Incidental Mutation 'R4595:Col9a2'
ID 344314
Institutional Source Beutler Lab
Gene Symbol Col9a2
Ensembl Gene ENSMUSG00000028626
Gene Name collagen, type IX, alpha 2
Synonyms Col9a-2
MMRRC Submission 041811-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4595 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 121039385-121055322 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 121045155 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Lysine to Asparagine at position 196 (K196N)
Ref Sequence ENSEMBL: ENSMUSP00000030372 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030372]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000030372
AA Change: K196N

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: K196N

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 noncoding transcript
Transcript: ENSMUST00000151987
Meta Mutation Damage Score 0.1445 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.2%
Validation Efficiency 94% (62/66)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik A T 12: 71,164,547 (GRCm38) E685V possibly damaging Het
2700049A03Rik G T 12: 71,164,546 (GRCm38) E685* probably null Het
4921536K21Rik A G 11: 3,890,052 (GRCm38) I115T probably benign Het
Acads A T 5: 115,113,064 (GRCm38) N120K probably damaging Het
Aco1 T A 4: 40,167,139 (GRCm38) C118S probably benign Het
Alpk2 T C 18: 65,289,748 (GRCm38) T1493A probably damaging Het
AU018091 A G 7: 3,158,428 (GRCm38) Y480H possibly damaging Het
Brd4 A T 17: 32,198,922 (GRCm38) I86N probably damaging Het
Ccdc180 A G 4: 45,945,023 (GRCm38) E1477G probably damaging Het
Ccne2 A G 4: 11,202,986 (GRCm38) N368S probably benign Het
Cenpp A T 13: 49,641,234 (GRCm38) F152L probably benign Het
Cfap46 T A 7: 139,652,404 (GRCm38) D881V possibly damaging Het
Chmp7 A G 14: 69,721,229 (GRCm38) V212A probably damaging Het
Copg2 T C 6: 30,749,450 (GRCm38) D814G probably damaging Het
Dcaf13 G A 15: 39,118,893 (GRCm38) G85R probably damaging Het
Dnah9 A G 11: 66,168,152 (GRCm38) S106P probably benign Het
Dpp8 A G 9: 65,075,803 (GRCm38) D739G probably damaging Het
Drd2 T A 9: 49,404,789 (GRCm38) M283K probably benign Het
Espl1 A G 15: 102,298,724 (GRCm38) T208A probably benign Het
Glul G A 1: 153,903,050 (GRCm38) G35D possibly damaging Het
Gm14412 T C 2: 177,315,212 (GRCm38) K297E unknown Het
Gm21976 A T 13: 98,305,810 (GRCm38) R120W probably damaging Het
Hipk3 T A 2: 104,441,277 (GRCm38) T437S probably benign Het
Kcnd3 C T 3: 105,658,766 (GRCm38) A421V probably damaging Het
Lipn T G 19: 34,081,350 (GRCm38) Y321D probably damaging Het
Lrwd1 A G 5: 136,123,956 (GRCm38) V484A probably benign Het
Madd T C 2: 91,167,664 (GRCm38) D673G possibly damaging Het
Marveld1 T A 19: 42,147,764 (GRCm38) L39Q probably damaging Het
Mfsd2b T C 12: 4,865,807 (GRCm38) T299A possibly damaging Het
Micu3 T C 8: 40,359,397 (GRCm38) probably benign Het
Mmp7 T C 9: 7,697,666 (GRCm38) V234A probably damaging Het
Nhsl1 T A 10: 18,527,609 (GRCm38) D1329E probably benign Het
Or4a15 C T 2: 89,363,325 (GRCm38) V35M probably damaging Het
Or4f14b T C 2: 111,944,652 (GRCm38) D268G possibly damaging Het
Or52a33 A G 7: 103,640,101 (GRCm38) F13S probably damaging Het
Pcdhb21 T A 18: 37,514,515 (GRCm38) D232E probably damaging Het
Pebp1 G T 5: 117,283,410 (GRCm38) D156E probably benign Het
Pik3cb A G 9: 99,055,406 (GRCm38) Y745H possibly damaging Het
Pld2 T C 11: 70,542,020 (GRCm38) L170P probably damaging Het
Ptch1 T C 13: 63,543,608 (GRCm38) D277G possibly damaging Het
Rab11fip1 A T 8: 27,154,575 (GRCm38) M394K probably damaging Het
Rhoq T C 17: 86,964,326 (GRCm38) Y57H probably benign Het
Setbp1 T C 18: 78,857,516 (GRCm38) I979V probably benign Het
Slc6a4 A G 11: 77,019,863 (GRCm38) I447V probably benign Het
Sos2 T C 12: 69,616,889 (GRCm38) K607R probably damaging Het
Stt3a T C 9: 36,735,512 (GRCm38) I602V probably damaging Het
Syne2 A T 12: 75,967,071 (GRCm38) Q3012L possibly damaging Het
Taf1b T A 12: 24,500,442 (GRCm38) F9I possibly damaging Het
Tex35 T A 1: 157,099,339 (GRCm38) Y195F probably benign Het
Tnc T C 4: 63,995,745 (GRCm38) T1277A probably damaging Het
Tnfsf15 G T 4: 63,729,943 (GRCm38) Y153* probably null Het
Trim5 C A 7: 104,265,432 (GRCm38) V477F probably damaging Het
Trp73 A G 4: 154,064,417 (GRCm38) I245T probably damaging Het
Zbtb16 C T 9: 48,832,080 (GRCm38) E311K possibly damaging Het
Zmynd19 A G 2: 24,958,988 (GRCm38) D165G probably damaging Het
Other mutations in Col9a2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01331:Col9a2 APN 4 121,045,192 (GRCm38) missense possibly damaging 0.95
IGL01978:Col9a2 APN 4 121,044,666 (GRCm38) missense unknown
IGL01995:Col9a2 APN 4 121,050,410 (GRCm38) critical splice donor site probably null
IGL02162:Col9a2 APN 4 121,054,334 (GRCm38) unclassified probably benign
IGL02931:Col9a2 APN 4 121,053,192 (GRCm38) missense probably benign 0.06
collision UTSW 4 121,049,716 (GRCm38) critical splice donor site probably null
gravity_wave UTSW 4 121,044,019 (GRCm38) critical splice donor site probably null
R0208:Col9a2 UTSW 4 121,052,288 (GRCm38) splice site probably benign
R0426:Col9a2 UTSW 4 121,044,660 (GRCm38) splice site probably benign
R0512:Col9a2 UTSW 4 121,054,307 (GRCm38) missense probably benign 0.22
R0973:Col9a2 UTSW 4 121,039,788 (GRCm38) critical splice donor site probably null
R1023:Col9a2 UTSW 4 121,044,010 (GRCm38) missense unknown
R1657:Col9a2 UTSW 4 121,040,974 (GRCm38) missense unknown
R1724:Col9a2 UTSW 4 121,053,902 (GRCm38) missense probably damaging 1.00
R2171:Col9a2 UTSW 4 121,045,001 (GRCm38) nonsense probably null
R2206:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2221:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2223:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2273:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2274:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2275:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2354:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2392:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2393:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R2394:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R3421:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R3426:Col9a2 UTSW 4 121,050,407 (GRCm38) missense possibly damaging 0.93
R3710:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R3821:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R3838:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R3839:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R4067:Col9a2 UTSW 4 121,052,389 (GRCm38) missense probably damaging 1.00
R4298:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R4299:Col9a2 UTSW 4 121,054,258 (GRCm38) missense probably damaging 0.98
R4942:Col9a2 UTSW 4 121,053,119 (GRCm38) missense possibly damaging 0.73
R5120:Col9a2 UTSW 4 121,039,772 (GRCm38) missense unknown
R5434:Col9a2 UTSW 4 121,040,965 (GRCm38) nonsense probably null
R6143:Col9a2 UTSW 4 121,053,863 (GRCm38) missense probably damaging 0.99
R7027:Col9a2 UTSW 4 121,044,019 (GRCm38) critical splice donor site probably null
R7056:Col9a2 UTSW 4 121,049,716 (GRCm38) critical splice donor site probably null
R7417:Col9a2 UTSW 4 121,054,292 (GRCm38) missense not run
R7571:Col9a2 UTSW 4 121,039,784 (GRCm38) missense unknown
R9120:Col9a2 UTSW 4 121,043,754 (GRCm38) splice site probably benign
R9341:Col9a2 UTSW 4 121,054,286 (GRCm38) missense probably benign 0.03
R9343:Col9a2 UTSW 4 121,054,286 (GRCm38) missense probably benign 0.03
R9389:Col9a2 UTSW 4 121,054,751 (GRCm38) missense probably benign 0.00
R9527:Col9a2 UTSW 4 121,042,331 (GRCm38) critical splice donor site probably null
R9620:Col9a2 UTSW 4 121,053,206 (GRCm38) critical splice donor site probably null
R9784:Col9a2 UTSW 4 121,041,029 (GRCm38) missense unknown
Z1176:Col9a2 UTSW 4 121,053,797 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ATTGCTCAGCTGGCCTTGAC -3'
(R):5'- AATAAGAGACCCAGTGGCCTC -3'

Sequencing Primer
(F):5'- ACCTCAAGGCCTTATAGGATTTTC -3'
(R):5'- TCCTGCCCCTCAGCACAG -3'
Posted On 2015-09-25