Incidental Mutation 'R6886:Col9a1'
ID 536924
Institutional Source Beutler Lab
Gene Symbol Col9a1
Ensembl Gene ENSMUSG00000026147
Gene Name collagen, type IX, alpha 1
Synonyms Col9a-1
MMRRC Submission 044980-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.092) question?
Stock # R6886 (G1)
Quality Score 225.009
Status Not validated
Chromosome 1
Chromosomal Location 24216691-24291765 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 24224426 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 203 (S203T)
Ref Sequence ENSEMBL: ENSMUSP00000051579 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054588]
AlphaFold no structure available at present
Predicted Effect unknown
Transcript: ENSMUST00000054588
AA Change: S203T
SMART Domains Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: S203T

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.3%
  • 20x: 97.7%
Validation Efficiency
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atp7b A T 8: 22,518,706 (GRCm39) M44K probably benign Het
Bad T C 19: 6,928,702 (GRCm39) probably benign Het
Bbs12 A G 3: 37,373,390 (GRCm39) D61G probably damaging Het
Bcr C T 10: 74,989,769 (GRCm39) R722C probably damaging Het
Carf C A 1: 60,175,413 (GRCm39) probably null Het
Ccdc181 A G 1: 164,107,665 (GRCm39) E116G probably damaging Het
Celsr1 A G 15: 85,915,855 (GRCm39) V706A probably benign Het
Ctsl T C 13: 64,512,961 (GRCm39) probably null Het
Exosc7 A T 9: 122,965,023 (GRCm39) E277D probably benign Het
Fam20b A T 1: 156,518,081 (GRCm39) W238R probably damaging Het
Fanci A T 7: 79,070,090 (GRCm39) H430L possibly damaging Het
Fstl4 A G 11: 53,077,277 (GRCm39) D678G probably damaging Het
Gm10801 TC TCGGC 2: 98,494,151 (GRCm39) probably benign Het
Gm11569 T A 11: 99,689,247 (GRCm39) probably benign Het
Igfn1 G A 1: 135,901,198 (GRCm39) R306W probably damaging Het
Il6 C T 5: 30,223,201 (GRCm39) probably benign Het
Khdc1c T C 1: 21,439,749 (GRCm39) L100P possibly damaging Het
Kif18a G A 2: 109,127,008 (GRCm39) R314H probably damaging Het
Kif26b A C 1: 178,701,703 (GRCm39) K694T probably damaging Het
Kndc1 A G 7: 139,493,485 (GRCm39) T484A probably benign Het
Lonrf1 T C 8: 36,696,191 (GRCm39) probably null Het
Man1a2 C T 3: 100,563,387 (GRCm39) G169D probably benign Het
Med6 G T 12: 81,638,159 (GRCm39) D17E probably damaging Het
Neb T C 2: 52,110,236 (GRCm39) K204R probably damaging Het
Nhlrc1 T A 13: 47,167,252 (GRCm39) N335I possibly damaging Het
Nlrp12 T C 7: 3,289,313 (GRCm39) M400V probably benign Het
Or7e173 G T 9: 19,938,428 (GRCm39) H269N probably benign Het
Or8k22 A T 2: 86,163,408 (GRCm39) C97* probably null Het
Pkhd1 C T 1: 20,417,504 (GRCm39) S2549N probably benign Het
Pramel26 A G 4: 143,539,332 (GRCm39) F54L probably benign Het
Rab4b A C 7: 26,872,381 (GRCm39) L145R probably damaging Het
Rad50 T C 11: 53,577,011 (GRCm39) I526V probably benign Het
Rel T C 11: 23,694,304 (GRCm39) H309R probably benign Het
Rnf2 G T 1: 151,349,017 (GRCm39) N34K possibly damaging Het
Serpina3m G T 12: 104,355,386 (GRCm39) V18F possibly damaging Het
Serpinb9c T C 13: 33,334,310 (GRCm39) K244R probably benign Het
Setbp1 T A 18: 78,900,715 (GRCm39) Y984F probably damaging Het
Slc12a5 T A 2: 164,824,825 (GRCm39) M410K probably benign Het
Smarca4 C T 9: 21,570,127 (GRCm39) A710V probably damaging Het
Snx19 C A 9: 30,340,231 (GRCm39) D456E probably damaging Het
Ssrp1 T A 2: 84,870,280 (GRCm39) D101E probably benign Het
Tax1bp1 A T 6: 52,710,208 (GRCm39) E162D probably benign Het
Tenm4 T A 7: 96,446,599 (GRCm39) M823K possibly damaging Het
Tesk1 A G 4: 43,443,592 (GRCm39) D53G possibly damaging Het
Tnrc6a T A 7: 122,786,668 (GRCm39) S1577T probably benign Het
Tpr A G 1: 150,299,716 (GRCm39) I1270V probably benign Het
Trp53bp2 T C 1: 182,256,608 (GRCm39) probably null Het
Ube4a A T 9: 44,860,141 (GRCm39) I307N probably damaging Het
Unc13b A G 4: 43,170,156 (GRCm39) probably benign Het
Vmn2r3 T C 3: 64,166,927 (GRCm39) K735E probably damaging Het
Vmn2r54 A G 7: 12,366,080 (GRCm39) F285L probably benign Het
Vmn2r81 T G 10: 79,103,988 (GRCm39) S204A possibly damaging Het
Washc1 A G 17: 66,426,061 (GRCm39) D453G probably damaging Het
Zfp329 T A 7: 12,544,025 (GRCm39) I500L probably benign Het
Zfp516 A G 18: 82,975,125 (GRCm39) D441G probably benign Het
Zfp644 T C 5: 106,785,777 (GRCm39) T257A possibly damaging 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
R0356:Col9a1 UTSW 1 24,224,328 (GRCm39) nonsense 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
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'- ACTGGAACATTTGGCAGATCCAG -3'
(R):5'- TCAAAGATGTCTTGGGCGCTC -3'

Sequencing Primer
(F):5'- TGGCAGATCCAGGATTCCG -3'
(R):5'- GCTCACCTTTAGCCATGCAGG -3'
Posted On 2018-10-18