Incidental Mutation 'R6118:Col2a1'
ID 485226
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 044267-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6118 (G1)
Quality Score 225.009
Status Not validated
Chromosome 15
Chromosomal Location 97873483-97902525 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 97896448 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 67 (D67G)
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: D135G
SMART Domains Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: D135G

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: D67G
SMART Domains Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: D67G

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: ENSMUST00000127879
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: ENSMUST00000133488
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139246
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140064
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230148
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.6%
  • 20x: 93.1%
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgb T G 10: 10,307,035 (GRCm39) K316N probably damaging Het
Als2 A T 1: 59,242,228 (GRCm39) V609E possibly damaging Het
Ank3 A G 10: 69,830,231 (GRCm39) I71V probably damaging Het
Antxr2 T A 5: 98,097,060 (GRCm39) D351V probably damaging Het
Arel1 A G 12: 84,988,713 (GRCm39) V12A possibly damaging Het
Atad1 C T 19: 32,664,697 (GRCm39) R239H possibly damaging Het
B3galnt2 A G 13: 14,166,094 (GRCm39) T330A probably damaging Het
Bag6 T A 17: 35,362,600 (GRCm39) I636N probably damaging Het
C1qtnf6 T C 15: 78,409,595 (GRCm39) D84G probably damaging Het
Ceacam20 T C 7: 19,705,654 (GRCm39) V215A possibly damaging Het
Chtf18 C T 17: 25,938,133 (GRCm39) D967N probably damaging Het
Cntnap2 T A 6: 47,170,011 (GRCm39) I1159K possibly damaging Het
Csde1 T A 3: 102,962,070 (GRCm39) V627E probably benign Het
Epb41l1 G A 2: 156,364,397 (GRCm39) E969K probably benign Het
Fam53c A C 18: 34,901,743 (GRCm39) E220A probably damaging Het
Gabbr2 C T 4: 46,736,459 (GRCm39) R474Q probably damaging Het
H2bc18 T A 3: 96,177,267 (GRCm39) V67E probably damaging Het
Hap1 G T 11: 100,246,620 (GRCm39) T95N probably benign Het
Jmjd1c A G 10: 67,075,791 (GRCm39) K1886R probably damaging Het
Kndc1 A G 7: 139,503,717 (GRCm39) D1007G probably damaging Het
Mcm2 C T 6: 88,864,818 (GRCm39) A553T probably damaging Het
Memo1 T C 17: 74,509,302 (GRCm39) Y239C possibly damaging Het
Meox2 GCACCACCACCACCACCACCA GCACCACCACCACCACCA 12: 37,159,030 (GRCm39) probably benign Het
Mptx2 G A 1: 173,102,414 (GRCm39) L92F probably benign Het
Obsl1 A G 1: 75,468,722 (GRCm39) probably benign Het
Or4c107 T A 2: 88,789,462 (GRCm39) Y217* probably null Het
Or8k35 T A 2: 86,424,758 (GRCm39) H138L probably benign Het
Pold3 A G 7: 99,745,614 (GRCm39) S180P possibly damaging Het
Rbm12b2 T C 4: 12,095,135 (GRCm39) S665P probably benign Het
Rfc4 A T 16: 22,939,693 (GRCm39) S86T probably damaging Het
Rfx6 T A 10: 51,587,962 (GRCm39) N277K possibly damaging Het
Ryr2 C A 13: 11,807,575 (GRCm39) V865F possibly damaging Het
Skint4 T A 4: 111,977,019 (GRCm39) probably null Het
Slc38a10 T C 11: 120,023,669 (GRCm39) Y249C probably damaging Het
Slco1b2 A G 6: 141,603,236 (GRCm39) T206A probably benign Het
Slco3a1 C T 7: 73,968,254 (GRCm39) D489N probably benign Het
Tasor2 C T 13: 3,631,891 (GRCm39) R870H possibly damaging Het
Tbc1d1 C T 5: 64,441,380 (GRCm39) L655F probably damaging Het
Tpp2 A T 1: 43,979,306 (GRCm39) I68F probably damaging Het
Trim30c G T 7: 104,031,288 (GRCm39) T509K probably benign Het
Zfp827 G T 8: 79,803,067 (GRCm39) K546N possibly damaging 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
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'- GGTACCAGGTTCTCCATCTCTG -3'
(R):5'- TGCACCCCTCTAACCAATGG -3'

Sequencing Primer
(F):5'- TCCATCTCTGCCACGGG -3'
(R):5'- TCTAACCAATGGGCTCATGG -3'
Posted On 2017-08-16