Incidental Mutation 'R7872:Col2a1'
ID 608204
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 045924-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7872 (G1)
Quality Score 225.009
Status Not validated
Chromosome 15
Chromosomal Location 97873483-97902525 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) G to A at 97898458 bp (GRCm39)
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*

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acta2 C T 19: 34,220,839 (GRCm39) D290N probably damaging Het
Adam18 T C 8: 25,101,116 (GRCm39) D682G probably benign Het
Ankrd46 A G 15: 36,485,989 (GRCm39) V88A possibly damaging Het
Ankub1 T A 3: 57,572,807 (GRCm39) K305I probably damaging Het
Atrn T A 2: 130,812,147 (GRCm39) probably null Het
Bambi A T 18: 3,511,406 (GRCm39) T76S probably benign Het
Cacna1a T A 8: 85,310,283 (GRCm39) V1447E probably damaging Het
Calcoco2 GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC 11: 95,990,808 (GRCm39) probably benign Het
Clcn2 A G 16: 20,527,210 (GRCm39) M629T probably damaging Het
Clcn4 T C 7: 7,290,780 (GRCm39) N673S probably benign Het
Col20a1 T C 2: 180,628,371 (GRCm39) F15S probably benign Het
Creb3 A G 4: 43,563,332 (GRCm39) E119G probably benign Het
Dnah5 A C 15: 28,245,830 (GRCm39) D556A probably damaging Het
Edar C T 10: 58,446,348 (GRCm39) M192I possibly damaging Het
Fam91a1 A G 15: 58,320,209 (GRCm39) M634V probably benign Het
Fbxo10 C T 4: 45,051,699 (GRCm39) V471I not run Het
Fer1l5 T C 1: 36,460,967 (GRCm39) F2032L probably benign Het
Gm5150 A C 3: 16,060,485 (GRCm39) M1R probably null Het
Grin1 T C 2: 25,188,202 (GRCm39) E509G probably benign Het
Igkv10-94 C T 6: 68,681,913 (GRCm39) probably benign Het
Il18bp A G 7: 101,666,002 (GRCm39) Y59H possibly damaging Het
Ints8 A T 4: 11,254,062 (GRCm39) C17S probably benign Het
Kcnmb1 T C 11: 33,916,275 (GRCm39) Y74H probably damaging Het
Kpna1 T C 16: 35,843,565 (GRCm39) V313A probably benign Het
Lrp4 C T 2: 91,321,061 (GRCm39) T1029I possibly damaging Het
Lrrc7 A T 3: 158,059,099 (GRCm39) C3S probably damaging Het
Lyst C A 13: 13,810,450 (GRCm39) H707N probably benign Het
Map3k20 A G 2: 72,202,098 (GRCm39) K148R probably damaging Het
Mcidas G A 13: 113,135,521 (GRCm39) G315S probably damaging Het
Miip C T 4: 147,947,375 (GRCm39) G236S probably benign Het
Mocs1 T A 17: 49,746,561 (GRCm39) I177N probably damaging Het
Muc5b A G 7: 141,399,850 (GRCm39) D441G unknown Het
Ncoa1 T C 12: 4,328,186 (GRCm39) N884S probably benign Het
Or12j4 A G 7: 140,046,696 (GRCm39) N194S probably damaging Het
Or51a39 A G 7: 102,363,389 (GRCm39) V77A probably benign Het
Padi6 A T 4: 140,455,073 (GRCm39) F621L probably damaging Het
Pde8b C A 13: 95,223,347 (GRCm39) M197I possibly damaging Het
Pear1 T A 3: 87,659,522 (GRCm39) I771L probably benign Het
Poli A G 18: 70,655,891 (GRCm39) L281P probably damaging Het
Prdm12 T C 2: 31,530,231 (GRCm39) W41R probably damaging Het
Prkdc T G 16: 15,532,870 (GRCm39) S1500A probably benign Het
Prune2 T A 19: 17,096,798 (GRCm39) H767Q probably benign Het
Rasgef1b G A 5: 99,382,403 (GRCm39) Q196* probably null Het
Rnpc3 A T 3: 113,416,096 (GRCm39) L121* probably null Het
Rpp14 A G 14: 8,083,724 (GRCm38) M1V probably null Het
Ryr2 T A 13: 11,610,610 (GRCm39) D4072V probably damaging Het
Sgms1 T C 19: 32,102,765 (GRCm39) H314R probably damaging Het
Six4 CT C 12: 73,151,013 (GRCm39) probably benign Het
Slc37a3 A T 6: 39,324,244 (GRCm39) Y335N probably damaging Het
Tcp11l1 A T 2: 104,536,837 (GRCm39) H9Q probably benign Het
Tnrc6a T A 7: 122,779,057 (GRCm39) M1256K probably damaging Het
Trpc6 A G 9: 8,609,910 (GRCm39) N126S probably damaging Het
Tut4 T G 4: 108,374,715 (GRCm39) C933G probably damaging Het
Ubr4 T C 4: 139,120,373 (GRCm39) F266S possibly damaging Het
Uimc1 A G 13: 55,217,550 (GRCm39) V424A possibly damaging Het
Utrn T C 10: 12,573,873 (GRCm39) I1066V probably benign Het
Vmn1r204 A G 13: 22,740,404 (GRCm39) T12A probably benign Het
Vmn1r57 T A 7: 5,223,613 (GRCm39) I46N possibly damaging Het
Vmn1r91 T C 7: 19,835,839 (GRCm39) Y253H probably benign Het
Vmn2r14 T A 5: 109,369,219 (GRCm39) H118L probably benign Het
Zfp775 A G 6: 48,597,404 (GRCm39) K426R probably benign Het
Other mutations in Col2a1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- GCATTTGCTGTGTCTCCGAG -3'
(R):5'- TGTCAGTTCAGCCTGTCTG -3'

Sequencing Primer
(F):5'- TAAATAAATTACGACCACTGGCAG -3'
(R):5'- CAGTTCAGCCTGTCTGGTGTG -3'
Posted On 2019-12-20