Incidental Mutation 'R1957:Col27a1'
ID 217893
Institutional Source Beutler Lab
Gene Symbol Col27a1
Ensembl Gene ENSMUSG00000045672
Gene Name collagen, type XXVII, alpha 1
Synonyms 5730512J02Rik
MMRRC Submission 039971-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1957 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 63132246-63253228 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 63196031 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 879 (A879S)
Ref Sequence ENSEMBL: ENSMUSP00000043816 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000036300] [ENSMUST00000183913] [ENSMUST00000184067]
AlphaFold Q5QNQ9
Predicted Effect probably benign
Transcript: ENSMUST00000036300
AA Change: A879S

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000043816
Gene: ENSMUSG00000045672
AA Change: A879S

DomainStartEndE-ValueType
signal peptide 1 39 N/A INTRINSIC
TSPN 43 223 1.1e-5 SMART
low complexity region 325 343 N/A INTRINSIC
low complexity region 356 372 N/A INTRINSIC
low complexity region 428 443 N/A INTRINSIC
low complexity region 455 467 N/A INTRINSIC
low complexity region 584 597 N/A INTRINSIC
Pfam:Collagen 609 670 2.1e-10 PFAM
Pfam:Collagen 666 731 3.7e-10 PFAM
low complexity region 790 808 N/A INTRINSIC
low complexity region 817 838 N/A INTRINSIC
low complexity region 858 880 N/A INTRINSIC
low complexity region 886 910 N/A INTRINSIC
low complexity region 912 946 N/A INTRINSIC
Pfam:Collagen 1012 1080 2.8e-8 PFAM
Pfam:Collagen 1033 1103 3e-9 PFAM
Pfam:Collagen 1063 1130 3.4e-9 PFAM
low complexity region 1150 1168 N/A INTRINSIC
Pfam:Collagen 1207 1281 5.5e-9 PFAM
Pfam:Collagen 1261 1324 8.4e-10 PFAM
Pfam:Collagen 1323 1384 3.8e-12 PFAM
low complexity region 1438 1466 N/A INTRINSIC
internal_repeat_4 1467 1502 1.5e-7 PROSPERO
internal_repeat_2 1468 1529 1.96e-8 PROSPERO
Pfam:Collagen 1544 1606 2.4e-9 PFAM
COLFI 1644 1845 1.28e-40 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125504
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148751
Predicted Effect probably benign
Transcript: ENSMUST00000183913
SMART Domains Protein: ENSMUSP00000139182
Gene: ENSMUSG00000045672

DomainStartEndE-ValueType
Pfam:Collagen 1 60 2.7e-12 PFAM
Pfam:Collagen 34 114 6.6e-8 PFAM
Pfam:Collagen 87 163 3.6e-9 PFAM
low complexity region 175 202 N/A INTRINSIC
low complexity region 214 232 N/A INTRINSIC
Pfam:Collagen 271 338 9.1e-11 PFAM
Pfam:Collagen 328 388 5.4e-11 PFAM
Pfam:Collagen 387 442 4.5e-10 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000184067
AA Change: A264S
SMART Domains Protein: ENSMUSP00000139173
Gene: ENSMUSG00000045672
AA Change: A264S

DomainStartEndE-ValueType
Pfam:Collagen 23 87 2.1e-8 PFAM
Pfam:Collagen 57 145 8.3e-8 PFAM
Pfam:Collagen 115 200 9.9e-8 PFAM
low complexity region 202 223 N/A INTRINSIC
low complexity region 243 265 N/A INTRINSIC
low complexity region 271 295 N/A INTRINSIC
low complexity region 297 331 N/A INTRINSIC
internal_repeat_1 337 442 5.17e-20 PROSPERO
Pfam:Collagen 448 515 1.5e-9 PFAM
Pfam:Collagen 478 543 2e-10 PFAM
Pfam:Collagen 502 566 2.5e-9 PFAM
Pfam:Collagen 532 617 4.4e-7 PFAM
Pfam:Collagen 594 660 8.2e-11 PFAM
Pfam:Collagen 649 709 1.4e-10 PFAM
Pfam:Collagen 708 769 2e-12 PFAM
Pfam:Collagen 752 829 5e-8 PFAM
Pfam:Collagen 878 939 2.2e-9 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.4%
Validation Efficiency 97% (117/121)
MGI Phenotype FUNCTION: This gene encodes the alpha-1 subunit of type XXVII collagen, one of the low abundance fibril-forming collagens found in cartilage. The encoded protein forms a homotrimeric triple helical procollagen that undergoes proteolytic processing during fibril formation. Transgenic mice lacking a portion of the collagenous domain in the encoded protein exhibit skeletal abnormalities, chondrodysplasia and die at birth because of a lung defect. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mice homozygous for an in frame deletion display neonatal lethality, respiratory failure, and severe chondrodysplasia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 114 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aaas C T 15: 102,247,068 (GRCm39) probably benign Het
Aadacl4fm5 G A 4: 144,504,389 (GRCm39) T254I possibly damaging Het
Abce1 A G 8: 80,412,578 (GRCm39) I583T probably benign Het
Abtb3 T C 10: 85,469,563 (GRCm39) L828P probably damaging Het
Adcy1 A T 11: 7,111,945 (GRCm39) T937S probably benign Het
Adgra2 A G 8: 27,601,196 (GRCm39) I279V possibly damaging Het
Adgrl4 A T 3: 151,216,416 (GRCm39) N533I possibly damaging Het
Adipor1 T C 1: 134,350,771 (GRCm39) S7P probably benign Het
Amelx A T X: 167,965,153 (GRCm39) probably null Het
Anks1b A T 10: 89,885,792 (GRCm39) T163S probably damaging Het
Apc A G 18: 34,450,388 (GRCm39) E2394G probably damaging Het
Arhgef39 C T 4: 43,499,309 (GRCm39) G56E probably damaging Het
Arnt C T 3: 95,355,704 (GRCm39) S16L possibly damaging Het
Arsj A G 3: 126,232,670 (GRCm39) N472S probably benign Het
Atg2b T C 12: 105,635,677 (GRCm39) Y197C probably damaging Het
B3gat1 A T 9: 26,667,248 (GRCm39) D160V possibly damaging Het
Bmp7 T C 2: 172,781,714 (GRCm39) E50G probably damaging Het
Bms1 T C 6: 118,369,939 (GRCm39) E869G probably damaging Het
Brd4 G A 17: 32,440,340 (GRCm39) P332L possibly damaging Het
C130074G19Rik T C 1: 184,615,095 (GRCm39) T32A probably benign Het
C1rl A T 6: 124,486,021 (GRCm39) Y464F probably damaging Het
Ccdc150 T A 1: 54,303,068 (GRCm39) M193K probably benign Het
Ccdc7a A G 8: 129,706,616 (GRCm39) S338P probably damaging Het
Cenpu T C 8: 47,025,872 (GRCm39) probably benign Het
Cep170 A C 1: 176,597,013 (GRCm39) V448G probably benign Het
Crtac1 C T 19: 42,276,383 (GRCm39) S515N possibly damaging Het
Cstad G A 2: 30,498,293 (GRCm39) V43M unknown Het
Daam1 T C 12: 72,029,529 (GRCm39) probably null Het
Dnmt1 C T 9: 20,838,442 (GRCm39) R207H probably benign Het
Dsg3 A G 18: 20,655,162 (GRCm39) N153S probably damaging Het
Dzip3 C A 16: 48,747,956 (GRCm39) L1151F probably damaging Het
Eml5 A T 12: 98,826,220 (GRCm39) H644Q probably damaging Het
Emsy A G 7: 98,297,027 (GRCm39) L52P probably damaging Het
Eno1 T A 4: 150,331,232 (GRCm39) probably null Het
Epha3 T A 16: 63,593,315 (GRCm39) T258S probably benign Het
Ern1 T C 11: 106,317,723 (GRCm39) T134A probably damaging Het
Fam151b G T 13: 92,614,410 (GRCm39) T26K probably damaging Het
Fam151b T A 13: 92,614,411 (GRCm39) T26S probably damaging Het
Fat1 T C 8: 45,493,719 (GRCm39) V3955A probably damaging Het
Fbn1 T C 2: 125,209,574 (GRCm39) N930S possibly damaging Het
Fgr A G 4: 132,725,673 (GRCm39) M361V probably benign Het
Fmo4 G A 1: 162,631,259 (GRCm39) T236I probably benign Het
Fndc7 G A 3: 108,790,825 (GRCm39) T67I probably damaging Het
Fxr2 A G 11: 69,534,766 (GRCm39) T216A probably benign Het
Gdf10 G A 14: 33,654,710 (GRCm39) A406T probably benign Het
Gm42669 A T 5: 107,656,738 (GRCm39) E355D possibly damaging Het
Gm5174 A T 10: 86,492,617 (GRCm39) noncoding transcript Het
Gm5431 A T 11: 48,779,224 (GRCm39) L844* probably null Het
Gm6489 T C 1: 31,326,452 (GRCm39) noncoding transcript Het
Gna11 A G 10: 81,366,678 (GRCm39) V344A probably damaging Het
Gtpbp3 A G 8: 71,943,099 (GRCm39) E170G probably damaging Het
H2az1 A C 3: 137,571,275 (GRCm39) probably benign Het
Heatr1 A G 13: 12,411,419 (GRCm39) N87D probably damaging Het
Iars2 T C 1: 185,027,868 (GRCm39) K687E possibly damaging Het
Ica1 T C 6: 8,749,736 (GRCm39) D71G possibly damaging Het
Ifnlr1 T C 4: 135,413,881 (GRCm39) L10P probably damaging Het
Il1r1 T A 1: 40,352,300 (GRCm39) L490* probably null Het
Ip6k3 A T 17: 27,370,142 (GRCm39) L92Q probably benign Het
Itgbl1 T A 14: 124,204,090 (GRCm39) F394I probably damaging Het
Kat6b T C 14: 21,678,947 (GRCm39) Y437H probably damaging Het
Kcnh5 G C 12: 74,944,358 (GRCm39) Q964E probably benign Het
Krt27 A T 11: 99,237,309 (GRCm39) probably null Het
Mki67 A T 7: 135,300,128 (GRCm39) D1635E probably benign Het
Mmp23 G T 4: 155,736,509 (GRCm39) H177Q possibly damaging Het
Myef2l G T 3: 10,154,346 (GRCm39) V372F probably benign Het
Mylk2 C A 2: 152,759,527 (GRCm39) Q406K possibly damaging Het
Myo1g A G 11: 6,462,159 (GRCm39) probably null Het
Myrf T C 19: 10,197,160 (GRCm39) T261A probably benign Het
Nmt2 C T 2: 3,326,419 (GRCm39) P486L possibly damaging Het
Oard1 T A 17: 48,722,304 (GRCm39) L100* probably null Het
Oca2 T C 7: 55,971,246 (GRCm39) I391T possibly damaging Het
Or51v14 T A 7: 103,260,618 (GRCm39) *314L probably null Het
Or5k17 T A 16: 58,746,530 (GRCm39) M135L probably benign Het
Or5p64 A C 7: 107,854,403 (GRCm39) L314* probably null Het
Or6c68 A T 10: 129,157,740 (GRCm39) I83F possibly damaging Het
Or8b39 T A 9: 37,996,419 (GRCm39) C96S probably damaging Het
Or9k2b C A 10: 130,015,847 (GRCm39) A301S possibly damaging Het
Pabpc4 T A 4: 123,180,658 (GRCm39) S127T probably damaging Het
Pcdhb1 A G 18: 37,398,760 (GRCm39) D237G probably damaging Het
Pdcd6ip T C 9: 113,537,090 (GRCm39) Y29C probably damaging Het
Phf3 C A 1: 30,870,601 (GRCm39) R95L probably damaging Het
Pkd1l2 A T 8: 117,757,421 (GRCm39) V1539D probably damaging Het
Plxna1 A T 6: 89,308,273 (GRCm39) D1271E probably damaging Het
Ppp3r2 A G 4: 49,681,726 (GRCm39) F75L probably damaging Het
Pth2r C A 1: 65,411,514 (GRCm39) D350E probably damaging Het
Rabgap1 T C 2: 37,373,774 (GRCm39) F262S possibly damaging Het
Rbbp6 T C 7: 122,589,511 (GRCm39) S438P probably benign Het
Rexo1 G A 10: 80,379,200 (GRCm39) R1038C probably damaging Het
Rnf10 A G 5: 115,398,381 (GRCm39) probably benign Het
Scyl1 C A 19: 5,810,132 (GRCm39) A565S probably benign Het
Septin4 A G 11: 87,481,193 (GRCm39) T378A probably benign Het
Sh3yl1 A G 12: 30,992,787 (GRCm39) probably null Het
Slc1a7 G T 4: 107,825,782 (GRCm39) D14Y probably benign Het
Slc32a1 T C 2: 158,455,963 (GRCm39) V206A probably damaging Het
Smyd5 G A 6: 85,415,121 (GRCm39) R43Q probably benign Het
Snrnp200 G A 2: 127,058,095 (GRCm39) A286T possibly damaging Het
Sp110 A C 1: 85,505,050 (GRCm39) F434C probably benign Het
Srebf2 T A 15: 82,079,155 (GRCm39) H794Q probably benign Het
Ssbp2 T C 13: 91,812,303 (GRCm39) probably benign Het
Sspo G A 6: 48,455,207 (GRCm39) G3023D probably damaging Het
St6galnac5 T A 3: 152,552,120 (GRCm39) Q149L probably benign Het
Stab2 A G 10: 86,697,334 (GRCm39) Y1985H probably benign Het
Suz12 A G 11: 79,889,926 (GRCm39) M146V probably benign Het
Tac2 A G 10: 127,564,349 (GRCm39) probably null Het
Thbd T C 2: 148,248,899 (GRCm39) E323G probably damaging Het
Tnfrsf26 T A 7: 143,171,660 (GRCm39) T98S probably damaging Het
Trim15 T C 17: 37,173,215 (GRCm39) probably benign Het
Trpt1 T C 19: 6,975,561 (GRCm39) V105A possibly damaging Het
Vcam1 T C 3: 115,919,606 (GRCm39) Y226C probably damaging Het
Vmn1r175 A G 7: 23,507,808 (GRCm39) V273A probably benign Het
Vmn2r109 A G 17: 20,784,969 (GRCm39) V17A probably benign Het
Vmn2r84 G A 10: 130,226,677 (GRCm39) A387V probably benign Het
Wdfy4 A T 14: 32,693,641 (GRCm39) L2728Q probably damaging Het
Zfp934 T A 13: 62,666,108 (GRCm39) T178S possibly damaging Het
Other mutations in Col27a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01305:Col27a1 APN 4 63,218,978 (GRCm39) splice site probably benign
IGL01461:Col27a1 APN 4 63,142,480 (GRCm39) missense probably damaging 1.00
IGL01534:Col27a1 APN 4 63,144,019 (GRCm39) missense probably benign 0.12
IGL01738:Col27a1 APN 4 63,182,016 (GRCm39) splice site probably benign
IGL01810:Col27a1 APN 4 63,143,868 (GRCm39) missense probably benign 0.21
IGL02127:Col27a1 APN 4 63,143,379 (GRCm39) missense possibly damaging 0.60
IGL02290:Col27a1 APN 4 63,144,163 (GRCm39) missense probably damaging 1.00
IGL02374:Col27a1 APN 4 63,211,486 (GRCm39) missense possibly damaging 0.86
IGL02548:Col27a1 APN 4 63,236,492 (GRCm39) splice site probably benign
IGL02792:Col27a1 APN 4 63,233,820 (GRCm39) missense unknown
IGL02931:Col27a1 APN 4 63,249,663 (GRCm39) utr 3 prime probably benign
IGL03107:Col27a1 APN 4 63,242,869 (GRCm39) splice site probably benign
IGL03121:Col27a1 APN 4 63,143,446 (GRCm39) missense probably benign 0.26
IGL03334:Col27a1 APN 4 63,232,959 (GRCm39) missense probably damaging 1.00
R0005:Col27a1 UTSW 4 63,143,637 (GRCm39) missense probably benign 0.04
R0025:Col27a1 UTSW 4 63,194,214 (GRCm39) missense probably damaging 1.00
R0141:Col27a1 UTSW 4 63,183,870 (GRCm39) critical splice acceptor site probably null
R0196:Col27a1 UTSW 4 63,142,503 (GRCm39) missense probably benign 0.02
R0359:Col27a1 UTSW 4 63,232,964 (GRCm39) critical splice donor site probably null
R0375:Col27a1 UTSW 4 63,143,898 (GRCm39) missense probably benign 0.23
R0432:Col27a1 UTSW 4 63,143,848 (GRCm39) missense possibly damaging 0.87
R0499:Col27a1 UTSW 4 63,218,978 (GRCm39) splice site probably benign
R0786:Col27a1 UTSW 4 63,209,815 (GRCm39) critical splice donor site probably null
R0891:Col27a1 UTSW 4 63,223,420 (GRCm39) critical splice acceptor site probably null
R1239:Col27a1 UTSW 4 63,237,152 (GRCm39) splice site probably benign
R1297:Col27a1 UTSW 4 63,183,868 (GRCm39) splice site probably benign
R1299:Col27a1 UTSW 4 63,183,868 (GRCm39) splice site probably benign
R1322:Col27a1 UTSW 4 63,246,803 (GRCm39) utr 3 prime probably benign
R1342:Col27a1 UTSW 4 63,175,351 (GRCm39) critical splice donor site probably null
R1446:Col27a1 UTSW 4 63,143,040 (GRCm39) missense probably damaging 1.00
R1629:Col27a1 UTSW 4 63,248,100 (GRCm39) utr 3 prime probably benign
R1644:Col27a1 UTSW 4 63,246,868 (GRCm39) utr 3 prime probably benign
R1774:Col27a1 UTSW 4 63,143,950 (GRCm39) missense probably damaging 1.00
R1807:Col27a1 UTSW 4 63,249,586 (GRCm39) utr 3 prime probably benign
R1952:Col27a1 UTSW 4 63,202,130 (GRCm39) splice site probably null
R1970:Col27a1 UTSW 4 63,191,354 (GRCm39) splice site probably benign
R2164:Col27a1 UTSW 4 63,143,661 (GRCm39) missense probably benign 0.21
R3774:Col27a1 UTSW 4 63,232,963 (GRCm39) missense probably benign 0.00
R4078:Col27a1 UTSW 4 63,142,669 (GRCm39) missense probably damaging 1.00
R4353:Col27a1 UTSW 4 63,143,868 (GRCm39) missense probably benign 0.21
R4611:Col27a1 UTSW 4 63,211,743 (GRCm39) missense probably damaging 1.00
R4708:Col27a1 UTSW 4 63,202,150 (GRCm39) missense probably benign 0.01
R4884:Col27a1 UTSW 4 63,194,197 (GRCm39) missense possibly damaging 0.77
R5149:Col27a1 UTSW 4 63,249,664 (GRCm39) utr 3 prime probably benign
R5411:Col27a1 UTSW 4 63,142,902 (GRCm39) missense probably damaging 1.00
R5451:Col27a1 UTSW 4 63,143,476 (GRCm39) missense probably damaging 0.98
R5615:Col27a1 UTSW 4 63,199,351 (GRCm39) missense probably damaging 0.96
R5657:Col27a1 UTSW 4 63,143,547 (GRCm39) missense probably damaging 0.97
R5838:Col27a1 UTSW 4 63,143,765 (GRCm39) missense probably damaging 1.00
R6230:Col27a1 UTSW 4 63,142,519 (GRCm39) missense probably damaging 1.00
R6326:Col27a1 UTSW 4 63,242,678 (GRCm39) utr 3 prime probably benign
R6457:Col27a1 UTSW 4 63,237,701 (GRCm39) utr 3 prime probably benign
R6624:Col27a1 UTSW 4 63,143,248 (GRCm39) missense probably benign 0.00
R6792:Col27a1 UTSW 4 63,235,740 (GRCm39) missense unknown
R6848:Col27a1 UTSW 4 63,220,608 (GRCm39) missense probably benign
R6962:Col27a1 UTSW 4 63,237,738 (GRCm39) utr 3 prime probably benign
R7053:Col27a1 UTSW 4 63,251,404 (GRCm39) utr 3 prime probably benign
R7206:Col27a1 UTSW 4 63,153,583 (GRCm39) missense probably benign 0.29
R7586:Col27a1 UTSW 4 63,143,278 (GRCm39) missense probably damaging 1.00
R7698:Col27a1 UTSW 4 63,143,955 (GRCm39) missense possibly damaging 0.78
R7714:Col27a1 UTSW 4 63,242,723 (GRCm39) critical splice donor site probably null
R7916:Col27a1 UTSW 4 63,142,789 (GRCm39) missense probably damaging 1.00
R7943:Col27a1 UTSW 4 63,236,520 (GRCm39) missense unknown
R7988:Col27a1 UTSW 4 63,249,559 (GRCm39) missense unknown
R8136:Col27a1 UTSW 4 63,202,190 (GRCm39) missense probably benign 0.06
R8243:Col27a1 UTSW 4 63,144,120 (GRCm39) missense probably damaging 1.00
R8245:Col27a1 UTSW 4 63,144,040 (GRCm39) missense probably damaging 0.97
R8350:Col27a1 UTSW 4 63,248,134 (GRCm39) missense unknown
R8437:Col27a1 UTSW 4 63,237,701 (GRCm39) utr 3 prime probably benign
R8450:Col27a1 UTSW 4 63,248,134 (GRCm39) missense unknown
R8542:Col27a1 UTSW 4 63,239,662 (GRCm39) splice site probably null
R8745:Col27a1 UTSW 4 63,144,153 (GRCm39) missense probably benign 0.02
R8821:Col27a1 UTSW 4 63,143,148 (GRCm39) missense probably benign 0.04
R8951:Col27a1 UTSW 4 63,191,311 (GRCm39) missense possibly damaging 0.92
R8970:Col27a1 UTSW 4 63,134,105 (GRCm39) missense unknown
R9115:Col27a1 UTSW 4 63,231,974 (GRCm39) missense unknown
R9185:Col27a1 UTSW 4 63,246,887 (GRCm39) missense unknown
R9291:Col27a1 UTSW 4 63,142,539 (GRCm39) missense probably damaging 0.99
R9404:Col27a1 UTSW 4 63,194,178 (GRCm39) missense possibly damaging 0.93
Z1176:Col27a1 UTSW 4 63,144,025 (GRCm39) missense probably damaging 0.99
Z1177:Col27a1 UTSW 4 63,199,526 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGAAGGCTGAAGTGACTTCC -3'
(R):5'- ATGTGTGATCCATACCAATTCCTTC -3'

Sequencing Primer
(F):5'- TGAAGTGACTTCCCGGGTCTC -3'
(R):5'- TCTCTGGGCACAACACTAAGAG -3'
Posted On 2014-08-01