Incidental Mutation 'R0356:Col9a1'
ID 29807
Institutional Source Beutler Lab
Gene Symbol Col9a1
Ensembl Gene ENSMUSG00000026147
Gene Name collagen, type IX, alpha 1
Synonyms Col9a-1
MMRRC Submission 038562-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.092) question?
Stock # R0356 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 24216691-24291765 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 24224328 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Stop codon at position 170 (L170*)
Ref Sequence ENSEMBL: ENSMUSP00000051579 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054588]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000054588
AA Change: L170*
SMART Domains Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: L170*

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
TSPN 50 244 5.73e-78 SMART
Pfam:Collagen 266 326 2e-11 PFAM
Pfam:Collagen 308 358 3.5e-9 PFAM
Pfam:Collagen 357 409 1.2e-8 PFAM
Pfam:Collagen 415 472 7.8e-11 PFAM
Pfam:Collagen 454 515 2.9e-11 PFAM
Pfam:Collagen 592 667 3.9e-8 PFAM
Pfam:Collagen 646 716 1.7e-9 PFAM
Pfam:Collagen 697 760 1.6e-10 PFAM
Pfam:Collagen 785 848 3.1e-11 PFAM
low complexity region 878 899 N/A INTRINSIC
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.6%
  • 10x: 94.4%
  • 20x: 86.1%
Validation Efficiency 100% (47/47)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted mutation show no conspicuous skeletal abnormalities at birth but develop early-onset degenerative joint disease resembling osteoarthritis as well as progressive hearing loss; restoration and remodeling of trabecular bone is perturbed with minimal effects on cortical bone. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9430097D07Rik T C 2: 32,464,418 (GRCm39) probably benign Het
Adgrg6 C T 10: 14,302,642 (GRCm39) V924M possibly damaging Het
Anxa9 A G 3: 95,215,387 (GRCm39) probably benign Het
Ap3d1 G T 10: 80,563,812 (GRCm39) S122R probably damaging Het
Arhgap5 T C 12: 52,563,091 (GRCm39) S21P probably damaging Het
Atp13a5 A G 16: 29,167,573 (GRCm39) probably benign Het
AU040320 A T 4: 126,731,155 (GRCm39) D618V probably damaging Het
Cbfa2t2 T A 2: 154,373,269 (GRCm39) D475E probably benign Het
Ccdc202 T A 14: 96,119,801 (GRCm39) V186E possibly damaging Het
Ccdc62 G A 5: 124,092,811 (GRCm39) V599I probably benign Het
Cenpj T C 14: 56,786,953 (GRCm39) E917G probably damaging Het
Cog5 T C 12: 31,887,180 (GRCm39) probably benign Het
Daxx T A 17: 34,132,867 (GRCm39) V627D probably benign Het
Dnah9 A G 11: 66,021,388 (GRCm39) probably null Het
Drg2 T A 11: 60,352,407 (GRCm39) V203E probably damaging Het
Fbxl17 G A 17: 63,663,846 (GRCm39) R67C probably damaging Het
Fer1l4 T C 2: 155,865,930 (GRCm39) Y1586C probably damaging Het
Gp6 A T 7: 4,373,141 (GRCm39) probably benign Het
Hhip T C 8: 80,724,121 (GRCm39) I374V probably benign Het
Hspa12b G T 2: 130,986,719 (GRCm39) V547L possibly damaging Het
Iars1 G A 13: 49,856,709 (GRCm39) V321I probably benign Het
Itga8 T C 2: 12,187,532 (GRCm39) M716V possibly damaging Het
Lcn5 T C 2: 25,550,705 (GRCm39) I131T probably damaging Het
Mki67 G A 7: 135,306,135 (GRCm39) T614M probably benign Het
Mmp3 G A 9: 7,451,768 (GRCm39) E369K probably benign Het
Myt1l A G 12: 29,861,500 (GRCm39) D94G unknown Het
Neil1 T C 9: 57,054,180 (GRCm39) I47V possibly damaging Het
Nr5a2 T C 1: 136,773,430 (GRCm39) N424S possibly damaging Het
Or1e21 A T 11: 73,344,906 (GRCm39) I44N possibly damaging Het
Or51f5 A T 7: 102,424,286 (GRCm39) D185V probably damaging Het
Or5b120 A G 19: 13,480,441 (GRCm39) T245A possibly damaging Het
Or7e166 G T 9: 19,624,743 (GRCm39) G207C probably damaging Het
Pakap C A 4: 57,855,628 (GRCm39) T360K possibly damaging Het
Pde8b G T 13: 95,182,962 (GRCm39) N265K probably damaging Het
Prpf40b T C 15: 99,203,080 (GRCm39) probably null Het
Samd9l T C 6: 3,375,107 (GRCm39) D718G possibly damaging Het
Sirpb1c T C 3: 15,887,309 (GRCm39) N175D possibly damaging Het
Srgap1 A T 10: 121,691,441 (GRCm39) probably null Het
Tgm5 T A 2: 120,884,055 (GRCm39) T313S probably damaging Het
Tigar A G 6: 127,068,145 (GRCm39) probably null Het
Tmprss11b A G 5: 86,808,326 (GRCm39) *417Q probably null Het
Trim32 G A 4: 65,531,491 (GRCm39) R16Q probably damaging Het
Ttll11 T C 2: 35,792,688 (GRCm39) D385G possibly damaging Het
Zfp426 T C 9: 20,382,541 (GRCm39) T135A probably benign Het
Other mutations in Col9a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00233:Col9a1 APN 1 24,224,306 (GRCm39) missense unknown
IGL00517:Col9a1 APN 1 24,234,615 (GRCm39) intron probably benign
IGL01125:Col9a1 APN 1 24,263,726 (GRCm39) critical splice acceptor site probably null
IGL01505:Col9a1 APN 1 24,224,205 (GRCm39) missense unknown
IGL01583:Col9a1 APN 1 24,224,225 (GRCm39) missense unknown
IGL01627:Col9a1 APN 1 24,218,689 (GRCm39) critical splice donor site probably null
IGL01773:Col9a1 APN 1 24,244,147 (GRCm39) missense probably benign 0.17
IGL02117:Col9a1 APN 1 24,276,574 (GRCm39) nonsense probably null
IGL02192:Col9a1 APN 1 24,261,068 (GRCm39) missense probably damaging 1.00
IGL02346:Col9a1 APN 1 24,262,690 (GRCm39) missense probably damaging 0.96
IGL02383:Col9a1 APN 1 24,224,339 (GRCm39) missense unknown
IGL02453:Col9a1 APN 1 24,218,438 (GRCm39) missense unknown
IGL02553:Col9a1 APN 1 24,261,018 (GRCm39) splice site probably benign
IGL03412:Col9a1 APN 1 24,249,508 (GRCm39) critical splice donor site probably null
IGL03493:Col9a1 APN 1 24,260,651 (GRCm39) splice site probably benign
ANU74:Col9a1 UTSW 1 24,224,409 (GRCm39) missense unknown
R0076:Col9a1 UTSW 1 24,276,578 (GRCm39) critical splice donor site probably null
R0076:Col9a1 UTSW 1 24,276,578 (GRCm39) critical splice donor site probably null
R0090:Col9a1 UTSW 1 24,262,643 (GRCm39) splice site probably null
R0562:Col9a1 UTSW 1 24,218,360 (GRCm39) splice site probably null
R0584:Col9a1 UTSW 1 24,263,571 (GRCm39) splice site probably benign
R0708:Col9a1 UTSW 1 24,276,342 (GRCm39) missense possibly damaging 0.92
R1342:Col9a1 UTSW 1 24,262,701 (GRCm39) critical splice donor site probably null
R1445:Col9a1 UTSW 1 24,276,579 (GRCm39) critical splice donor site probably null
R1791:Col9a1 UTSW 1 24,224,386 (GRCm39) missense unknown
R1938:Col9a1 UTSW 1 24,261,554 (GRCm39) missense probably damaging 1.00
R2214:Col9a1 UTSW 1 24,247,283 (GRCm39) missense probably damaging 1.00
R2240:Col9a1 UTSW 1 24,218,582 (GRCm39) missense unknown
R3757:Col9a1 UTSW 1 24,271,312 (GRCm39) critical splice donor site probably null
R3891:Col9a1 UTSW 1 24,224,517 (GRCm39) critical splice donor site probably null
R4249:Col9a1 UTSW 1 24,283,462 (GRCm39) missense probably damaging 1.00
R4690:Col9a1 UTSW 1 24,263,787 (GRCm39) splice site probably null
R4918:Col9a1 UTSW 1 24,276,339 (GRCm39) missense possibly damaging 0.74
R4988:Col9a1 UTSW 1 24,224,273 (GRCm39) missense unknown
R5144:Col9a1 UTSW 1 24,278,434 (GRCm39) missense probably benign 0.08
R5327:Col9a1 UTSW 1 24,234,620 (GRCm39) critical splice donor site probably null
R5511:Col9a1 UTSW 1 24,218,619 (GRCm39) missense unknown
R5519:Col9a1 UTSW 1 24,269,335 (GRCm39) splice site probably null
R5564:Col9a1 UTSW 1 24,234,436 (GRCm39) start gained probably benign
R6076:Col9a1 UTSW 1 24,234,457 (GRCm39) start gained probably benign
R6478:Col9a1 UTSW 1 24,224,486 (GRCm39) missense unknown
R6886:Col9a1 UTSW 1 24,224,426 (GRCm39) missense unknown
R7177:Col9a1 UTSW 1 24,234,498 (GRCm39) missense unknown
R7259:Col9a1 UTSW 1 24,224,424 (GRCm39) missense unknown
R7268:Col9a1 UTSW 1 24,246,479 (GRCm39) missense possibly damaging 0.89
R7347:Col9a1 UTSW 1 24,218,484 (GRCm39) splice site probably null
R7644:Col9a1 UTSW 1 24,224,243 (GRCm39) missense unknown
R7860:Col9a1 UTSW 1 24,276,261 (GRCm39) missense probably damaging 1.00
R8267:Col9a1 UTSW 1 24,224,267 (GRCm39) missense unknown
R8296:Col9a1 UTSW 1 24,217,380 (GRCm39) missense unknown
R8737:Col9a1 UTSW 1 24,224,127 (GRCm39) missense unknown
R8773:Col9a1 UTSW 1 24,224,208 (GRCm39) missense unknown
R8795:Col9a1 UTSW 1 24,233,812 (GRCm39) missense unknown
R8878:Col9a1 UTSW 1 24,236,048 (GRCm39) critical splice donor site probably null
R8956:Col9a1 UTSW 1 24,276,300 (GRCm39) missense probably damaging 1.00
R8978:Col9a1 UTSW 1 24,278,396 (GRCm39) missense probably damaging 1.00
R9096:Col9a1 UTSW 1 24,224,207 (GRCm39) missense unknown
R9097:Col9a1 UTSW 1 24,224,207 (GRCm39) missense unknown
R9205:Col9a1 UTSW 1 24,224,175 (GRCm39) missense unknown
R9534:Col9a1 UTSW 1 24,224,250 (GRCm39) missense unknown
Z1176:Col9a1 UTSW 1 24,253,669 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TTCACACTGTAGCCTTTCCGCAGG -3'
(R):5'- GTTTTCCCAGCACTGCAAAGCC -3'

Sequencing Primer
(F):5'- AGGCATTTGTATCCCAGTGGAC -3'
(R):5'- GCCATCCGCATCAATCTGG -3'
Posted On 2013-04-24