Mutagenetix > Incidental Mutation

Incidental Mutation 'R7872:Col2a1'

608204

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

045924-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7872 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

97975602-98004695 bp(-) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to A at 98000577 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Stop codon at position 39 (Q39*)

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

probably null
Transcript: ENSMUST00000023123
AA Change: Q39*

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: Q39*

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

probably benign
Transcript: ENSMUST00000088355

SMART Domains

Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acta2	C	T	19: 34,243,439	D290N	probably damaging	Het
Adam18	T	C	8: 24,611,100	D682G	probably benign	Het
Ankrd46	A	G	15: 36,485,843	V88A	possibly damaging	Het
Ankub1	T	A	3: 57,665,386	K305I	probably damaging	Het
Atrn	T	A	2: 130,970,227		probably null	Het
Bambi	A	T	18: 3,511,406	T76S	probably benign	Het
Cacna1a	T	A	8: 84,583,654	V1447E	probably damaging	Het
Calcoco2	GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC	GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC	11: 96,099,982		probably benign	Het
Clcn2	A	G	16: 20,708,460	M629T	probably damaging	Het
Clcn4	T	C	7: 7,287,781	N673S	probably benign	Het
Col20a1	T	C	2: 180,986,578	F15S	probably benign	Het
Creb3	A	G	4: 43,563,332	E119G	probably benign	Het
Dnah5	A	C	15: 28,245,684	D556A	probably damaging	Het
Edar	C	T	10: 58,610,526	M192I	possibly damaging	Het
Fam91a1	A	G	15: 58,448,360	M634V	probably benign	Het
Fbxo10	C	T	4: 45,051,699	V471I	not run	Het
Fer1l5	T	C	1: 36,421,886	F2032L	probably benign	Het
Gm5150	A	C	3: 16,006,321	M1R	probably null	Het
Grin1	T	C	2: 25,298,190	E509G	probably benign	Het
Igkv10-94	C	T	6: 68,704,929		probably benign	Het
Il18bp	A	G	7: 102,016,795	Y59H	possibly damaging	Het
Ints8	A	T	4: 11,254,062	C17S	probably benign	Het
Kcnmb1	T	C	11: 33,966,275	Y74H	probably damaging	Het
Kpna1	T	C	16: 36,023,195	V313A	probably benign	Het
Lrp4	C	T	2: 91,490,716	T1029I	possibly damaging	Het
Lrrc7	A	T	3: 158,353,462	C3S	probably damaging	Het
Lyst	C	A	13: 13,635,865	H707N	probably benign	Het
Map3k20	A	G	2: 72,371,754	K148R	probably damaging	Het
Mcidas	G	A	13: 112,998,987	G315S	probably damaging	Het
Miip	C	T	4: 147,862,918	G236S	probably benign	Het
Mocs1	T	A	17: 49,439,533	I177N	probably damaging	Het
Muc5b	A	G	7: 141,846,113	D441G	unknown	Het
Ncoa1	T	C	12: 4,278,186	N884S	probably benign	Het
Olfr33	A	G	7: 102,714,182	V77A	probably benign	Het
Olfr533	A	G	7: 140,466,783	N194S	probably damaging	Het
Padi6	A	T	4: 140,727,762	F621L	probably damaging	Het
Pde8b	C	A	13: 95,086,839	M197I	possibly damaging	Het
Pear1	T	A	3: 87,752,215	I771L	probably benign	Het
Poli	A	G	18: 70,522,820	L281P	probably damaging	Het
Prdm12	T	C	2: 31,640,219	W41R	probably damaging	Het
Prkdc	T	G	16: 15,715,006	S1500A	probably benign	Het
Prune2	T	A	19: 17,119,434	H767Q	probably benign	Het
Rasgef1b	G	A	5: 99,234,544	Q196*	probably null	Het
Rnpc3	A	T	3: 113,622,447	L121*	probably null	Het
Rpp14	A	G	14: 8,083,724	M1V	probably null	Het
Ryr2	T	A	13: 11,595,724	D4072V	probably damaging	Het
Sgms1	T	C	19: 32,125,365	H314R	probably damaging	Het
Six4	CT	C	12: 73,104,239		probably benign	Het
Slc37a3	A	T	6: 39,347,310	Y335N	probably damaging	Het
Tcp11l1	A	T	2: 104,706,492	H9Q	probably benign	Het
Tnrc6a	T	A	7: 123,179,834	M1256K	probably damaging	Het
Trpc6	A	G	9: 8,609,909	N126S	probably damaging	Het
Ubr4	T	C	4: 139,393,062	F266S	possibly damaging	Het
Uimc1	A	G	13: 55,069,737	V424A	possibly damaging	Het
Utrn	T	C	10: 12,698,129	I1066V	probably benign	Het
Vmn1r204	A	G	13: 22,556,234	T12A	probably benign	Het
Vmn1r57	T	A	7: 5,220,614	I46N	possibly damaging	Het
Vmn1r91	T	C	7: 20,101,914	Y253H	probably benign	Het
Vmn2r14	T	A	5: 109,221,353	H118L	probably benign	Het
Zcchc11	T	G	4: 108,517,518	C933G	probably damaging	Het
Zfp775	A	G	6: 48,620,470	K426R	probably benign	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
R7665:Col2a1	UTSW	15	97976700	missense	unknown
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'- GCATTTGCTGTGTCTCCGAG -3'
(R):5'- TGTCAGTTCAGCCTGTCTG -3'

Sequencing Primer
(F):5'- TAAATAAATTACGACCACTGGCAG -3'
(R):5'- CAGTTCAGCCTGTCTGGTGTG -3'

Posted On

2019-12-20