Incidental Mutation 'R0477:Col9a3'
ID 41839
Institutional Source Beutler Lab
Gene Symbol Col9a3
Ensembl Gene ENSMUSG00000027570
Gene Name collagen, type IX, alpha 3
Synonyms
MMRRC Submission 038677-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.186) question?
Stock # R0477 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 2
Chromosomal Location 180239895-180263985 bp(+) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to G at 180251263 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000128718 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000103059] [ENSMUST00000132527]
AlphaFold A2ACT7
Predicted Effect probably benign
Transcript: ENSMUST00000103059
SMART Domains Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570

DomainStartEndE-ValueType
Pfam:Collagen 21 80 7.7e-12 PFAM
Pfam:Collagen 58 114 4.2e-9 PFAM
low complexity region 126 162 N/A INTRINSIC
Pfam:Collagen 174 236 4.1e-12 PFAM
Pfam:Collagen 213 292 8e-9 PFAM
internal_repeat_1 315 366 1.58e-12 PROSPERO
internal_repeat_2 360 382 2.94e-6 PROSPERO
low complexity region 384 396 N/A INTRINSIC
Pfam:Collagen 456 518 1.8e-11 PFAM
Pfam:Collagen 545 606 3.8e-11 PFAM
low complexity region 635 656 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129090
Predicted Effect probably benign
Transcript: ENSMUST00000132527
SMART Domains Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570

DomainStartEndE-ValueType
Pfam:Collagen 21 80 7.9e-12 PFAM
Pfam:Collagen 58 114 4.3e-9 PFAM
Pfam:Collagen 109 166 4.5e-8 PFAM
Pfam:Collagen 174 236 4.2e-12 PFAM
Pfam:Collagen 213 292 8.2e-9 PFAM
internal_repeat_1 315 366 1.58e-12 PROSPERO
internal_repeat_2 360 382 2.94e-6 PROSPERO
low complexity region 384 396 N/A INTRINSIC
Pfam:Collagen 402 474 8.2e-8 PFAM
Pfam:Collagen 456 518 1.8e-11 PFAM
Pfam:Collagen 545 606 3.9e-11 PFAM
Pfam:Collagen 603 662 2.5e-8 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141056
Predicted Effect noncoding transcript
Transcript: ENSMUST00000165879
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.4%
  • 20x: 93.1%
Validation Efficiency 98% (57/58)
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, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
6030468B19Rik A T 11: 117,693,787 (GRCm39) I85F probably benign Het
Abca8a T A 11: 109,956,051 (GRCm39) I778L probably benign Het
Abcc5 T C 16: 20,187,319 (GRCm39) N889S possibly damaging Het
Abcc5 T C 16: 20,217,635 (GRCm39) N359D probably damaging Het
Adam23 A G 1: 63,596,559 (GRCm39) probably benign Het
Adamts3 A T 5: 89,832,366 (GRCm39) D913E probably benign Het
Ap1b1 G T 11: 4,981,787 (GRCm39) C538F probably benign Het
Ash1l T A 3: 88,890,766 (GRCm39) S882T probably benign Het
C9 A T 15: 6,487,664 (GRCm39) E43D probably benign Het
Cacna2d1 T C 5: 16,399,796 (GRCm39) probably null Het
Ces2a A G 8: 105,464,169 (GRCm39) E267G probably damaging Het
Cfap61 A G 2: 145,781,836 (GRCm39) D23G probably damaging Het
Cstl1 T C 2: 148,592,908 (GRCm39) V21A probably benign Het
Cth A T 3: 157,610,812 (GRCm39) L340Q probably damaging Het
Dnah8 T A 17: 30,974,054 (GRCm39) M2813K probably damaging Het
Fam107a A T 14: 8,301,168 (GRCm38) Y21N probably benign Het
Fam184a G A 10: 53,531,175 (GRCm39) T733M probably damaging Het
Fer1l4 A G 2: 155,894,806 (GRCm39) V21A probably benign Het
Foxc2 A T 8: 121,844,774 (GRCm39) Y474F probably damaging Het
Hnf4g G T 3: 3,716,851 (GRCm39) probably benign Het
Hnrnpll T C 17: 80,369,261 (GRCm39) D54G unknown Het
Hydin A G 8: 111,145,130 (GRCm39) Y827C probably damaging Het
Il23r A G 6: 67,429,361 (GRCm39) V327A probably benign Het
Itih4 T A 14: 30,611,631 (GRCm39) V118D probably damaging Het
Kmt2d G A 15: 98,751,462 (GRCm39) probably benign Het
Lamb1 A G 12: 31,376,268 (GRCm39) D1546G possibly damaging Het
Large1 A T 8: 73,544,710 (GRCm39) D689E probably damaging Het
Map1a T C 2: 121,132,582 (GRCm39) S895P probably damaging Het
Mdn1 A C 4: 32,750,928 (GRCm39) E4487A probably benign Het
Myo15a T C 11: 60,411,740 (GRCm39) probably null Het
Nlrp4f C A 13: 65,338,720 (GRCm39) R639L probably benign Het
Or4f52 A G 2: 111,062,009 (GRCm39) F43S probably benign Het
Or8h10 T A 2: 86,808,567 (GRCm39) D191V probably damaging Het
Pcdh9 T C 14: 94,125,114 (GRCm39) N229S probably damaging Het
Pcnx2 A G 8: 126,488,306 (GRCm39) V1746A probably damaging Het
Phf12 A T 11: 77,913,896 (GRCm39) H446L possibly damaging Het
Phlpp2 A G 8: 110,622,138 (GRCm39) probably null Het
Psmb9 A C 17: 34,401,238 (GRCm39) V207G probably damaging Het
Ptprh C A 7: 4,600,997 (GRCm39) D127Y possibly damaging Het
Rabep1 T G 11: 70,811,733 (GRCm39) M535R probably damaging Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Scin T C 12: 40,110,515 (GRCm39) D711G probably damaging Het
Slfn4 T C 11: 83,079,507 (GRCm39) I6T probably benign Het
Sos1 T A 17: 80,742,363 (GRCm39) E388V possibly damaging Het
Spag5 A C 11: 78,205,024 (GRCm39) Q603P probably damaging Het
Supv3l1 G T 10: 62,266,364 (GRCm39) T604N probably damaging Het
Tbx5 A G 5: 120,021,184 (GRCm39) S397G possibly damaging Het
Tmprss5 A G 9: 49,026,465 (GRCm39) D383G possibly damaging Het
Trim43b A G 9: 88,972,654 (GRCm39) W167R probably damaging Het
Unc80 A T 1: 66,609,160 (GRCm39) D1283V probably damaging Het
Upf1 A T 8: 70,786,730 (GRCm39) V918D probably benign Het
Vmn2r100 A G 17: 19,742,776 (GRCm39) I383M probably benign Het
Zc3h3 G T 15: 75,648,932 (GRCm39) S733R possibly damaging Het
Zcchc2 C T 1: 105,958,000 (GRCm39) P426S possibly damaging Het
Zkscan7 A G 9: 122,719,874 (GRCm39) probably null Het
Other mutations in Col9a3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01022:Col9a3 APN 2 180,258,227 (GRCm39) missense probably damaging 0.96
IGL01542:Col9a3 APN 2 180,251,109 (GRCm39) splice site probably benign
IGL01727:Col9a3 APN 2 180,258,358 (GRCm39) critical splice donor site probably null
IGL02558:Col9a3 APN 2 180,248,599 (GRCm39) critical splice acceptor site probably null
IGL03112:Col9a3 APN 2 180,249,435 (GRCm39) missense possibly damaging 0.60
IGL02796:Col9a3 UTSW 2 180,255,955 (GRCm39) missense probably damaging 1.00
R0022:Col9a3 UTSW 2 180,261,549 (GRCm39) missense probably damaging 1.00
R0022:Col9a3 UTSW 2 180,261,549 (GRCm39) missense probably damaging 1.00
R0046:Col9a3 UTSW 2 180,251,280 (GRCm39) missense possibly damaging 0.47
R0046:Col9a3 UTSW 2 180,251,280 (GRCm39) missense possibly damaging 0.47
R0890:Col9a3 UTSW 2 180,251,856 (GRCm39) missense probably benign 0.23
R1934:Col9a3 UTSW 2 180,248,927 (GRCm39) missense probably damaging 0.98
R4355:Col9a3 UTSW 2 180,248,271 (GRCm39) missense probably benign 0.00
R4571:Col9a3 UTSW 2 180,258,159 (GRCm39) splice site probably benign
R4688:Col9a3 UTSW 2 180,249,424 (GRCm39) missense probably damaging 0.99
R4731:Col9a3 UTSW 2 180,252,474 (GRCm39) missense probably damaging 0.99
R4742:Col9a3 UTSW 2 180,245,180 (GRCm39) missense unknown
R4847:Col9a3 UTSW 2 180,257,318 (GRCm39) missense probably damaging 1.00
R4985:Col9a3 UTSW 2 180,245,193 (GRCm39) missense unknown
R5488:Col9a3 UTSW 2 180,258,318 (GRCm39) missense probably damaging 1.00
R5489:Col9a3 UTSW 2 180,258,318 (GRCm39) missense probably damaging 1.00
R5573:Col9a3 UTSW 2 180,261,525 (GRCm39) missense probably benign 0.17
R5575:Col9a3 UTSW 2 180,240,639 (GRCm39) intron probably benign
R6820:Col9a3 UTSW 2 180,248,927 (GRCm39) missense probably damaging 0.98
R7114:Col9a3 UTSW 2 180,245,590 (GRCm39) missense unknown
R7710:Col9a3 UTSW 2 180,251,158 (GRCm39) missense probably damaging 0.98
R8177:Col9a3 UTSW 2 180,249,450 (GRCm39) missense probably damaging 0.97
R8342:Col9a3 UTSW 2 180,245,183 (GRCm39) missense unknown
R8472:Col9a3 UTSW 2 180,247,057 (GRCm39) missense probably damaging 1.00
R8783:Col9a3 UTSW 2 180,255,970 (GRCm39) missense probably damaging 0.98
R9683:Col9a3 UTSW 2 180,248,322 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- ACCTGACTCCTGAGAAGAAAGGGTG -3'
(R):5'- GGTAAAGTCTCCTCAGCCTGATGC -3'

Sequencing Primer
(F):5'- ATCTCTGACAGTGGCACATAG -3'
(R):5'- CTCCCAGGAAATGTTCTCAGG -3'
Posted On 2013-05-23