Mutagenetix > Incidental Mutation

Incidental Mutation 'R7392:Col2a1'

573544

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

045474-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7392 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

97873483-97902525 bp(-) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to A at 97878032 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Stop codon at position 1036 (R1036*)

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: R1036*

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: R1036*

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 null
Transcript: ENSMUST00000088355
AA Change: R968*

SMART Domains

Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: R968*

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: 98.8%

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610021A01Rik	T	A	7: 41,275,990 (GRCm39)	F564L	probably damaging	Het
Abcc2	T	C	19: 43,797,126 (GRCm39)	I499T	probably damaging	Het
Adamts13	C	T	2: 26,879,336 (GRCm39)	R630C	probably damaging	Het
Adgrv1	A	T	13: 81,708,808 (GRCm39)	F1199I	probably damaging	Het
Agbl5	G	A	5: 31,048,115 (GRCm39)		probably null	Het
Anks1b	A	G	10: 90,516,648 (GRCm39)	D881G	possibly damaging	Het
Arap2	A	T	5: 62,855,728 (GRCm39)	S569R	possibly damaging	Het
Arhgap15	T	C	2: 43,953,786 (GRCm39)	S171P	possibly damaging	Het
Arhgef11	G	A	3: 87,624,482 (GRCm39)		probably null	Het
Baz1a	C	A	12: 54,945,550 (GRCm39)	L1271F	probably damaging	Het
Bdnf	A	C	2: 109,554,275 (GRCm39)	K216N	probably benign	Het
Bmp7	C	T	2: 172,711,998 (GRCm39)	D409N	probably damaging	Het
Bnip5	A	T	17: 29,127,351 (GRCm39)	D219E	probably benign	Het
Cacna1c	T	A	6: 118,718,881 (GRCm39)	I390F		Het
Chd8	A	G	14: 52,470,312 (GRCm39)	S433P	probably benign	Het
Clrn2	A	G	5: 45,621,251 (GRCm39)	E215G	possibly damaging	Het
Col19a1	T	G	1: 24,573,115 (GRCm39)	D219A	unknown	Het
Copg1	T	A	6: 87,867,257 (GRCm39)	V110D	probably benign	Het
Cpd	C	T	11: 76,692,605 (GRCm39)	G744D	probably damaging	Het
Crygs	G	A	16: 22,625,252 (GRCm39)	P63L	probably benign	Het
Dcn	A	G	10: 97,345,860 (GRCm39)	D224G	probably damaging	Het
Dnah7a	T	C	1: 53,540,820 (GRCm39)	E2518G	probably benign	Het
Efcab6	C	A	15: 83,873,152 (GRCm39)	R197L	probably benign	Het
Efr3b	T	A	12: 4,019,588 (GRCm39)	Y723F	probably benign	Het
Enam	A	G	5: 88,649,523 (GRCm39)	N344S	probably damaging	Het
Erich4	A	G	7: 25,315,101 (GRCm39)	I58T	possibly damaging	Het
Esrp1	A	G	4: 11,338,809 (GRCm39)	V665A	probably benign	Het
Etf1	G	A	18: 35,039,103 (GRCm39)	T388I	probably benign	Het
Faf1	A	G	4: 109,652,040 (GRCm39)	T244A	probably benign	Het
Fbn1	T	C	2: 125,185,844 (GRCm39)	D1610G	probably damaging	Het
Fcgbpl1	C	T	7: 27,863,797 (GRCm39)	T2523M	possibly damaging	Het
Frem1	G	T	4: 82,932,064 (GRCm39)	F212L	probably benign	Het
Fuom	T	A	7: 139,681,073 (GRCm39)	D85V	probably damaging	Het
Gcfc2	T	C	6: 81,919,993 (GRCm39)		probably null	Het
Gpr37	C	T	6: 25,688,786 (GRCm39)	A104T	probably benign	Het
Hsp90ab1	G	C	17: 45,879,974 (GRCm39)	T514S	probably benign	Het
Ifnl2	A	G	7: 28,209,094 (GRCm39)	F74L	probably benign	Het
Ipo11	G	A	13: 107,028,199 (GRCm39)	R367*	probably null	Het
Itpr2	T	C	6: 146,260,838 (GRCm39)	D963G	possibly damaging	Het
Krt15	A	T	11: 100,026,386 (GRCm39)	V100E	possibly damaging	Het
Lrch3	T	A	16: 32,807,125 (GRCm39)	L466*	probably null	Het
Lrfn5	A	T	12: 61,887,090 (GRCm39)	T293S	probably benign	Het
Lrp5	A	G	19: 3,660,199 (GRCm39)	I955T	probably damaging	Het
Lrrc4b	C	T	7: 44,111,439 (GRCm39)	T437M	probably damaging	Het
Man1a	A	G	10: 53,795,283 (GRCm39)	Y657H	probably damaging	Het
Mapkap1	G	T	2: 34,325,166 (GRCm39)	R94L	probably damaging	Het
Mtmr4	T	A	11: 87,495,383 (GRCm39)	L480Q	probably damaging	Het
Mycbp2	T	C	14: 103,389,627 (GRCm39)	I3504M	probably damaging	Het
Mycbp2	A	T	14: 103,480,564 (GRCm39)	C1169S	probably damaging	Het
Myo15a	T	C	11: 60,396,802 (GRCm39)	S1455P		Het
Niban1	A	G	1: 151,571,975 (GRCm39)	T307A	probably damaging	Het
Nid2	A	G	14: 19,818,724 (GRCm39)	D406G	probably benign	Het
Nrip2	A	G	6: 128,381,913 (GRCm39)	I69V	probably benign	Het
Nthl1	G	A	17: 24,857,598 (GRCm39)	V266I	probably benign	Het
Or2ag16	T	C	7: 106,352,589 (GRCm39)	E2G	possibly damaging	Het
Or5an6	G	T	19: 12,371,829 (GRCm39)	L67F	probably damaging	Het
Or5b21	A	G	19: 12,839,951 (GRCm39)	T271A	probably benign	Het
Or5g23	A	C	2: 85,438,832 (GRCm39)	C141G	possibly damaging	Het
Or5p75-ps1	C	A	7: 108,107,291 (GRCm39)	H9Q	possibly damaging	Het
Or8k25	A	G	2: 86,243,496 (GRCm39)	V300A	probably benign	Het
Or8s5	A	G	15: 98,238,192 (GRCm39)	V226A	probably benign	Het
Pcdhb1	A	C	18: 37,398,171 (GRCm39)	S41R	possibly damaging	Het
Pdcd11	T	A	19: 47,116,436 (GRCm39)	F1529I	probably damaging	Het
Plcd3	C	A	11: 102,992,383 (GRCm39)		probably benign	Het
Qdpr	T	C	5: 45,596,718 (GRCm39)	M149V	probably benign	Het
R3hcc1	T	A	14: 69,943,329 (GRCm39)		probably null	Het
Rasgrf2	T	C	13: 92,041,856 (GRCm39)	Y392C		Het
Slc8a3	A	C	12: 81,361,577 (GRCm39)	V414G	probably damaging	Het
Slco1a6	A	G	6: 142,103,003 (GRCm39)	S54P	probably benign	Het
Sos1	C	A	17: 80,731,629 (GRCm39)	V624F	probably damaging	Het
Spdef	T	C	17: 27,936,262 (GRCm39)	D227G	probably benign	Het
Sptb	G	T	12: 76,671,003 (GRCm39)	Q447K	probably damaging	Het
Srsf12	A	T	4: 33,209,265 (GRCm39)	R62W	unknown	Het
Stag3	T	C	5: 138,289,628 (GRCm39)	L266P	probably damaging	Het
Sult2b1	T	C	7: 45,391,862 (GRCm39)		probably benign	Het
Taf1a	A	G	1: 183,190,095 (GRCm39)	T66A		Het
Tfg	A	T	16: 56,532,972 (GRCm39)		probably null	Het
Trim34b	A	G	7: 103,985,604 (GRCm39)	N413S	probably benign	Het
Txndc15	T	A	13: 55,869,399 (GRCm39)	M184K	probably damaging	Het
Umodl1	A	C	17: 31,201,306 (GRCm39)	S412R	probably damaging	Het
Zbtb8b	T	A	4: 129,326,683 (GRCm39)	M161L	probably benign	Het
Zfp597	A	T	16: 3,684,369 (GRCm39)	V129E	probably benign	Het
Zfp790	T	C	7: 29,528,050 (GRCm39)	I245T	possibly 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
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
R8306:Col2a1	UTSW	15	97,888,849 (GRCm39)	critical splice acceptor site	probably null
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'- GAGGATTCACTTAGAGCCACTCTC -3'
(R):5'- GAGCATCCCTTTGTTGGCTG -3'

Sequencing Primer
(F):5'- GTTTACTCTCCCACTCTGGTCTGAAG -3'
(R):5'- TGGCTGATTCTGCTGAAGAG -3'

Posted On

2019-09-13