Incidental Mutation 'R5411:Col10a1'
ID 427488
Institutional Source Beutler Lab
Gene Symbol Col10a1
Ensembl Gene ENSMUSG00000039462
Gene Name collagen, type X, alpha 1
Synonyms Col10, Col10a-1
MMRRC Submission 042980-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.121) question?
Stock # R5411 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 34265977-34273081 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 34270553 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 175 (E175G)
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

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

DomainStartEndE-ValueType
Pfam:5_nucleotid 1 189 8.8e-25 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000105511
AA Change: E175G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: E175G

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.2%
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acat1 C A 9: 53,493,946 (GRCm39) V392F probably damaging Het
Ache C T 5: 137,288,326 (GRCm39) P11S possibly damaging Het
Ache T A 5: 137,288,692 (GRCm39) probably null Het
Acoxl A T 2: 127,696,821 (GRCm39) H23L probably benign Het
Adamtsl1 G A 4: 86,306,650 (GRCm39) probably null Het
Adar T A 3: 89,646,519 (GRCm39) F45I probably benign Het
Adgrf4 A C 17: 42,978,104 (GRCm39) L413R probably damaging Het
Atp6v1g3 A T 1: 138,215,627 (GRCm39) I96F probably benign Het
Brsk2 T C 7: 141,554,594 (GRCm39) M653T probably benign Het
Cacna1s G T 1: 136,033,549 (GRCm39) V1275L probably benign Het
Ces3b T C 8: 105,815,264 (GRCm39) V5A possibly damaging Het
Chpt1 A T 10: 88,312,969 (GRCm39) I281N probably damaging Het
Col27a1 T C 4: 63,142,902 (GRCm39) S197P probably damaging Het
Csmd1 T A 8: 15,960,471 (GRCm39) R3315W probably damaging Het
Ctnna2 T C 6: 77,091,914 (GRCm39) E443G probably damaging Het
Dhx9 G T 1: 153,356,969 (GRCm39) S93R probably benign Het
Efcab8 A G 2: 153,625,676 (GRCm39) H112R probably damaging Het
Eif3d A T 15: 77,843,887 (GRCm39) N486K probably damaging Het
Esp8 C T 17: 40,840,909 (GRCm39) R57* probably null Het
Eya3 A T 4: 132,417,090 (GRCm39) I130F probably damaging Het
Fat2 G T 11: 55,143,052 (GRCm39) L4266I probably benign Het
Fras1 T A 5: 96,793,019 (GRCm39) D983E probably benign Het
Gcc2 T C 10: 58,106,791 (GRCm39) S640P probably damaging Het
Gys2 C T 6: 142,394,147 (GRCm39) G464R probably damaging Het
Heatr5a G A 12: 51,935,026 (GRCm39) T1659I probably damaging Het
Il17ra A G 6: 120,458,403 (GRCm39) D518G probably damaging Het
Kcnk13 A G 12: 100,027,510 (GRCm39) Y195C probably damaging Het
Kmt2a T A 9: 44,759,782 (GRCm39) H722L probably damaging Het
Luzp1 C A 4: 136,270,653 (GRCm39) Q959K possibly damaging Het
Mep1b T A 18: 21,219,306 (GRCm39) H153Q probably damaging Het
Mfsd13b A T 7: 120,599,346 (GRCm39) I381F probably benign Het
Mvk A G 5: 114,597,034 (GRCm39) T334A probably benign Het
Naa30 T C 14: 49,425,008 (GRCm39) V320A probably damaging Het
Naip5 C T 13: 100,382,254 (GRCm39) G152S possibly damaging Het
Neb A C 2: 52,185,384 (GRCm39) S949R probably damaging Het
Nfya A T 17: 48,699,046 (GRCm39) I214N possibly damaging Het
Nsf G T 11: 103,773,637 (GRCm39) N292K probably damaging Het
Nup133 T C 8: 124,653,945 (GRCm39) T505A probably benign Het
Or4c1 A C 2: 89,133,920 (GRCm39) S5R probably benign Het
Or4p7 A G 2: 88,221,605 (GRCm39) T5A probably benign Het
Or5h24 T A 16: 58,919,067 (GRCm39) H96L unknown Het
Or9s23 A T 1: 92,501,546 (GRCm39) T218S probably benign Het
P4ha3 A T 7: 99,943,022 (GRCm39) R136W probably damaging Het
Parp12 A G 6: 39,067,142 (GRCm39) V550A probably damaging Het
Phf11a T C 14: 59,532,387 (GRCm39) D16G probably benign Het
Pramel31 T A 4: 144,088,207 (GRCm39) M1K probably null Het
Rab3gap2 A G 1: 185,009,342 (GRCm39) probably null Het
Sco1 A G 11: 66,954,784 (GRCm39) D263G probably damaging Het
Sfi1 A ATCTTCCCAAAGCCAGTGC 11: 3,103,384 (GRCm39) probably benign Homo
Sfpq T A 4: 126,915,516 (GRCm39) S103T unknown Het
Shisa7 G A 7: 4,832,975 (GRCm39) R263C probably damaging Het
Ssc4d T A 5: 135,992,254 (GRCm39) D144V probably benign Het
Stxbp5l G A 16: 36,950,213 (GRCm39) P1044L probably damaging Het
Tgm6 G A 2: 129,987,116 (GRCm39) R528Q probably benign Het
Tlr3 A T 8: 45,849,992 (GRCm39) H892Q probably benign Het
Tmc2 A G 2: 130,082,035 (GRCm39) H406R probably damaging Het
Tmtc1 A T 6: 148,345,397 (GRCm39) probably null Het
Ttc19 A G 11: 62,174,977 (GRCm39) I139M probably benign Het
Utrn G A 10: 12,524,929 (GRCm39) R2185C probably benign Het
Wdfy4 T C 14: 32,681,959 (GRCm39) N3004S probably damaging Het
Wdr3 C A 3: 100,050,300 (GRCm39) G746W probably damaging Het
Zfp335 T A 2: 164,744,165 (GRCm39) Q500L probably damaging Het
Zfp804b A T 5: 6,820,071 (GRCm39) D961E probably benign Het
Zkscan16 CTTCAGCTTTCA CTTCA 4: 58,956,745 (GRCm39) probably null Het
Other mutations in Col10a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03005:Col10a1 APN 10 34,271,734 (GRCm39) missense probably damaging 1.00
IGL03028:Col10a1 APN 10 34,271,012 (GRCm39) missense probably benign 0.19
R0580:Col10a1 UTSW 10 34,270,948 (GRCm39) missense probably benign 0.31
R0691:Col10a1 UTSW 10 34,271,692 (GRCm39) missense possibly damaging 0.94
R1187:Col10a1 UTSW 10 34,270,834 (GRCm39) missense probably benign 0.13
R1597:Col10a1 UTSW 10 34,271,074 (GRCm39) missense probably damaging 0.99
R1724:Col10a1 UTSW 10 34,271,714 (GRCm39) missense probably damaging 1.00
R1826:Col10a1 UTSW 10 34,270,645 (GRCm39) missense probably damaging 1.00
R1834:Col10a1 UTSW 10 34,271,011 (GRCm39) missense probably damaging 1.00
R2156:Col10a1 UTSW 10 34,271,696 (GRCm39) missense probably benign 0.30
R3687:Col10a1 UTSW 10 34,271,494 (GRCm39) missense probably benign 0.12
R4208:Col10a1 UTSW 10 34,271,539 (GRCm39) missense probably damaging 0.99
R4929:Col10a1 UTSW 10 34,271,120 (GRCm39) missense probably benign 0.00
R5433:Col10a1 UTSW 10 34,266,735 (GRCm39) intron probably benign
R5481:Col10a1 UTSW 10 34,271,660 (GRCm39) missense probably benign 0.09
R6036:Col10a1 UTSW 10 34,271,278 (GRCm39) missense probably benign
R6036:Col10a1 UTSW 10 34,271,278 (GRCm39) missense probably benign
R6208:Col10a1 UTSW 10 34,270,582 (GRCm39) missense possibly damaging 0.69
R6223:Col10a1 UTSW 10 34,271,183 (GRCm39) missense probably damaging 1.00
R7019:Col10a1 UTSW 10 34,270,947 (GRCm39) missense probably damaging 0.96
R7642:Col10a1 UTSW 10 34,271,638 (GRCm39) missense probably benign 0.00
R7784:Col10a1 UTSW 10 34,270,214 (GRCm39) missense unknown
R8072:Col10a1 UTSW 10 34,266,663 (GRCm39) missense unknown
R8711:Col10a1 UTSW 10 34,270,824 (GRCm39) missense probably damaging 1.00
Z1176:Col10a1 UTSW 10 34,271,174 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACCAGGAATATCAGCCACGG -3'
(R):5'- GAAACCCCGGTCACCTTTGATG -3'

Sequencing Primer
(F):5'- ATATCAGCCACGGGGAAGCC -3'
(R):5'- ACCTTTGATGCCCGGCTG -3'
Posted On 2016-09-01