Incidental Mutation 'R3838:Col2a1'
ID 277023
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 040779-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3838 (G1)
Quality Score 225
Status Not validated
Chromosome 15
Chromosomal Location 97873483-97902525 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 97886857 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 345 (D345G)
Ref Sequence ENSEMBL: ENSMUSP00000085693 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023123] [ENSMUST00000088355] [ENSMUST00000131560]
AlphaFold P28481
Predicted Effect unknown
Transcript: ENSMUST00000023123
AA Change: D413G
SMART Domains Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: D413G

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 unknown
Transcript: ENSMUST00000088355
AA Change: D345G
SMART Domains Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: D345G

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128547
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131560
SMART Domains Protein: ENSMUSP00000116951
Gene: ENSMUSG00000022483

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
VWC 34 88 1.59e-21 SMART
low complexity region 109 132 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131910
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.8%
  • 20x: 96.4%
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930486L24Rik A G 13: 60,993,041 (GRCm39) Y213H probably damaging Het
Alg8 C T 7: 97,037,752 (GRCm39) H379Y probably damaging Het
Arhgef25 T C 10: 127,025,605 (GRCm39) T12A probably benign Het
Arid4a A G 12: 71,122,559 (GRCm39) E980G possibly damaging Het
Aspm C T 1: 139,405,792 (GRCm39) H1560Y probably benign Het
Atg10 A T 13: 91,085,499 (GRCm39) I150K probably damaging Het
Bud13 A C 9: 46,201,490 (GRCm39) Q387P possibly damaging Het
Champ1 A G 8: 13,929,939 (GRCm39) Y699C probably damaging Het
Clstn1 A G 4: 149,722,790 (GRCm39) E476G probably damaging Het
Col9a2 C G 4: 120,911,455 (GRCm39) R599G probably damaging Het
Dnajb2 G A 1: 75,218,124 (GRCm39) probably null Het
Dock4 G T 12: 40,844,623 (GRCm39) probably null Het
Epx A T 11: 87,765,656 (GRCm39) L101Q probably damaging Het
F13a1 A T 13: 37,231,398 (GRCm39) N21K probably damaging Het
Fam13c C T 10: 70,378,478 (GRCm39) S336L probably damaging Het
Foxj3 T A 4: 119,473,821 (GRCm39) H215Q possibly damaging Het
Gcnt4 A T 13: 97,083,522 (GRCm39) R273* probably null Het
Gpam T C 19: 55,068,890 (GRCm39) N450S probably benign Het
Hivep2 C A 10: 14,004,713 (GRCm39) T437K probably benign Het
Hmcn2 T C 2: 31,303,419 (GRCm39) L3020P probably damaging Het
Hmgcr A G 13: 96,795,597 (GRCm39) I324T probably benign Het
Ighmbp2 T C 19: 3,321,658 (GRCm39) Y367C probably benign Het
Lrrc14b A G 13: 74,511,664 (GRCm39) C139R possibly damaging Het
Lsamp A T 16: 41,954,675 (GRCm39) E174V possibly damaging Het
Mid1ip1 T C X: 10,584,620 (GRCm39) V51A possibly damaging Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Msn C A X: 95,203,805 (GRCm39) Q303K probably damaging Het
Myh7b A G 2: 155,474,909 (GRCm39) K1816E probably damaging Het
Nap1l1 T A 10: 111,331,183 (GRCm39) probably null Het
Nme2 T A 11: 93,840,803 (GRCm39) E252D probably benign Het
Ntpcr G A 8: 126,464,111 (GRCm39) V79M probably damaging Het
Ogdh C T 11: 6,288,627 (GRCm39) R235* probably null Het
Or10d1 A G 9: 39,484,267 (GRCm39) V96A probably benign Het
Or10w1 A G 19: 13,632,321 (GRCm39) D176G probably benign Het
Or9k2 C A 10: 129,998,275 (GRCm39) E307* probably null Het
P3r3urf A G 4: 116,030,718 (GRCm39) T41A probably benign Het
Pcdh20 T C 14: 88,705,899 (GRCm39) N467S probably benign Het
Pkhd1 G A 1: 20,604,853 (GRCm39) T1154I possibly damaging Het
Polq G T 16: 36,898,711 (GRCm39) R2157I probably damaging Het
Reep6 C A 10: 80,171,723 (GRCm39) A533E probably damaging Het
Senp2 T C 16: 21,828,485 (GRCm39) S32P probably damaging Het
Septin11 T A 5: 93,296,258 (GRCm39) I52N probably damaging Het
Shld2 T C 14: 33,967,325 (GRCm39) D77G probably benign Het
Slc17a4 C T 13: 24,085,752 (GRCm39) R387H probably benign Het
Spdye4b C T 5: 143,178,084 (GRCm39) T11I probably benign Het
Srrt C T 5: 137,300,387 (GRCm39) probably null Het
Sspo T A 6: 48,457,754 (GRCm39) C3085S probably damaging Het
Stim1 C T 7: 102,060,503 (GRCm39) T182I possibly damaging Het
Thbs2 C A 17: 14,908,113 (GRCm39) V217L probably benign Het
Thpo G A 16: 20,547,498 (GRCm39) R38C probably damaging Het
Tmem210 A G 2: 25,178,444 (GRCm39) E35G possibly damaging Het
Trim12c T A 7: 103,990,075 (GRCm39) probably benign Het
Tvp23b A G 11: 62,774,455 (GRCm39) H33R possibly damaging Het
Usp14 A G 18: 10,024,532 (GRCm39) probably null Het
Vmn2r73 A G 7: 85,507,258 (GRCm39) W685R probably benign Het
Zfp618 G A 4: 63,051,801 (GRCm39) A861T probably benign Het
Zfp715 A G 7: 42,949,180 (GRCm39) V260A 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
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
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'- ACCAGTTGCACCTTGAGGAC -3'
(R):5'- ACTAAATGGTCATGCTGGCC -3'

Sequencing Primer
(F):5'- ACCTTGAGGACCGGGAG -3'
(R):5'- GGTCATGCTGGCCAAACAC -3'
Posted On 2015-04-06