Mutagenetix > Incidental Mutation

Incidental Mutation 'R8306:Col2a1'

641101

Institutional Source

Beutler Lab

Gene Symbol

Col2a1

Ensembl Gene

ENSMUSG00000022483

Gene Name

collagen, type II, alpha 1

Synonyms

Rgsc413, M100413, Rgsc856, Col2a-1, M100856, Del1, Col2a, Col2, Lpk

MMRRC Submission

067792-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8306 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

97873483-97902525 bp(-) (GRCm39)

Type of Mutation

critical splice acceptor site

DNA Base Change (assembly)

T to C at 97888849 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

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

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483

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: 99.9%
10x: 99.7%
20x: 99.1%

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aarsd1	C	A	11: 101,302,194 (GRCm39)	V158F	probably damaging	Het
Abtb3	T	A	10: 85,434,409 (GRCm39)	C22*	probably null	Het
Adam1b	T	C	5: 121,641,212 (GRCm39)		probably benign	Het
Ambn	G	A	5: 88,607,281 (GRCm39)	E50K	possibly damaging	Het
Ash1l	A	G	3: 88,873,259 (GRCm39)	D14G	probably benign	Het
Asphd1	C	T	7: 126,547,784 (GRCm39)	R173H	probably damaging	Het
Atr	A	T	9: 95,802,423 (GRCm39)	T1772S		Het
Best3	T	C	10: 116,838,515 (GRCm39)	L191P	probably damaging	Het
Bola1	A	T	3: 96,104,517 (GRCm39)	S26T	probably benign	Het
Borcs6	T	C	11: 68,950,646 (GRCm39)	L8P	probably benign	Het
Brca1	T	G	11: 101,416,463 (GRCm39)	Q557P	probably damaging	Het
Brca2	G	A	5: 150,460,128 (GRCm39)	E468K	possibly damaging	Het
Capza2	T	A	6: 17,637,131 (GRCm39)	L4Q	probably benign	Het
Cc2d2b	T	A	19: 40,804,228 (GRCm39)	Y918*	probably null	Het
Ccdc163	T	C	4: 116,567,472 (GRCm39)	L67P	probably damaging	Het
Ccdc172	C	A	19: 58,525,022 (GRCm39)	Q160K	probably damaging	Het
Ccp110	T	A	7: 118,321,903 (GRCm39)	D519E	probably benign	Het
Cd300ld2	T	C	11: 114,904,648 (GRCm39)	Q73R	probably benign	Het
Cfap46	T	A	7: 139,236,496 (GRCm39)	D608V		Het
Cfap69	T	G	5: 5,654,287 (GRCm39)	Y549S	probably benign	Het
Cilp	G	A	9: 65,186,286 (GRCm39)	G794S	probably damaging	Het
Clu	A	C	14: 66,217,211 (GRCm39)	Q348P	probably damaging	Het
Cnot1	A	T	8: 96,473,649 (GRCm39)	N1153K	probably benign	Het
Col6a6	A	T	9: 105,661,272 (GRCm39)	I279N	probably damaging	Het
Dop1a	A	G	9: 86,402,259 (GRCm39)	D1153G	possibly damaging	Het
Dpyd	A	G	3: 119,205,822 (GRCm39)	K888E	probably benign	Het
Eif2ak4	T	C	2: 118,287,656 (GRCm39)	I1208T	possibly damaging	Het
Epha1	T	C	6: 42,335,722 (GRCm39)	I972V	probably damaging	Het
Fam13c	C	T	10: 70,388,983 (GRCm39)	T503I	probably benign	Het
Fbxo43	T	A	15: 36,162,013 (GRCm39)	Q398L	probably benign	Het
Fbxo44	A	G	4: 148,243,089 (GRCm39)	I57T	probably benign	Het
Flnc	T	C	6: 29,449,369 (GRCm39)	I1422T	probably benign	Het
Flrt2	T	C	12: 95,746,076 (GRCm39)	L138P	probably damaging	Het
Frem3	A	G	8: 81,338,840 (GRCm39)	K378E	possibly damaging	Het
Ganc	T	A	2: 120,252,560 (GRCm39)	D128E	probably benign	Het
Gm19965	T	C	1: 116,749,515 (GRCm39)	S399P		Het
H2-Q1	A	T	17: 35,539,997 (GRCm39)	K89*	probably null	Het
H2-Q2	A	T	17: 35,561,301 (GRCm39)		probably benign	Het
Hmmr	G	A	11: 40,612,499 (GRCm39)	S206F	probably damaging	Het
Homer2	T	A	7: 81,274,014 (GRCm39)	S125C	possibly damaging	Het
Hormad2	T	C	11: 4,358,714 (GRCm39)	K231R	probably benign	Het
Kif17	A	C	4: 138,005,220 (GRCm39)	K262Q	probably damaging	Het
Kif20a	G	A	18: 34,761,444 (GRCm39)	S279N	probably benign	Het
Lrp12	T	C	15: 39,741,450 (GRCm39)	N441D	probably damaging	Het
Lta4h	G	T	10: 93,318,126 (GRCm39)	L515F	possibly damaging	Het
Mavs	T	C	2: 131,088,470 (GRCm39)	S425P	probably benign	Het
Mcat	A	C	15: 83,439,592 (GRCm39)	D99E	probably damaging	Het
Nav2	C	A	7: 49,195,765 (GRCm39)	T1047K	probably benign	Het
Neb	T	A	2: 52,099,657 (GRCm39)	Y4731F	probably damaging	Het
Nectin4	G	C	1: 171,211,325 (GRCm39)	R283P	probably null	Het
Notch3	G	A	17: 32,377,086 (GRCm39)	T273I	probably damaging	Het
Or4c11c	G	A	2: 88,661,633 (GRCm39)	M57I	possibly damaging	Het
Or5i1	A	T	2: 87,613,830 (GRCm39)	*317C	probably null	Het
Or6b2b	T	G	1: 92,419,247 (GRCm39)	I77L	possibly damaging	Het
Or6z7	T	A	7: 6,483,868 (GRCm39)	I96F	possibly damaging	Het
Pcdha12	A	T	18: 37,155,638 (GRCm39)	T786S	probably benign	Het
Pde9a	A	G	17: 31,692,186 (GRCm39)	K520E	probably benign	Het
Piezo2	A	C	18: 63,208,801 (GRCm39)	L1404R	probably damaging	Het
Rrbp1	T	C	2: 143,792,416 (GRCm39)	S1321G	probably benign	Het
Rtkn	T	C	6: 83,128,897 (GRCm39)	V464A	probably damaging	Het
Rtn4rl1	T	C	11: 75,156,147 (GRCm39)	F193S	probably damaging	Het
Samd4	G	A	14: 47,122,374 (GRCm39)	V33I	probably damaging	Het
Scn5a	A	G	9: 119,350,357 (GRCm39)	L839P	probably damaging	Het
Slc6a17	C	A	3: 107,380,985 (GRCm39)	V507L	probably benign	Het
Stradb	C	A	1: 59,030,356 (GRCm39)	N203K	unknown	Het
Tenm2	T	C	11: 35,960,196 (GRCm39)	T1044A	possibly damaging	Het
Tmem245	A	C	4: 56,886,037 (GRCm39)	W860G	probably damaging	Het
Tpst2	G	A	5: 112,455,803 (GRCm39)	R114H	probably damaging	Het
Trappc10	C	T	10: 78,036,460 (GRCm39)	D920N	possibly damaging	Het
Vmn1r59	T	A	7: 5,456,966 (GRCm39)	I265L	probably benign	Het
Zbtb20	A	C	16: 43,439,100 (GRCm39)	D667A	probably damaging	Het
Zbtb4	T	A	11: 69,668,309 (GRCm39)	I344N	probably damaging	Het
Zdbf2	T	A	1: 63,343,234 (GRCm39)	C538S	possibly damaging	Het
Zmym6	A	T	4: 127,016,355 (GRCm39)	H712L	probably damaging	Het

Other mutations in Col2a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01025:Col2a1	APN	15	97,874,054 (GRCm39)	missense	unknown
IGL01286:Col2a1	APN	15	97,892,759 (GRCm39)	missense	unknown
IGL01369:Col2a1	APN	15	97,875,707 (GRCm39)	missense	unknown
IGL01747:Col2a1	APN	15	97,889,273 (GRCm39)	splice site	probably benign
IGL02086:Col2a1	APN	15	97,884,618 (GRCm39)	splice site	probably null
IGL02549:Col2a1	APN	15	97,875,680 (GRCm39)	missense	unknown
IGL03289:Col2a1	APN	15	97,878,762 (GRCm39)	missense	unknown
IGL03369:Col2a1	APN	15	97,879,923 (GRCm39)	missense	unknown
Foreseen	UTSW	15	97,874,674 (GRCm39)	missense	unknown
FR4304:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
FR4340:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
FR4342:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
FR4589:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
LCD18:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
R0124:Col2a1	UTSW	15	97,896,743 (GRCm39)	missense	unknown
R0227:Col2a1	UTSW	15	97,874,636 (GRCm39)	missense	unknown
R0690:Col2a1	UTSW	15	97,878,073 (GRCm39)	missense	unknown
R1434:Col2a1	UTSW	15	97,877,532 (GRCm39)	missense	probably damaging	0.96
R1473:Col2a1	UTSW	15	97,880,789 (GRCm39)	splice site	probably benign
R1577:Col2a1	UTSW	15	97,877,083 (GRCm39)	missense	probably damaging	1.00
R1598:Col2a1	UTSW	15	97,877,131 (GRCm39)	missense	probably damaging	0.99
R1837:Col2a1	UTSW	15	97,894,522 (GRCm39)	splice site	probably benign
R2153:Col2a1	UTSW	15	97,885,461 (GRCm39)	missense	unknown
R2965:Col2a1	UTSW	15	97,873,976 (GRCm39)	missense	unknown
R2966:Col2a1	UTSW	15	97,873,976 (GRCm39)	missense	unknown
R3710:Col2a1	UTSW	15	97,888,788 (GRCm39)	splice site	probably benign
R3838:Col2a1	UTSW	15	97,898,462 (GRCm39)	intron	probably benign
R3838:Col2a1	UTSW	15	97,886,857 (GRCm39)	missense	unknown
R4112:Col2a1	UTSW	15	97,881,582 (GRCm39)	missense	probably benign	0.18
R4417:Col2a1	UTSW	15	97,896,466 (GRCm39)	missense	unknown
R4656:Col2a1	UTSW	15	97,874,057 (GRCm39)	missense	unknown
R4960:Col2a1	UTSW	15	97,874,030 (GRCm39)	missense	unknown
R5008:Col2a1	UTSW	15	97,877,550 (GRCm39)	missense	probably benign	0.28
R5435:Col2a1	UTSW	15	97,898,391 (GRCm39)	intron	probably benign
R5473:Col2a1	UTSW	15	97,885,370 (GRCm39)	missense	unknown
R6042:Col2a1	UTSW	15	97,898,451 (GRCm39)	intron	probably benign
R6118:Col2a1	UTSW	15	97,896,448 (GRCm39)	missense	unknown
R6183:Col2a1	UTSW	15	97,886,671 (GRCm39)	missense	unknown
R6187:Col2a1	UTSW	15	97,886,671 (GRCm39)	missense	unknown
R6401:Col2a1	UTSW	15	97,883,773 (GRCm39)	missense	unknown
R6550:Col2a1	UTSW	15	97,874,674 (GRCm39)	missense	unknown
R6568:Col2a1	UTSW	15	97,875,157 (GRCm39)	missense	unknown
R6988:Col2a1	UTSW	15	97,902,335 (GRCm39)	missense	unknown
R7060:Col2a1	UTSW	15	97,874,022 (GRCm39)	missense	unknown
R7069:Col2a1	UTSW	15	97,896,469 (GRCm39)	missense	unknown
R7167:Col2a1	UTSW	15	97,898,337 (GRCm39)	missense	unknown
R7294:Col2a1	UTSW	15	97,885,168 (GRCm39)	splice site	probably null
R7392:Col2a1	UTSW	15	97,878,032 (GRCm39)	nonsense	probably null
R7491:Col2a1	UTSW	15	97,874,040 (GRCm39)	missense	not run
R7583:Col2a1	UTSW	15	97,874,065 (GRCm39)	missense	unknown
R7665:Col2a1	UTSW	15	97,874,581 (GRCm39)	missense	unknown
R7872:Col2a1	UTSW	15	97,898,458 (GRCm39)	nonsense	probably null
R8177:Col2a1	UTSW	15	97,874,654 (GRCm39)	missense	unknown
R9343:Col2a1	UTSW	15	97,877,775 (GRCm39)	missense	probably damaging	0.99
R9458:Col2a1	UTSW	15	97,876,242 (GRCm39)	missense	unknown
Z1177:Col2a1	UTSW	15	97,896,226 (GRCm39)	missense	unknown
Z1177:Col2a1	UTSW	15	97,881,854 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTGGACTTCAGCCTCTACAACC -3'
(R):5'- GTGGCTTCTCACAGACTCAG -3'

Sequencing Primer
(F):5'- TCTGTCAGAGAGAGATGCTGG -3'
(R):5'- TGGCTTCTCACAGACTCAGAAACTC -3'

Posted On

2020-07-28