGETGKN GGFGRRGPPG AKGNKGGPGQ PGFEGEQGTR
GAQGPAGPAG PPGLIGEQGI SGPRGSGGAA GAPGERGRTG PLGRKGEPGE PGPKGGIGNR
GPRGETGDDG RDGVGSEGRR GKKGERGFPG YPGPKGNPGE PGLNGTTGPK GIRGRRGNSG
PPGIVGQKGD PGYPGPAGPK GNRGDSIDQC ALIQSIKDKC PCCYGPLECP VFPTELAFAL
DTSEGVNQDT FGRMRDVVLS IVNDLTIAES NCPRGARVAV VTYNNEVTTE IRFADSKRKS
VLLDKIKNLQ VALTSKQQSL ETAMSFVARN TFKRVRNGFL MRKVAVFFSN TPTRASPQLR
EAVLKLSDAG ITPLFLTRQE DRQLINALQI NNTAVGHALV LPAGRDLTDF LENVLTCHVC
LDICNIDPSC GFGSWRPSFR DRRAAGSDVD IDMAFILDSA ETTTLFQFNE MKKYIAYLVR
QLDMSPDPKA SQHFARVAVV QHAPSESVDN ASMPPVKVEF SLTDYGSKEK LVDFLSRGMT
QLQGTRALGS AIEYTIENVF ESAPNPRDLK IVVLMLTGEV PEQQLEEAQR VILQAKCKGY
FFVVLGIGRK VNIKEVYTFA SEPNDVFFKL VDKSTELNEE PLMRFGRLLP SFVSSENAFY
LSPDIRKQCD WFQGDQPTKN LVKFGHKQVN VPNNVTSSPT SNPVTTTKPV TTTKPVTTTT
KPVTTTTKPV TIINQPSVKP AAAKPAPAKP VAAKPVATKM ATVRPPVAVK PATAAKPVAA
KPAAVRPPAA AAAKPVATKP EVPRPQAAKP AATKPATTKP MVKMSREVQV FEITENSAKL
HWERAEPPGP YFYDLTVTSA HDQSLVLKQN LTVTDRVIGG LLAGQTYHVA VVCYLRSQVR
ATYHGSFSTK KSQPPPPQPA RSASSSTINL MVSTEPLALT ETDICKLPKD EGTCRDFILK
WYYDPNTKSC ARFWYGGCGG NENKFGSQKE CEKVCAPVLA KPGVISVMGT *

mutated AA sequence

MRKHRHLPLV AVFCLFLSGF PTTHAQQQQA VIEVNKRDIV FLVDGSSALG LANFNAIRDF
IAKVIQRLEI GQDLIQVAVA QYADTVRPEF YFNTHPTKRE VITAVRKMKP LDGSALYTGS
ALDFVRNNLF TSSAGYRAAE GIPKLLVLIT GGKSLDEISQ PAQELKRSSI MAFAIGNKGA
DQAELEEIAF DSSLVFIPAE FRAAPLQGML PGLLAPLRTL SGTPEESKRD ILFLFDGSAN
LVGQFPVVRD FLYKIIDELN VKPEGTRIAV AQYSDDVKVE SRFDEHQSKP EILNLVKRMK
IKTGKALNLG YALDYAQRYI FVKSAGSRIE DGVLQFLVLL VAGRSSDRVD GPASNLKQSG
VVPFIFQAKN ADPAELEQIV LSPAFILAAE SLPKIGDLHP QIVNLLKSVH NGAPAPVSGE
KDVVFLLDGS EGVRSGFPLL KEFVQRVVES LDVGQDRVRV AVVQYSDRTR PEFYLNSYMN
KQDVVNAVRQ LTLLGGPTPN TGAALEFVLR NILVSSAGSR ITEGVPQLLI VLTADRSGDD
VRNPSVVVKR GGAVPIGIGI GNADITEMQT ISFIPDFAVA IPTFRQLGTV QQVISERVTQ
LTREELSRLQ PVLQPLPSPG VGGKRDVVFL IDGSQSAGPE FQYVRTLIER LVDYLDVGFD
TTRVAVIQFS DDPKVEFLLN AHSSKDEVQN AVQRLRPKGG RQINVGNALE YVSRNIFKRP
LGSRIEEGVP QFLVLISSGK SDDEVDDPAV ELKQFGVAPF TIARNADQEE LVKISLSPEY
VFSVSTFREL PSLEQKLLTP ITTLTSEQIQ KLLASTRYPP PAVESDAADI VFLIDSSEGV
RPDGFAHIRD FVSRIVRRLN IGPSKVRVGV VQFSNDVFPE FYLKTYRSQA PVLDAIRRLR
LRGGSPLNTG KALEFVARNL FVKSAGSRIE DGVPQHLVLV LGGKSQDDVS RFAQVIRSSG
IVSLGVGDRN IDRTELQTIT NDPRLVFTVR EFRELPNIEE RIMNSFGPSA ATPAPPGVDT
PPPSRPEKKK ADIVFLLDGS INFRRDSFQE VLRFVSEIVD TVYEDGDSIQ VGLVQYNSDP
TDEFFLKDFS TKRQIIDAIN KVVYKGGRHA NTKVGLEHLR VNHFVPEAGS RLDQRVPQIA
FVITGGKSVE DAQDVSLALT QRGVKVFAVG VRNIDSEEVG KIASNSATAF RVGNVQELSE
LSEQVLETLH DAMHETLCPG VTDAAKACNL DVILGFDGSR DQNVFVAQKG FESKVDAILN
RISQMHRVSC SGGRSPTVRV SVVANTPSGP VEAFDFDEYQ PEMLEKFRNM RSQHPYVLTE
DTLKVYLNKF RQSSPDSVKV VIHFTDGADG DLADLHRASE NLRQEGVRAL ILVGLERVVN
LERLMHLEFG RGFMYDRPLR LNLLDLDYEL AEQLDNIAEK ACCGVPCKCS GQRGDRGPIG
SIGPKGIPGE DGYRGYPGDE GGPGERGPPG VNGTQGFQGC PGQRGVKGSR GFPGEKGEVG
EIGLDGLDGE DGDKGLPGSS GEKGNPGRRG DKGPRGEKGE RGDVGIRGDP GNPGQDSQER
GPKGETGDLG PMGVPGRDGV PGGPGETGKN GGFGRRGPPG AKGNKGGPGQ PGFEGEQGTR
GAQGPAGPAG PPGLIGEQGI SGPRGSGGAA GAPGERGRTG PLGRKGEPGE PGPKGGIGNR
GPRGETGDDG RDGVGSEGRR GKKGERGFPG YPGPKGNPGE PGLNGTTGPK GIRGRRGNSG
PPGIVGQKGD PGYPGPAGPK GNRGDSIDQC ALIQSIKDKC PCCYGPLECP VFPTELAFAL
DTSEGVNQDT FGRMRDVVLS IVNDLTIAES NCPRGARVAV VTYNNEVTTE IRFADSKRKS
VLLDKIKNLQ VALTSKQQSL ETAMSFVARN TFKRVRNGFL MRKVAVFFSN TPTRASPQLR
EAVLKLSDAG ITPLFLTRQE DRQLINALQI NNTAVGHALV LPAGRDLTDF LENVLTCHVC
LDICNIDPSC GFGSWRPSFR DRRAAGSDVD IDMAFILDSA ETTTLFQFNE MKKYIAYLVR
QLDMSPDPKA SQHFARVAVV QHAPSESVDN ASMPPVKVEF SLTDYGSKEK LVDFLSRGMT
QLQGTRALGS AIEYTIENVF ESAPNPRDLK IVVLMLTGEV PEQQLEEAQR VILQAKCKGY
FFVVLGIGRK VNIKEVYTFA SEPNDVFFKL VDKSTELNEE PLMRFGRLLP SFVSSENAFY
LSPDIRKQCD WFQGDQPTKN LVKFGHKQVN VPNNVTSSPT SNPVTTTKPV TTTKPVTTTT
KPVTTTTKPV TIINQPSVKP AAAKPAPAKP VAAKPVATKT ATVRPPVAVK PATAAKPVAA
KPAAVRPPAA AAAKPVATKP EVPRPQAAKP AATKPATTKP MVKMSREVQV FEITENSAKL
HWERAEPPGP YFYDLTVTSA HDQSLVLKQN LTVTDRVIGG LLAGQTYHVA VVCYLRSQVR
ATYHGSFSTK KSQPPPPQPA RSASSSTINL MVSTEPLALT ETDICKLPKD EGTCRDFILK
WYYDPNTKSC ARFWYGGCGG NENKFGSQKE CEKVCAPVLA KPGVISVMGT *

speed

1.15 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