Incidental Mutation 'R5615:Col27a1'
ID 501162
Institutional Source Beutler Lab
Gene Symbol Col27a1
Ensembl Gene ENSMUSG00000045672
Gene Name collagen, type XXVII, alpha 1
Synonyms 5730512J02Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5615 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 63132246-63253228 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 63199351 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Asparagine at position 912 (K912N)
Ref Sequence ENSEMBL: ENSMUSP00000043816 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000036300] [ENSMUST00000183913] [ENSMUST00000184067]
AlphaFold Q5QNQ9
Predicted Effect probably damaging
Transcript: ENSMUST00000036300
AA Change: K912N

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000043816
Gene: ENSMUSG00000045672
AA Change: K912N

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: ENSMUST00000149856
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: K297N
SMART Domains Protein: ENSMUSP00000139173
Gene: ENSMUSG00000045672
AA Change: K297N

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
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.5%
  • 10x: 97.6%
  • 20x: 92.4%
Validation Efficiency
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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 A T 1: 71,346,218 (GRCm39) L884H probably damaging Het
Ahr A G 12: 35,553,884 (GRCm39) V745A probably benign Het
Ankrd17 A T 5: 90,431,295 (GRCm39) S830T possibly damaging Het
Aox1 A G 1: 58,136,125 (GRCm39) T1123A probably benign Het
Arhgef11 T C 3: 87,629,792 (GRCm39) probably null Het
Bcas3 T A 11: 85,361,587 (GRCm39) C250S probably damaging Het
Bckdk T C 7: 127,506,489 (GRCm39) I272T probably damaging Het
Cacna1e T C 1: 154,287,916 (GRCm39) K1897E probably damaging Het
Cd180 A T 13: 102,842,711 (GRCm39) I586F probably benign Het
Cep290 A G 10: 100,367,012 (GRCm39) D1121G probably damaging Het
Clasrp A G 7: 19,320,372 (GRCm39) probably benign Het
Dock4 G T 12: 40,699,479 (GRCm39) R231L probably benign Het
Ell G A 8: 71,043,382 (GRCm39) S505N probably benign Het
Ephb6 A G 6: 41,596,225 (GRCm39) T833A probably benign Het
Hemk1 T A 9: 107,208,023 (GRCm39) probably null Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Hspa12a T C 19: 58,793,082 (GRCm39) I368V possibly damaging Het
Igkv3-3 A T 6: 70,664,214 (GRCm39) T19S probably benign Het
Itpr1 G A 6: 108,465,561 (GRCm39) A2158T possibly damaging Het
Lancl2 T C 6: 57,699,496 (GRCm39) Y104H probably damaging Het
Leng8 G T 7: 4,147,957 (GRCm39) E634* probably null Het
Lrrk1 A T 7: 65,937,363 (GRCm39) C930S probably damaging Het
Lvrn C T 18: 46,983,395 (GRCm39) S46L possibly damaging Het
Mcidas G A 13: 113,133,959 (GRCm39) V148I probably benign Het
Mprip A T 11: 59,649,313 (GRCm39) T1006S probably benign Het
Mrgprb3 T A 7: 48,293,234 (GRCm39) M106L probably benign Het
Mroh2a GCCC GC 1: 88,159,979 (GRCm39) probably null Het
Mtor G A 4: 148,622,733 (GRCm39) V1938I possibly damaging Het
Muc2 A G 7: 141,277,446 (GRCm39) D46G probably damaging Het
Nfkb2 G T 19: 46,296,006 (GRCm39) E170D probably benign Het
Or10ag52 T A 2: 87,044,083 (GRCm39) F282L probably benign Het
Or6c215 A T 10: 129,637,636 (GRCm39) C253S probably damaging Het
Osbp2 C T 11: 3,813,356 (GRCm39) G171D probably benign Het
Otud6b A T 4: 14,818,187 (GRCm39) M238K possibly damaging Het
Pcdhac2 G A 18: 37,279,476 (GRCm39) G819R probably benign Het
Pcdhac2 G T 18: 37,279,477 (GRCm39) G819V probably benign Het
Pcdhga12 T G 18: 37,901,132 (GRCm39) S655A probably damaging Het
Pkd1l3 A G 8: 110,356,842 (GRCm39) I756V probably benign Het
Plekhd1 T A 12: 80,767,364 (GRCm39) S251T probably damaging Het
Ppp2r1a A T 17: 21,179,249 (GRCm39) T96S probably benign Het
Qser1 A C 2: 104,620,039 (GRCm39) S258A possibly damaging Het
Rsph4a G A 10: 33,785,324 (GRCm39) A412T probably benign Het
Sanbr A T 11: 23,556,759 (GRCm39) L407H probably damaging Het
Sass6 T A 3: 116,401,135 (GRCm39) C159S probably benign Het
Scaf4 T C 16: 90,048,848 (GRCm39) Q322R unknown Het
Sema6d C T 2: 124,498,821 (GRCm39) H244Y probably damaging Het
Sigirr T G 7: 140,672,632 (GRCm39) L163F probably damaging Het
Spata31d1c C A 13: 65,183,078 (GRCm39) L207I possibly damaging Het
Tacstd2 A G 6: 67,512,033 (GRCm39) F220L probably damaging Het
Tdpoz4 A T 3: 93,704,806 (GRCm39) T368S probably benign Het
Tnxb C A 17: 34,902,392 (GRCm39) Q1082K probably damaging Het
Trim41 GCCTAGGCGCCCA G 11: 48,698,192 (GRCm39) probably benign Het
Trpm6 C T 19: 18,807,297 (GRCm39) R1014C probably damaging Het
Ugt1a10 TTCATCA TTCA 1: 88,143,880 (GRCm39) probably benign Het
Vmn2r114 ATTT ATT 17: 23,509,906 (GRCm39) probably null Het
Vmn2r61 T A 7: 41,916,677 (GRCm39) M430K probably benign Het
Vmn2r61 A G 7: 41,949,917 (GRCm39) E779G probably damaging Het
Zfp599 T C 9: 22,165,165 (GRCm39) D70G probably benign Het
Zmym1 A T 4: 126,943,191 (GRCm39) I301N probably 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
R1957:Col27a1 UTSW 4 63,196,031 (GRCm39) missense probably benign 0.03
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
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'- CTGAAAAGTCAGGCTTGGGG -3'
(R):5'- AGGGCTATCTTACCTCAGGC -3'

Sequencing Primer
(F):5'- GGGATCAAGTAGCTGACCTACC -3'
(R):5'- TTACCTCAGGCCCCAGCTG -3'
Posted On 2017-12-01