Incidental Mutation 'R1445:Col9a1'
ID 158745
Institutional Source Beutler Lab
Gene Symbol Col9a1
Ensembl Gene ENSMUSG00000026147
Gene Name collagen, type IX, alpha 1
Synonyms Col9a-1
MMRRC Submission 039500-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.092) question?
Stock # R1445 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 24216691-24291765 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to C at 24276579 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000085687 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054588] [ENSMUST00000054588] [ENSMUST00000054588] [ENSMUST00000054588] [ENSMUST00000088349] [ENSMUST00000088349] [ENSMUST00000088349] [ENSMUST00000088349] [ENSMUST00000088349]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000054588
SMART Domains Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

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
Predicted Effect probably null
Transcript: ENSMUST00000054588
SMART Domains Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

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
Predicted Effect probably null
Transcript: ENSMUST00000054588
SMART Domains Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

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
Predicted Effect probably null
Transcript: ENSMUST00000054588
SMART Domains Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

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
Predicted Effect probably null
Transcript: ENSMUST00000088349
SMART Domains Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

DomainStartEndE-ValueType
low complexity region 7 22 N/A INTRINSIC
Pfam:Collagen 24 85 1.5e-11 PFAM
Pfam:Collagen 66 117 2.7e-9 PFAM
Pfam:Collagen 115 168 2.8e-8 PFAM
Pfam:Collagen 174 231 5.5e-11 PFAM
Pfam:Collagen 213 274 1.9e-11 PFAM
low complexity region 353 391 N/A INTRINSIC
Pfam:Collagen 405 479 1.3e-9 PFAM
Pfam:Collagen 456 519 1e-10 PFAM
Pfam:Collagen 544 607 2.4e-11 PFAM
low complexity region 637 658 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000088349
SMART Domains Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

DomainStartEndE-ValueType
low complexity region 7 22 N/A INTRINSIC
Pfam:Collagen 24 85 1.5e-11 PFAM
Pfam:Collagen 66 117 2.7e-9 PFAM
Pfam:Collagen 115 168 2.8e-8 PFAM
Pfam:Collagen 174 231 5.5e-11 PFAM
Pfam:Collagen 213 274 1.9e-11 PFAM
low complexity region 353 391 N/A INTRINSIC
Pfam:Collagen 405 479 1.3e-9 PFAM
Pfam:Collagen 456 519 1e-10 PFAM
Pfam:Collagen 544 607 2.4e-11 PFAM
low complexity region 637 658 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000088349
SMART Domains Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

DomainStartEndE-ValueType
low complexity region 7 22 N/A INTRINSIC
Pfam:Collagen 24 85 1.5e-11 PFAM
Pfam:Collagen 66 117 2.7e-9 PFAM
Pfam:Collagen 115 168 2.8e-8 PFAM
Pfam:Collagen 174 231 5.5e-11 PFAM
Pfam:Collagen 213 274 1.9e-11 PFAM
low complexity region 353 391 N/A INTRINSIC
Pfam:Collagen 405 479 1.3e-9 PFAM
Pfam:Collagen 456 519 1e-10 PFAM
Pfam:Collagen 544 607 2.4e-11 PFAM
low complexity region 637 658 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000088349
SMART Domains Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

DomainStartEndE-ValueType
low complexity region 7 22 N/A INTRINSIC
Pfam:Collagen 24 85 1.5e-11 PFAM
Pfam:Collagen 66 117 2.7e-9 PFAM
Pfam:Collagen 115 168 2.8e-8 PFAM
Pfam:Collagen 174 231 5.5e-11 PFAM
Pfam:Collagen 213 274 1.9e-11 PFAM
low complexity region 353 391 N/A INTRINSIC
Pfam:Collagen 405 479 1.3e-9 PFAM
Pfam:Collagen 456 519 1e-10 PFAM
Pfam:Collagen 544 607 2.4e-11 PFAM
low complexity region 637 658 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000088349
SMART Domains Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

DomainStartEndE-ValueType
low complexity region 7 22 N/A INTRINSIC
Pfam:Collagen 24 85 1.5e-11 PFAM
Pfam:Collagen 66 117 2.7e-9 PFAM
Pfam:Collagen 115 168 2.8e-8 PFAM
Pfam:Collagen 174 231 5.5e-11 PFAM
Pfam:Collagen 213 274 1.9e-11 PFAM
low complexity region 353 391 N/A INTRINSIC
Pfam:Collagen 405 479 1.3e-9 PFAM
Pfam:Collagen 456 519 1e-10 PFAM
Pfam:Collagen 544 607 2.4e-11 PFAM
low complexity region 637 658 N/A INTRINSIC
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.7%
  • 10x: 93.9%
  • 20x: 84.0%
Validation Efficiency 96% (101/105)
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: 94 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700061I17Rik G T 3: 116,861,385 (GRCm39) noncoding transcript Het
2300003K06Rik G T 11: 99,728,793 (GRCm39) Q17K probably benign Het
Abca16 T C 7: 120,119,256 (GRCm39) V999A probably benign Het
Actn3 C T 19: 4,915,483 (GRCm39) probably benign Het
Agap2 T A 10: 126,926,981 (GRCm39) probably benign Het
Ago3 C A 4: 126,265,580 (GRCm39) R278L probably benign Het
Aldh1a2 T C 9: 71,192,492 (GRCm39) V449A possibly damaging Het
Alkbh2 C T 5: 114,262,287 (GRCm39) E148K probably damaging Het
Aplnr A G 2: 84,967,353 (GRCm39) Y126C probably damaging Het
Apob T C 12: 8,066,084 (GRCm39) I4351T possibly damaging Het
Ash1l T C 3: 88,914,659 (GRCm39) L1763P probably benign Het
Aspn T C 13: 49,710,849 (GRCm39) S165P possibly damaging Het
Atg13 A T 2: 91,510,335 (GRCm39) V349E probably damaging Het
Atp1b2 T A 11: 69,493,309 (GRCm39) probably null Het
B3glct A T 5: 149,677,604 (GRCm39) D411V probably damaging Het
Bcar3 A T 3: 122,316,840 (GRCm39) I255F probably damaging Het
Cacna1b G A 2: 24,608,148 (GRCm39) probably benign Het
Cep164 T G 9: 45,690,198 (GRCm39) E675A possibly damaging Het
Chd1l C T 3: 97,490,047 (GRCm39) E503K probably benign Het
Chst8 C A 7: 34,447,593 (GRCm39) M8I possibly damaging Het
Clec4n A G 6: 123,212,475 (GRCm39) E67G probably benign Het
Cobll1 A T 2: 64,929,480 (GRCm39) D653E probably damaging Het
Crip2 T C 12: 113,107,124 (GRCm39) L30P probably damaging Het
Ctbp1 C T 5: 33,418,407 (GRCm39) V22I probably benign Het
Cwc22 T C 2: 77,747,521 (GRCm39) probably benign Het
Cyp4a32 C A 4: 115,460,147 (GRCm39) Y119* probably null Het
Dido1 G T 2: 180,313,263 (GRCm39) A463E possibly damaging Het
Dnah7a G A 1: 53,567,956 (GRCm39) P1880L probably benign Het
Dock2 T A 11: 34,189,705 (GRCm39) T1489S probably benign Het
Dsp A G 13: 38,375,907 (GRCm39) T1231A probably damaging Het
Eif2ak1 G T 5: 143,810,717 (GRCm39) probably benign Het
Entrep1 G A 19: 23,998,998 (GRCm39) T140M probably damaging Het
Epc1 A T 18: 6,452,360 (GRCm39) M233K probably damaging Het
Gigyf2 A G 1: 87,371,360 (GRCm39) probably benign Het
Greb1 T G 12: 16,757,852 (GRCm39) H58P probably damaging Het
Gtpbp1 T C 15: 79,597,649 (GRCm39) I348T possibly damaging Het
Hck A T 2: 152,970,192 (GRCm39) N64Y probably benign Het
Herc2 T C 7: 55,818,744 (GRCm39) S2812P probably damaging Het
Inpp4b T A 8: 82,679,463 (GRCm39) probably null Het
Kcnq5 A C 1: 21,475,248 (GRCm39) S473A probably benign Het
Lrat T G 3: 82,810,676 (GRCm39) D115A probably damaging Het
Lyst A G 13: 13,814,639 (GRCm39) I1131M possibly damaging Het
Man2a2 T C 7: 80,018,310 (GRCm39) D160G probably benign Het
Marf1 C T 16: 13,933,688 (GRCm39) D1567N probably benign Het
Mars1 T C 10: 127,133,857 (GRCm39) D680G possibly damaging Het
Mat1a T C 14: 40,843,797 (GRCm39) S339P probably damaging Het
Megf8 T C 7: 25,042,081 (GRCm39) S1300P probably damaging Het
Mga T C 2: 119,733,179 (GRCm39) L9S probably damaging Het
Mllt6 T C 11: 97,563,277 (GRCm39) probably benign Het
Mrpl37 A G 4: 106,921,692 (GRCm39) L179P probably benign Het
Mtnr1a G T 8: 45,540,782 (GRCm39) V248L probably benign Het
Mylk T C 16: 34,635,835 (GRCm39) S19P possibly damaging Het
Or11g1 A G 14: 50,651,858 (GRCm39) T286A probably damaging Het
Pacc1 A G 1: 191,080,559 (GRCm39) probably benign Het
Parp8 A T 13: 117,161,886 (GRCm39) probably null Het
Pcnx2 T C 8: 126,479,023 (GRCm39) D2075G probably damaging Het
Pigo A T 4: 43,021,460 (GRCm39) I494K probably benign Het
Pkd1l1 A T 11: 8,820,313 (GRCm39) D1217E probably benign Het
Pkhd1l1 T C 15: 44,369,040 (GRCm39) V895A probably benign Het
Plcb4 A T 2: 135,842,109 (GRCm39) H1031L possibly damaging Het
Plxnb1 A G 9: 108,937,989 (GRCm39) K1245R probably null Het
Pold1 C T 7: 44,192,181 (GRCm39) probably benign Het
Ptprq T C 10: 107,498,423 (GRCm39) I885V probably damaging Het
Ptprz1 A G 6: 23,050,473 (GRCm39) D1398G probably damaging Het
Pygm G A 19: 6,439,917 (GRCm39) A364T probably benign Het
Rbl1 T C 2: 157,035,018 (GRCm39) N354S probably benign Het
Scgb2b19 C T 7: 32,979,037 (GRCm39) probably null Het
Slc26a8 C T 17: 28,867,187 (GRCm39) V545M possibly damaging Het
Slc27a1 T A 8: 72,036,757 (GRCm39) probably null Het
Smpd1 A G 7: 105,205,881 (GRCm39) D416G possibly damaging Het
Sorbs3 A G 14: 70,431,095 (GRCm39) V284A probably benign Het
Stfa2l1 T C 16: 35,982,154 (GRCm39) V75A probably damaging Het
Syndig1 A G 2: 149,772,841 (GRCm39) D166G probably damaging Het
Tcp10a G A 17: 7,593,406 (GRCm39) probably null Het
Themis2 T A 4: 132,510,212 (GRCm39) I663F possibly damaging Het
Thrap3 T C 4: 126,070,129 (GRCm39) Q586R probably damaging Het
Tinag C A 9: 76,952,798 (GRCm39) C62F probably damaging Het
Tmod1 T C 4: 46,090,884 (GRCm39) Y146H probably damaging Het
Tmprss4 T A 9: 45,095,683 (GRCm39) I54F possibly damaging Het
Tnks A C 8: 35,301,757 (GRCm39) probably benign Het
Trim43a GATTTATTTATTTATTTATTTATTTATTTATTTATTTATT GATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 9: 88,465,042 (GRCm39) probably benign Het
Trpc6 A G 9: 8,680,538 (GRCm39) E844G probably benign Het
Ubtd2 C T 11: 32,466,125 (GRCm39) R115W probably damaging Het
Ubxn6 T C 17: 56,376,042 (GRCm39) D373G probably benign Het
Upf1 T A 8: 70,794,174 (GRCm39) Q244L probably benign Het
Usp33 A G 3: 152,074,271 (GRCm39) I372M probably damaging Het
Usp34 A G 11: 23,301,629 (GRCm39) E351G probably damaging Het
Utrn A G 10: 12,554,318 (GRCm39) probably benign Het
Vmn1r78 A G 7: 11,886,508 (GRCm39) K40E possibly damaging Het
Vmn2r7 T A 3: 64,632,223 (GRCm39) M80L probably benign Het
Vps13a G T 19: 16,678,602 (GRCm39) Y1126* probably null Het
Wfdc11 T C 2: 164,506,366 (GRCm39) N60S probably benign Het
Wnk2 C T 13: 49,224,586 (GRCm39) D992N probably damaging Het
Zpbp2 C A 11: 98,444,670 (GRCm39) T66K probably 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
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'- ATTGGTAGCCCCACCAATCTCAGC -3'
(R):5'- GCCTGAGGACAATGCCAGATACAC -3'

Sequencing Primer
(F):5'- GCCAAGTGGAAAACTGTCTC -3'
(R):5'- AAGTTACCCTCCCTGTTGGAATTG -3'
Posted On 2014-03-14