Incidental Mutation 'R6036:Col10a1'
ID 479220
Institutional Source Beutler Lab
Gene Symbol Col10a1
Ensembl Gene ENSMUSG00000039462
Gene Name collagen, type X, alpha 1
Synonyms Col10a-1, Col10
MMRRC Submission 043257-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.125) question?
Stock # R6036 (G1)
Quality Score 176.009
Status Not validated
Chromosome 10
Chromosomal Location 34389981-34397085 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 34395282 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 417 (T417A)
Ref Sequence ENSEMBL: ENSMUSP00000101150 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047885] [ENSMUST00000099973] [ENSMUST00000105511] [ENSMUST00000105512] [ENSMUST00000213269]
AlphaFold Q05306
Predicted Effect probably benign
Transcript: ENSMUST00000047885
SMART Domains Protein: ENSMUSP00000047126
Gene: ENSMUSG00000039480

Pfam:5_nucleotid 1 382 2.6e-58 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000099973
SMART Domains Protein: ENSMUSP00000097553
Gene: ENSMUSG00000039480

Pfam:5_nucleotid 1 189 8.8e-25 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000105511
AA Change: T417A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: T417A

signal peptide 1 18 N/A INTRINSIC
low complexity region 60 101 N/A INTRINSIC
Pfam:Collagen 103 155 1.4e-9 PFAM
Pfam:Collagen 153 218 1.4e-8 PFAM
Pfam:Collagen 193 250 2.6e-9 PFAM
Pfam:Collagen 206 264 3.8e-8 PFAM
low complexity region 282 323 N/A INTRINSIC
internal_repeat_2 329 361 2.25e-6 PROSPERO
internal_repeat_1 331 365 5.9e-14 PROSPERO
low complexity region 368 383 N/A INTRINSIC
low complexity region 391 410 N/A INTRINSIC
Pfam:Collagen 413 483 9.3e-10 PFAM
low complexity region 487 517 N/A INTRINSIC
C1Q 545 680 2.85e-79 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000105512
SMART Domains Protein: ENSMUSP00000101151
Gene: ENSMUSG00000039480

Pfam:5_nucleotid 1 372 8.7e-54 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130290
Predicted Effect probably benign
Transcript: ENSMUST00000213269
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.0%
  • 10x: 92.6%
  • 20x: 72.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X collagen is a homotrimer. Mutations in this gene are associated with Schmid type metaphyseal chondrodysplasia (SMCD) and Japanese type spondylometaphyseal dysplasia (SMD). [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations may exhibit abnormal trabecular bone, thinner growth plate resting zone and articular cartilage, and altered bone content. Mice homozygous for another knock-out allele exhibit altered B and T cell populations and TH1/TH2responses. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi3 T C 11: 95,832,858 (GRCm38) probably benign Het
Ago1 C T 4: 126,443,228 (GRCm38) R228H probably damaging Het
Alpk3 G A 7: 81,093,257 (GRCm38) V941M probably benign Het
Ano4 A G 10: 88,982,265 (GRCm38) W588R possibly damaging Het
Atp6v1a A G 16: 44,098,831 (GRCm38) Y464H probably benign Het
Barx2 A T 9: 31,913,008 (GRCm38) D28E probably damaging Het
Cabp5 A T 7: 13,401,335 (GRCm38) M67L probably damaging Het
Dnah2 C T 11: 69,458,920 (GRCm38) R2399Q probably benign Het
Eif4enif1 T C 11: 3,239,420 (GRCm38) S227P probably damaging Het
Erv3 G A 2: 131,856,005 (GRCm38) H145Y possibly damaging Het
Exoc5 T C 14: 49,014,322 (GRCm38) T591A possibly damaging Het
F5 A T 1: 164,184,996 (GRCm38) E493V probably damaging Het
Gm8444 G T 15: 81,843,593 (GRCm38) probably benign Het
Gria4 T A 9: 4,537,646 (GRCm38) I221L probably benign Het
Hc T C 2: 35,039,684 (GRCm38) T249A probably benign Het
Herc2 A G 7: 56,068,053 (GRCm38) T48A probably benign Het
Hist1h2bl A T 13: 21,715,978 (GRCm38) S56T probably damaging Het
Hp A G 8: 109,576,774 (GRCm38) probably null Het
Ifna15 T G 4: 88,558,073 (GRCm38) D58A possibly damaging Het
Kcnj1 A T 9: 32,397,125 (GRCm38) M262L probably benign Het
Krt83 A C 15: 101,487,531 (GRCm38) I320S possibly damaging Het
Megf10 A G 18: 57,242,727 (GRCm38) N242D probably damaging Het
Nup155 A G 15: 8,128,411 (GRCm38) T451A probably benign Het
Olfr1277 C T 2: 111,269,612 (GRCm38) G252R probably damaging Het
Olfr1288 T C 2: 111,478,988 (GRCm38) L68P probably damaging Het
Olfr559 T A 7: 102,724,485 (GRCm38) I2F probably benign Het
Olfr701 A T 7: 106,818,460 (GRCm38) I126F probably damaging Het
Olfr930 A G 9: 38,930,920 (GRCm38) I250V probably damaging Het
Pdzd8 G A 19: 59,305,209 (GRCm38) P403S probably damaging Het
Piezo2 G A 18: 63,114,948 (GRCm38) Q494* probably null Het
Plag1 T C 4: 3,904,618 (GRCm38) E191G possibly damaging Het
Pou4f2 A T 8: 78,435,474 (GRCm38) S167T probably damaging Het
Scd4 G A 19: 44,344,792 (GRCm38) D319N probably damaging Het
Senp2 A T 16: 22,028,558 (GRCm38) R279* probably null Het
Sh3rf3 G A 10: 58,813,984 (GRCm38) G137D probably benign Het
Simc1 C T 13: 54,524,621 (GRCm38) P261S probably benign Het
Slc26a1 T A 5: 108,673,570 (GRCm38) D151V probably damaging Het
Snx29 A G 16: 11,738,437 (GRCm38) probably null Het
Stard9 C T 2: 120,700,075 (GRCm38) A2271V probably benign Het
Stat6 A G 10: 127,655,444 (GRCm38) N485D possibly damaging Het
Tpcn2 T C 7: 145,268,869 (GRCm38) T280A possibly damaging Het
Ttc23 A G 7: 67,711,366 (GRCm38) I378V possibly damaging Het
Ttc29 A G 8: 78,325,576 (GRCm38) D362G probably benign Het
Ttll7 A G 3: 146,940,162 (GRCm38) I592V probably benign Het
Ugt3a1 A T 15: 9,306,086 (GRCm38) H107L probably benign Het
Vmn1r70 A G 7: 10,633,903 (GRCm38) Q87R probably damaging Het
Wdfy4 G T 14: 33,146,990 (GRCm38) S360R probably damaging Het
Zfp780b A G 7: 27,963,568 (GRCm38) Y521H probably damaging Het
Other mutations in Col10a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03005:Col10a1 APN 10 34,395,738 (GRCm38) missense probably damaging 1.00
IGL03028:Col10a1 APN 10 34,395,016 (GRCm38) missense probably benign 0.19
R0580:Col10a1 UTSW 10 34,394,952 (GRCm38) missense probably benign 0.31
R0691:Col10a1 UTSW 10 34,395,696 (GRCm38) missense possibly damaging 0.94
R1187:Col10a1 UTSW 10 34,394,838 (GRCm38) missense probably benign 0.13
R1597:Col10a1 UTSW 10 34,395,078 (GRCm38) missense probably damaging 0.99
R1724:Col10a1 UTSW 10 34,395,718 (GRCm38) missense probably damaging 1.00
R1826:Col10a1 UTSW 10 34,394,649 (GRCm38) missense probably damaging 1.00
R1834:Col10a1 UTSW 10 34,395,015 (GRCm38) missense probably damaging 1.00
R2156:Col10a1 UTSW 10 34,395,700 (GRCm38) missense probably benign 0.30
R3687:Col10a1 UTSW 10 34,395,498 (GRCm38) missense probably benign 0.12
R4208:Col10a1 UTSW 10 34,395,543 (GRCm38) missense probably damaging 0.99
R4929:Col10a1 UTSW 10 34,395,124 (GRCm38) missense probably benign 0.00
R5411:Col10a1 UTSW 10 34,394,557 (GRCm38) missense probably damaging 1.00
R5433:Col10a1 UTSW 10 34,390,739 (GRCm38) intron probably benign
R5481:Col10a1 UTSW 10 34,395,664 (GRCm38) missense probably benign 0.09
R6036:Col10a1 UTSW 10 34,395,282 (GRCm38) missense probably benign
R6208:Col10a1 UTSW 10 34,394,586 (GRCm38) missense possibly damaging 0.69
R6223:Col10a1 UTSW 10 34,395,187 (GRCm38) missense probably damaging 1.00
R7019:Col10a1 UTSW 10 34,394,951 (GRCm38) missense probably damaging 0.96
R7642:Col10a1 UTSW 10 34,395,642 (GRCm38) missense probably benign 0.00
R7784:Col10a1 UTSW 10 34,394,218 (GRCm38) missense unknown
R8072:Col10a1 UTSW 10 34,390,667 (GRCm38) missense unknown
R8711:Col10a1 UTSW 10 34,394,828 (GRCm38) missense probably damaging 1.00
Z1176:Col10a1 UTSW 10 34,395,178 (GRCm38) missense probably damaging 1.00
Predicted Primers
Posted On 2017-06-26