Mutagenetix > Incidental Mutation

Incidental Mutation 'R7665:Col2a1'

591890

Institutional Source

Beutler Lab

Gene Symbol

Col2a1

Ensembl Gene

ENSMUSG00000022483

Gene Name

collagen, type II, alpha 1

Synonyms

M100856, Col2a, Col2a-1, Del1, Col2, Rgsc856, Lpk

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7665 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

97975602-98004695 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 97976700 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 1420 (E1420G)

Ref Sequence

ENSEMBL: ENSMUSP00000023123 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023123] [ENSMUST00000088355]

AlphaFold

P28481

PDB Structure

ANTI CITRULLINATED COLLAGEN TYPE 2 ANTIBODY ACC4 IN COMPLEX WITH A CITRULLINATED PEPTIDE [X-RAY DIFFRACTION]
Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide [X-RAY DIFFRACTION]

Predicted Effect

unknown
Transcript: ENSMUST00000023123
AA Change: E1420G

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: E1420G

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
VWC	34	88	1.59e-21	SMART
Pfam:Collagen	115	175	1.3e-11	PFAM
Pfam:Collagen	199	260	7.2e-11	PFAM
Pfam:Collagen	258	317	1.3e-12	PFAM
Pfam:Collagen	312	377	4e-9	PFAM
low complexity region	395	411	N/A	INTRINSIC
low complexity region	416	451	N/A	INTRINSIC
internal_repeat_5	456	468	5.45e-5	PROSPERO
low complexity region	471	513	N/A	INTRINSIC
internal_repeat_3	516	619	3.99e-13	PROSPERO
internal_repeat_1	524	567	1.6e-17	PROSPERO
low complexity region	621	633	N/A	INTRINSIC
low complexity region	636	655	N/A	INTRINSIC
low complexity region	659	687	N/A	INTRINSIC
low complexity region	696	753	N/A	INTRINSIC
internal_repeat_5	756	768	5.45e-5	PROSPERO
low complexity region	783	804	N/A	INTRINSIC
Pfam:Collagen	852	918	1.1e-8	PFAM
Pfam:Collagen	876	941	1.9e-9	PFAM
Pfam:Collagen	900	966	2.4e-9	PFAM
Pfam:Collagen	983	1049	2.1e-10	PFAM
low complexity region	1062	1081	N/A	INTRINSIC
Pfam:Collagen	1101	1172	3.4e-9	PFAM
Pfam:Collagen	1158	1218	1.3e-9	PFAM
COLFI	1252	1487	3.06e-184	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000088355
AA Change: E1352G

SMART Domains

Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: E1352G

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Pfam:Collagen	47	107	1.2e-11	PFAM
Pfam:Collagen	131	192	7.2e-11	PFAM
Pfam:Collagen	190	249	1.3e-12	PFAM
low complexity region	262	314	N/A	INTRINSIC
Pfam:Collagen	327	405	3.5e-7	PFAM
Pfam:Collagen	361	429	7.6e-10	PFAM
internal_repeat_3	448	551	1.3e-13	PROSPERO
internal_repeat_7	454	466	2.86e-5	PROSPERO
internal_repeat_1	456	499	4.05e-18	PROSPERO
internal_repeat_6	481	504	1.7e-5	PROSPERO
low complexity region	553	565	N/A	INTRINSIC
low complexity region	568	587	N/A	INTRINSIC
low complexity region	591	619	N/A	INTRINSIC
low complexity region	628	685	N/A	INTRINSIC
internal_repeat_4	688	712	8.3e-12	PROSPERO
low complexity region	715	736	N/A	INTRINSIC
low complexity region	747	784	N/A	INTRINSIC
Pfam:Collagen	808	878	9.8e-9	PFAM
Pfam:Collagen	832	898	2.1e-9	PFAM
Pfam:Collagen	916	979	7.2e-10	PFAM
Pfam:Collagen	937	1005	2.1e-8	PFAM
Pfam:Collagen	973	1049	6e-7	PFAM
Pfam:Collagen	1030	1094	1.5e-10	PFAM
Pfam:Collagen	1088	1150	1.4e-9	PFAM
COLFI	1184	1419	3.06e-184	SMART

Meta Mutation Damage Score

0.8469

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

100% (72/72)

MGI Phenotype

FUNCTION: This gene encodes the alpha-1 subunit of the fibril-forming type II collagen, the major component of cartilage and the vitreous humor of the eye. The encoded preproprotein forms homotrimeric, triple helical procollagen that undergoes proteolytic processing during fibirl formation. Mice harboring certain mutations in this gene exhibit severe chondrodysplasia characterized by short limbs and trunch, craniofacial deformities and cleft palate. A complete lack of the encoded protein in mice results in postnatal lethality. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mutations in this locus affect cartilage development. Homozygotes die perinatally with anomalies such as shortened limbs without epiphiseal growth plates, cleft palate and persistence of notochord. Heterozygotes are dwarfed with reduced cartilage matrix. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930519G04Rik	A	G	5: 114,874,323		probably null	Het
A830018L16Rik	T	C	1: 11,972,099	S448P	probably damaging	Het
Abca4	C	T	3: 122,044,490		probably benign	Het
Ackr2	A	G	9: 121,909,308	M250V	probably benign	Het
Actn4	A	G	7: 28,916,207	I147T	probably damaging	Het
Adgrv1	C	T	13: 81,499,142	S3093N	probably damaging	Het
Arid5b	C	T	10: 68,098,587	G495E	probably benign	Het
Armh1	C	A	4: 117,213,741	A396S	probably benign	Het
Brwd1	G	A	16: 96,041,343	T798M	probably benign	Het
Cdk13	G	A	13: 17,772,553	T540I	possibly damaging	Het
Cdkn1c	A	G	7: 143,460,634	V25A	possibly damaging	Het
Dbf4	G	A	5: 8,397,867	P448S	probably damaging	Het
Dnajb7	T	C	15: 81,407,419	N239S	probably benign	Het
Dnttip1	A	G	2: 164,754,141	D102G	probably damaging	Het
Dpp8	T	A	9: 65,078,718	V830D	probably damaging	Het
Eef1g	T	C	19: 8,968,289	V29A	probably benign	Het
Enpp2	T	A	15: 54,839,394	Y906F	probably damaging	Het
Epb41l4a	A	G	18: 34,006,016	L23P	possibly damaging	Het
Epp13	G	A	7: 6,269,892		probably null	Het
Exoc1	T	A	5: 76,543,573	M248K	probably benign	Het
Fam83b	T	C	9: 76,490,875	Y982C	probably damaging	Het
Fat4	C	T	3: 38,889,178	A740V	probably benign	Het
Fsip2	T	A	2: 82,981,805	S2823T	probably benign	Het
Gckr	T	C	5: 31,297,555			Het
Gpr150	A	T	13: 76,055,974	V284E	probably damaging	Het
Grtp1	T	G	8: 13,177,103	I344L	probably benign	Het
Heatr5a	T	A	12: 51,961,530	N10I	probably damaging	Het
Herc2	C	A	7: 56,153,155	L2109I	probably damaging	Het
Hs1bp3	T	A	12: 8,317,935	D61E	probably damaging	Het
Ifit1bl1	T	A	19: 34,594,883	Y58F	probably benign	Het
Itfg1	A	G	8: 85,764,350	F317L	probably benign	Het
Itsn1	T	C	16: 91,841,603	I764T	unknown	Het
Med8	A	C	4: 118,411,656		probably null	Het
Mpeg1	C	A	19: 12,463,094	P639T	probably damaging	Het
Nedd9	A	G	13: 41,316,309	L456P	probably benign	Het
Neo1	A	G	9: 58,925,795	S556P	probably damaging	Het
Nphp3	T	A	9: 104,005,393		probably null	Het
Nup205	T	C	6: 35,177,620	V53A	possibly damaging	Het
Nvl	A	T	1: 181,134,944	S154T	probably benign	Het
Olfr239	G	T	17: 33,199,629	G194*	probably null	Het
Olfr391-ps	A	T	11: 73,798,961	N265K	probably benign	Het
Olfr615	A	T	7: 103,561,316	I280F	probably benign	Het
Olfr706	A	T	7: 106,886,673	V48D	possibly damaging	Het
Olfr827	T	A	10: 130,211,261		probably null	Het
Olfr92	A	G	17: 37,111,391	M197T	probably benign	Het
Parvg	T	C	15: 84,337,801	I243T	probably damaging	Het
Paxip1	T	A	5: 27,765,738	M538L	unknown	Het
Pgghg	G	T	7: 140,945,469	D428Y	probably damaging	Het
Pik3cd	C	T	4: 149,654,050	V777M	possibly damaging	Het
Plcl2	A	C	17: 50,607,157	K398T	probably benign	Het
Plxna1	A	T	6: 89,324,538		probably null	Het
Rbbp6	T	C	7: 122,994,686	Y514H	possibly damaging	Het
Rbbp6	T	A	7: 122,990,032		probably null	Het
Scin	T	A	12: 40,069,415	N538I	probably damaging	Het
Sdcbp	A	G	4: 6,385,144	D121G	probably benign	Het
Sgk1	T	C	10: 21,996,662	I311T	probably damaging	Het
Shq1	A	C	6: 100,573,756	L407W	probably damaging	Het
Sipa1	A	T	19: 5,651,671	S979T	probably benign	Het
Slc25a37	G	T	14: 69,249,579	T85K	probably benign	Het
Soga3	T	A	10: 29,196,397	Y562N	probably damaging	Het
Spag9	A	T	11: 94,013,654	Q112L	probably damaging	Het
Spg11	A	T	2: 122,066,267	V1686E	probably damaging	Het
Stap2	A	G	17: 55,997,909	V291A	probably benign	Het
Tnk2	C	T	16: 32,680,526	R886C	probably damaging	Het
Tnrc6c	T	A	11: 117,720,951	D138E	possibly damaging	Het
Unc13c	A	G	9: 73,680,474	S1426P	probably benign	Het
Vav1	G	A	17: 57,297,086	V163M	probably damaging	Het
Vmn2r67	T	A	7: 85,151,988	K247*	probably null	Het
Zc2hc1c	T	C	12: 85,296,562	V491A	possibly damaging	Het
Zfp51	A	G	17: 21,463,581	T153A	probably benign	Het
Zyx	A	G	6: 42,356,162	E374G	probably damaging	Het

Other mutations in Col2a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01025:Col2a1	APN	15	97976173	missense	unknown
IGL01286:Col2a1	APN	15	97994878	missense	unknown
IGL01369:Col2a1	APN	15	97977826	missense	unknown
IGL01747:Col2a1	APN	15	97991392	splice site	probably benign
IGL02086:Col2a1	APN	15	97986737	splice site	probably null
IGL02549:Col2a1	APN	15	97977799	missense	unknown
IGL03289:Col2a1	APN	15	97980881	missense	unknown
IGL03369:Col2a1	APN	15	97982042	missense	unknown
Foreseen	UTSW	15	97976793	missense	unknown
FR4304:Col2a1	UTSW	15	97988981	splice site	probably null
FR4340:Col2a1	UTSW	15	97988981	splice site	probably null
FR4342:Col2a1	UTSW	15	97988981	splice site	probably null
FR4589:Col2a1	UTSW	15	97988981	splice site	probably null
LCD18:Col2a1	UTSW	15	97988981	splice site	probably null
R0124:Col2a1	UTSW	15	97998862	missense	unknown
R0227:Col2a1	UTSW	15	97976755	missense	unknown
R0690:Col2a1	UTSW	15	97980192	missense	unknown
R1434:Col2a1	UTSW	15	97979651	missense	probably damaging	0.96
R1473:Col2a1	UTSW	15	97982908	splice site	probably benign
R1577:Col2a1	UTSW	15	97979202	missense	probably damaging	1.00
R1598:Col2a1	UTSW	15	97979250	missense	probably damaging	0.99
R1837:Col2a1	UTSW	15	97996641	splice site	probably benign
R2153:Col2a1	UTSW	15	97987580	missense	unknown
R2965:Col2a1	UTSW	15	97976095	missense	unknown
R2966:Col2a1	UTSW	15	97976095	missense	unknown
R3710:Col2a1	UTSW	15	97990907	splice site	probably benign
R3838:Col2a1	UTSW	15	97988976	missense	unknown
R3838:Col2a1	UTSW	15	98000581	intron	probably benign
R4112:Col2a1	UTSW	15	97983701	missense	probably benign	0.18
R4417:Col2a1	UTSW	15	97998585	missense	unknown
R4656:Col2a1	UTSW	15	97976176	missense	unknown
R4960:Col2a1	UTSW	15	97976149	missense	unknown
R5008:Col2a1	UTSW	15	97979669	missense	probably benign	0.28
R5435:Col2a1	UTSW	15	98000510	intron	probably benign
R5473:Col2a1	UTSW	15	97987489	missense	unknown
R6042:Col2a1	UTSW	15	98000570	intron	probably benign
R6118:Col2a1	UTSW	15	97998567	missense	unknown
R6183:Col2a1	UTSW	15	97988790	missense	unknown
R6187:Col2a1	UTSW	15	97988790	missense	unknown
R6401:Col2a1	UTSW	15	97985892	missense	unknown
R6550:Col2a1	UTSW	15	97976793	missense	unknown
R6568:Col2a1	UTSW	15	97977276	missense	unknown
R6988:Col2a1	UTSW	15	98004454	missense	unknown
R7060:Col2a1	UTSW	15	97976141	missense	unknown
R7069:Col2a1	UTSW	15	97998588	missense	unknown
R7167:Col2a1	UTSW	15	98000456	missense	unknown
R7294:Col2a1	UTSW	15	97987287	splice site	probably null
R7392:Col2a1	UTSW	15	97980151	nonsense	probably null
R7491:Col2a1	UTSW	15	97976159	missense	not run
R7583:Col2a1	UTSW	15	97976184	missense	unknown
R7872:Col2a1	UTSW	15	98000577	nonsense	probably null
R8177:Col2a1	UTSW	15	97976773	missense	unknown
R8306:Col2a1	UTSW	15	97990968	critical splice acceptor site	probably null
R9343:Col2a1	UTSW	15	97979894	missense	probably damaging	0.99
R9458:Col2a1	UTSW	15	97978361	missense	unknown
Z1177:Col2a1	UTSW	15	97983973	missense	probably damaging	1.00
Z1177:Col2a1	UTSW	15	97998345	missense	unknown

Predicted Primers

PCR Primer
(F):5'- CAGCATCTTTATTGCCTCTGAATGAG -3'
(R):5'- AGTTCAGCTATGGCGATGGC -3'

Sequencing Primer
(F):5'- AGCCAGTATGGTATACGCTCC -3'
(R):5'- TATGGCGATGGCAACCTG -3'

Posted On

2019-11-12