Incidental Mutation 'IGL01022:Col9a3'
ID 53464
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Col9a3
Ensembl Gene ENSMUSG00000027570
Gene Name collagen, type IX, alpha 3
Synonyms
Accession Numbers
Essential gene? Probably non essential (E-score: 0.186) question?
Stock # IGL01022
Quality Score
Status
Chromosome 2
Chromosomal Location 180239895-180263985 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 180258227 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 549 (I549F)
Ref Sequence ENSEMBL: ENSMUSP00000128718 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000103059] [ENSMUST00000132527]
AlphaFold A2ACT7
Predicted Effect probably damaging
Transcript: ENSMUST00000103059
AA Change: I549F

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: I549F

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 damaging
Transcript: ENSMUST00000132527
AA Change: I549F

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: I549F

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: ENSMUST00000165224
Predicted Effect noncoding transcript
Transcript: ENSMUST00000165879
Coding Region Coverage
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, 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: 29 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts14 A G 10: 61,038,721 (GRCm39) S927P probably benign Het
Arfgef1 G T 1: 10,244,301 (GRCm39) F987L probably damaging Het
Asph A T 4: 9,601,344 (GRCm39) N191K possibly damaging Het
Bmpr1b A T 3: 141,577,099 (GRCm39) C71S probably damaging Het
Bod1l A T 5: 41,951,652 (GRCm39) S2920T probably damaging Het
Camta2 G A 11: 70,562,308 (GRCm39) R1030* probably null Het
Chd8 T C 14: 52,474,450 (GRCm39) T194A probably benign Het
Fstl4 A G 11: 53,077,568 (GRCm39) N775S probably benign Het
Gm10800 T A 2: 98,497,576 (GRCm39) probably benign Het
Gm5117 T A 8: 32,228,515 (GRCm39) noncoding transcript Het
Hap1 A G 11: 100,240,374 (GRCm39) L112P probably benign Het
Hcls1 C A 16: 36,771,488 (GRCm39) probably benign Het
Kmt2c A G 5: 25,507,699 (GRCm39) probably benign Het
Lct T A 1: 128,228,596 (GRCm39) I966L probably benign Het
Myo1h A T 5: 114,474,361 (GRCm39) I451F possibly damaging Het
Notch4 G A 17: 34,784,671 (GRCm39) C128Y probably damaging Het
Oca2 T A 7: 55,974,504 (GRCm39) N484K probably damaging Het
Or51f1e T G 7: 102,747,077 (GRCm39) L43R probably damaging Het
Or7a42 A T 10: 78,791,188 (GRCm39) I50F possibly damaging Het
Rprd2 T A 3: 95,671,066 (GRCm39) R1362* probably null Het
Sema3a C T 5: 13,523,433 (GRCm39) T134I probably damaging Het
Sfta2 C T 17: 35,961,336 (GRCm39) T74I possibly damaging Het
Slfn10-ps C T 11: 82,926,353 (GRCm39) noncoding transcript Het
Spag11a A T 8: 19,208,005 (GRCm39) Q15H probably damaging Het
Tbc1d22a G A 15: 86,185,756 (GRCm39) D282N probably damaging Het
Tmbim6 G A 15: 99,300,003 (GRCm39) V40M possibly damaging Het
Tmem259 A G 10: 79,819,808 (GRCm39) V22A probably damaging Het
Tnik T C 3: 28,679,377 (GRCm39) probably null Het
Unc13c T C 9: 73,424,610 (GRCm39) D2002G probably benign Het
Other mutations in Col9a3
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
R0477:Col9a3 UTSW 2 180,251,263 (GRCm39) splice site probably benign
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
Posted On 2013-06-28