Incidental Mutation 'R7177:Col9a1'
ID 558655
Institutional Source Beutler Lab
Gene Symbol Col9a1
Ensembl Gene ENSMUSG00000026147
Gene Name collagen, type IX, alpha 1
Synonyms Col9a-1
MMRRC Submission 045268-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.092) question?
Stock # R7177 (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 24234498 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 13 (L13Q)
Ref Sequence ENSEMBL: ENSMUSP00000085687 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054588] [ENSMUST00000088349]
AlphaFold no structure available at present
Predicted Effect probably benign
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 unknown
Transcript: ENSMUST00000088349
AA Change: L13Q
SMART Domains Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147
AA Change: L13Q

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
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: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930550C14Rik T C 9: 53,325,685 (GRCm39) L74S probably damaging Het
5730409E04Rik A G 4: 126,505,525 (GRCm39) S18G probably benign Het
Adam29 A G 8: 56,325,659 (GRCm39) I265T probably benign Het
Aff4 C T 11: 53,297,466 (GRCm39) S896L probably benign Het
Ankrd27 T C 7: 35,318,822 (GRCm39) I571T probably damaging Het
Bdp1 C A 13: 100,186,478 (GRCm39) R1658I probably damaging Het
Carm1 C T 9: 21,458,323 (GRCm39) T7M unknown Het
Ccdc183 A G 2: 25,506,296 (GRCm39) V100A probably damaging Het
Cd86 CA CAA 16: 36,426,917 (GRCm39) probably null Het
Ceacam2 T G 7: 25,220,341 (GRCm39) D239A probably benign Het
Cfap96 T A 8: 46,423,444 (GRCm39) E89D possibly damaging Het
Cimap1c T A 9: 56,757,262 (GRCm39) M139L possibly damaging Het
Cmya5 T C 13: 93,231,836 (GRCm39) D1084G probably benign Het
Cog5 T A 12: 31,810,888 (GRCm39) I194K probably damaging Het
Col20a1 C T 2: 180,636,007 (GRCm39) Q211* probably null Het
Cracr2a A T 6: 127,585,669 (GRCm39) M156L probably benign Het
Cts8 C T 13: 61,399,505 (GRCm39) M151I possibly damaging Het
Cyp2ab1 A T 16: 20,135,469 (GRCm39) L11Q probably null Het
Dhrs13 T A 11: 77,925,208 (GRCm39) C160S probably benign Het
Enthd1 T A 15: 80,358,415 (GRCm39) E368D probably damaging Het
Fbh1 A G 2: 11,760,522 (GRCm39) I676T probably damaging Het
Fcgrt T C 7: 44,751,421 (GRCm39) R176G probably benign Het
Gatd1 A G 7: 140,990,947 (GRCm39) F67L possibly damaging Het
Gm4353 G A 7: 115,683,727 (GRCm39) P23S probably damaging Het
Gm6882 T A 7: 21,161,677 (GRCm39) I64F possibly damaging Het
Grwd1 A T 7: 45,480,204 (GRCm39) M1K probably null Het
Hook2 T A 8: 85,718,046 (GRCm39) S58T probably benign Het
Iqch T G 9: 63,329,117 (GRCm39) *1072C probably null Het
Kmt2d G A 15: 98,748,267 (GRCm39) T3019I unknown Het
Lmx1a T C 1: 167,674,247 (GRCm39) S356P probably benign Het
Lrig3 A G 10: 125,842,712 (GRCm39) M546V probably benign Het
Lrrc1 C A 9: 77,379,504 (GRCm39) E96* probably null Het
Lrtm2 C A 6: 119,294,113 (GRCm39) M339I probably damaging Het
Map10 T C 8: 126,398,584 (GRCm39) V659A probably benign Het
Map7d1 A G 4: 126,130,778 (GRCm39) C384R probably damaging Het
Mcur1 T C 13: 43,698,012 (GRCm39) D296G probably damaging Het
Mettl24 A T 10: 40,686,508 (GRCm39) H295L probably damaging Het
Mgat4f T C 1: 134,318,163 (GRCm39) S312P probably benign Het
Mpl A G 4: 118,305,741 (GRCm39) probably null Het
Mrps5 T C 2: 127,437,617 (GRCm39) V148A probably benign Het
N4bp2 T C 5: 65,964,891 (GRCm39) V980A probably damaging Het
Ncaph A T 2: 126,958,506 (GRCm39) D504E probably damaging Het
Nxph1 A G 6: 9,247,497 (GRCm39) N156S probably damaging Het
Or2t26 T A 11: 49,040,012 (GRCm39) C309* probably null Het
Or4f14b T A 2: 111,775,501 (GRCm39) Q100L probably damaging Het
Pafah1b3 T A 7: 24,994,657 (GRCm39) I186L probably benign Het
Papola C A 12: 105,775,790 (GRCm39) N235K possibly damaging Het
Pcnx3 A T 19: 5,737,527 (GRCm39) M98K probably benign Het
Pip4p1 A C 14: 51,167,634 (GRCm39) M104R possibly damaging Het
Pkhd1l1 A G 15: 44,330,800 (GRCm39) N125S probably damaging Het
Pls1 T A 9: 95,655,612 (GRCm39) H380L probably benign Het
Plxna1 T C 6: 89,300,311 (GRCm39) T1591A possibly damaging Het
Pparg T G 6: 115,418,581 (GRCm39) S147A probably benign Het
Prdm10 T C 9: 31,279,003 (GRCm39) S1025P probably benign Het
Prkcd T A 14: 30,321,664 (GRCm39) H510L probably damaging Het
Ptprh T A 7: 4,572,480 (GRCm39) E499D possibly damaging Het
Rad51ap1 A G 6: 126,901,983 (GRCm39) S256P probably benign Het
Rad54b A G 4: 11,599,755 (GRCm39) T320A probably damaging Het
Rnf207 A G 4: 152,396,634 (GRCm39) I459T probably benign Het
Runx2 G A 17: 45,125,079 (GRCm39) P80L probably damaging Het
Ryr3 A T 2: 112,731,188 (GRCm39) D727E probably damaging Het
Sdk2 C T 11: 113,720,795 (GRCm39) R1378H possibly damaging Het
Slc7a11 A G 3: 50,397,680 (GRCm39) S11P probably benign Het
Sox4 A G 13: 29,137,000 (GRCm39) V2A probably damaging Het
Srf A G 17: 46,866,318 (GRCm39) F146S probably damaging Het
Srrm2 T C 17: 24,035,747 (GRCm39) V797A unknown Het
Stk32c T C 7: 138,684,218 (GRCm39) D463G possibly damaging Het
Syne2 C A 12: 76,018,654 (GRCm39) Y3384* probably null Het
Tektl1 T C 10: 78,588,324 (GRCm39) D162G probably damaging Het
Traip T A 9: 107,838,184 (GRCm39) M139K possibly damaging Het
Trappc2l T A 8: 123,341,051 (GRCm39) F100Y probably damaging Het
Ush1c T C 7: 45,878,643 (GRCm39) D124G probably damaging Het
Uty A G Y: 1,099,691 (GRCm39) V1168A probably benign Het
Vmn2r25 T C 6: 123,816,882 (GRCm39) D233G possibly damaging Het
Zdbf2 C T 1: 63,334,120 (GRCm39) R31C 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
R6886:Col9a1 UTSW 1 24,224,426 (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'- AAGAAACCCAGGTCCCCTTG -3'
(R):5'- GGGTACTCTGACTTCTCACACC -3'

Sequencing Primer
(F):5'- TTGGCCAGGCACCTTTG -3'
(R):5'- GTACTCTGACTTCTCACACCCAGAAC -3'
Posted On 2019-06-26