Incidental Mutation 'R3821:Col9a2'
ID 274906
Institutional Source Beutler Lab
Gene Symbol Col9a2
Ensembl Gene ENSMUSG00000028626
Gene Name collagen, type IX, alpha 2
Synonyms Col9a-2
MMRRC Submission 040883-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3821 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 120896763-120912522 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to G at 120911455 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glycine at position 599 (R599G)
Ref Sequence ENSEMBL: ENSMUSP00000030372 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030372] [ENSMUST00000058754]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000030372
AA Change: R599G

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: R599G

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
Pfam:Collagen 24 82 7.3e-12 PFAM
Pfam:Collagen 59 115 2.4e-10 PFAM
Pfam:Collagen 113 170 2e-8 PFAM
Pfam:Collagen 176 236 8.9e-11 PFAM
low complexity region 258 277 N/A INTRINSIC
low complexity region 288 315 N/A INTRINSIC
Pfam:Collagen 357 435 4.4e-8 PFAM
Pfam:Collagen 459 523 6.1e-11 PFAM
Pfam:Collagen 548 610 4.5e-11 PFAM
low complexity region 639 661 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000058754
SMART Domains Protein: ENSMUSP00000053900
Gene: ENSMUSG00000043207

DomainStartEndE-ValueType
Pfam:Peptidase_M48_N 41 225 2.5e-70 PFAM
Pfam:Peptidase_M48 228 473 5.5e-75 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140119
Meta Mutation Damage Score 0.3183 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 100% (67/67)
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. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aarsd1 T A 11: 101,301,971 (GRCm39) I332F probably damaging Het
Abcd2 C T 15: 91,058,908 (GRCm39) G512D probably damaging Het
Acp3 G T 9: 104,201,916 (GRCm39) Q76K probably damaging Het
Adamtsl3 G T 7: 82,255,687 (GRCm39) probably benign Het
Alox8 T A 11: 69,077,308 (GRCm39) I481F probably damaging Het
Anp32e A T 3: 95,842,181 (GRCm39) I100L probably benign Het
Arpin G A 7: 79,579,408 (GRCm39) R72C probably damaging Het
C6 A G 15: 4,819,066 (GRCm39) E466G probably benign Het
Ccdc13 C A 9: 121,660,085 (GRCm39) L76F probably damaging Het
Cd44 T C 2: 102,731,738 (GRCm39) probably null Het
Clgn A G 8: 84,147,106 (GRCm39) I353V probably null Het
Cnot6 A T 11: 49,579,999 (GRCm39) S98T probably benign Het
Cramp1 G A 17: 25,193,756 (GRCm39) T908I probably damaging Het
Dnah9 C A 11: 65,741,829 (GRCm39) probably null Het
Ehd3 A T 17: 74,134,390 (GRCm39) I250F probably benign Het
Eml2 T C 7: 18,936,911 (GRCm39) V555A possibly damaging Het
Erbb4 A G 1: 68,345,072 (GRCm39) S550P probably damaging Het
Fchsd1 A G 18: 38,102,510 (GRCm39) probably benign Het
Flad1 T A 3: 89,318,494 (GRCm39) I20F probably damaging Het
Frem2 A T 3: 53,559,836 (GRCm39) L1557Q probably damaging Het
Gbf1 T C 19: 46,253,246 (GRCm39) I506T probably damaging Het
Gm20730 C T 6: 43,058,656 (GRCm39) S52N probably benign Het
Hoxc9 A G 15: 102,890,596 (GRCm39) K171R probably benign Het
Hscb A T 5: 110,984,194 (GRCm39) D52E probably damaging Het
Htr1b A T 9: 81,514,487 (GRCm39) I40N probably benign Het
Ido2 T C 8: 25,023,771 (GRCm39) I356V probably benign Het
Insyn2b T C 11: 34,353,007 (GRCm39) S350P probably benign Het
Irs1 T C 1: 82,267,770 (GRCm39) T149A probably benign Het
Itgam A G 7: 127,711,458 (GRCm39) probably null Het
Itpr2 A T 6: 146,319,224 (GRCm39) H244Q probably damaging Het
Kcnma1 A G 14: 23,417,679 (GRCm39) I846T probably damaging Het
Kdm3a A T 6: 71,588,661 (GRCm39) D449E probably benign Het
Lama1 C A 17: 68,086,041 (GRCm39) probably null Het
Lhfpl4 A G 6: 113,171,069 (GRCm39) V39A probably benign Het
Marf1 A T 16: 13,960,418 (GRCm39) L542Q probably damaging Het
Mns1 A G 9: 72,346,730 (GRCm39) E71G probably damaging Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Mrpl19 C A 6: 81,938,987 (GRCm39) E272* probably null Het
Ncoa6 T A 2: 155,248,858 (GRCm39) N1482I probably damaging Het
Neto2 C A 8: 86,389,924 (GRCm39) E180* probably null Het
Or2a51 A G 6: 43,178,604 (GRCm39) T9A probably benign Het
Pcdhga10 A G 18: 37,880,995 (GRCm39) N252S probably damaging Het
Pcdhgb7 C A 18: 37,885,286 (GRCm39) T152K possibly damaging Het
Ptprb G T 10: 116,185,979 (GRCm39) R1678L probably benign Het
Ptprg A T 14: 12,226,375 (GRCm38) I1323L probably benign Het
Rab40b T A 11: 121,248,874 (GRCm39) N127I probably damaging Het
Scn10a A G 9: 119,467,699 (GRCm39) C814R probably benign Het
Sdhb C T 4: 140,706,399 (GRCm39) R279* probably null Het
Shroom4 C T X: 6,536,276 (GRCm39) Q1165* probably null Het
Slc17a4 C T 13: 24,085,752 (GRCm39) R387H probably benign Het
Slc20a2 A G 8: 23,028,918 (GRCm39) I130V probably benign Het
Slitrk3 T C 3: 72,956,549 (GRCm39) Y741C possibly damaging Het
Tas1r1 G T 4: 152,119,138 (GRCm39) L144I probably benign Het
Tenm2 A T 11: 35,915,147 (GRCm39) I2129N probably damaging Het
Tmbim1 A G 1: 74,333,089 (GRCm39) V92A probably damaging Het
Tmem131 T A 1: 36,847,477 (GRCm39) H1207L probably damaging Het
Tmem209 G T 6: 30,505,959 (GRCm39) P116T probably damaging Het
Tmem8b C A 4: 43,689,745 (GRCm39) H800N probably damaging Het
Tnfsf8 A G 4: 63,779,127 (GRCm39) V57A probably benign Het
Topaz1 A G 9: 122,626,848 (GRCm39) D1492G possibly damaging Het
Trank1 G A 9: 111,207,887 (GRCm39) G1711R probably damaging Het
Trpc6 A T 9: 8,610,279 (GRCm39) D249V probably damaging Het
Ubr3 G A 2: 69,824,157 (GRCm39) probably null Het
Ufc1 A G 1: 171,117,172 (GRCm39) probably benign Het
Unc5cl T C 17: 48,767,001 (GRCm39) L125P possibly damaging Het
Usb1 G A 8: 96,060,061 (GRCm39) S57N probably benign Het
Wdfy1 A G 1: 79,684,017 (GRCm39) S373P probably benign Het
Zfp618 G A 4: 63,051,801 (GRCm39) A861T probably benign Het
Zfp831 T C 2: 174,485,816 (GRCm39) S164P possibly damaging Het
Other mutations in Col9a2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01331:Col9a2 APN 4 120,902,389 (GRCm39) missense possibly damaging 0.95
IGL01978:Col9a2 APN 4 120,901,863 (GRCm39) missense unknown
IGL01995:Col9a2 APN 4 120,907,607 (GRCm39) critical splice donor site probably null
IGL02162:Col9a2 APN 4 120,911,531 (GRCm39) unclassified probably benign
IGL02931:Col9a2 APN 4 120,910,389 (GRCm39) missense probably benign 0.06
collision UTSW 4 120,906,913 (GRCm39) critical splice donor site probably null
gravity_wave UTSW 4 120,901,216 (GRCm39) critical splice donor site probably null
R0208:Col9a2 UTSW 4 120,909,485 (GRCm39) splice site probably benign
R0426:Col9a2 UTSW 4 120,901,857 (GRCm39) splice site probably benign
R0512:Col9a2 UTSW 4 120,911,504 (GRCm39) missense probably benign 0.22
R0973:Col9a2 UTSW 4 120,896,985 (GRCm39) critical splice donor site probably null
R1023:Col9a2 UTSW 4 120,901,207 (GRCm39) missense unknown
R1657:Col9a2 UTSW 4 120,898,171 (GRCm39) missense unknown
R1724:Col9a2 UTSW 4 120,911,099 (GRCm39) missense probably damaging 1.00
R2171:Col9a2 UTSW 4 120,902,198 (GRCm39) nonsense probably null
R2206:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2221:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2223:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2273:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2274:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2275:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2354:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2392:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2393:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R2394:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R3421:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R3426:Col9a2 UTSW 4 120,907,604 (GRCm39) missense possibly damaging 0.93
R3710:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R3838:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R3839:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R4067:Col9a2 UTSW 4 120,909,586 (GRCm39) missense probably damaging 1.00
R4298:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R4299:Col9a2 UTSW 4 120,911,455 (GRCm39) missense probably damaging 0.98
R4595:Col9a2 UTSW 4 120,902,352 (GRCm39) missense probably benign 0.04
R4942:Col9a2 UTSW 4 120,910,316 (GRCm39) missense possibly damaging 0.73
R5120:Col9a2 UTSW 4 120,896,969 (GRCm39) missense unknown
R5434:Col9a2 UTSW 4 120,898,162 (GRCm39) nonsense probably null
R6143:Col9a2 UTSW 4 120,911,060 (GRCm39) missense probably damaging 0.99
R7027:Col9a2 UTSW 4 120,901,216 (GRCm39) critical splice donor site probably null
R7056:Col9a2 UTSW 4 120,906,913 (GRCm39) critical splice donor site probably null
R7417:Col9a2 UTSW 4 120,911,489 (GRCm39) missense not run
R7571:Col9a2 UTSW 4 120,896,981 (GRCm39) missense unknown
R9120:Col9a2 UTSW 4 120,900,951 (GRCm39) splice site probably benign
R9341:Col9a2 UTSW 4 120,911,483 (GRCm39) missense probably benign 0.03
R9343:Col9a2 UTSW 4 120,911,483 (GRCm39) missense probably benign 0.03
R9389:Col9a2 UTSW 4 120,911,948 (GRCm39) missense probably benign 0.00
R9527:Col9a2 UTSW 4 120,899,528 (GRCm39) critical splice donor site probably null
R9620:Col9a2 UTSW 4 120,910,403 (GRCm39) critical splice donor site probably null
R9784:Col9a2 UTSW 4 120,898,226 (GRCm39) missense unknown
Z1176:Col9a2 UTSW 4 120,910,994 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGAACCTCCCAAATCTTATCTGGATC -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'

Sequencing Primer
(F):5'- ATCTGGATCTCCCTTTATCTAACCAG -3'
(R):5'- AGAGACACCTCCAGCTTGG -3'
Posted On 2015-04-02