Incidental Mutation 'R5344:Col11a1'
ID 422476
Institutional Source Beutler Lab
Gene Symbol Col11a1
Ensembl Gene ENSMUSG00000027966
Gene Name collagen, type XI, alpha 1
Synonyms C530001D20Rik
MMRRC Submission 042923-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.939) question?
Stock # R5344 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 113824189-114014367 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to A at 114002011 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000089793 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000092155] [ENSMUST00000184978]
AlphaFold Q61245
Predicted Effect probably null
Transcript: ENSMUST00000092155
SMART Domains Protein: ENSMUSP00000089793
Gene: ENSMUSG00000027966

DomainStartEndE-ValueType
TSPN 37 228 1.83e-62 SMART
LamG 96 227 5.87e-11 SMART
low complexity region 256 276 N/A INTRINSIC
internal_repeat_4 357 431 3.12e-6 PROSPERO
Pfam:Collagen 433 491 2.6e-9 PFAM
Pfam:Collagen 525 586 5.9e-9 PFAM
low complexity region 611 632 N/A INTRINSIC
low complexity region 638 677 N/A INTRINSIC
Pfam:Collagen 721 805 3.6e-8 PFAM
internal_repeat_3 814 854 3.55e-9 PROSPERO
internal_repeat_1 818 869 2.01e-16 PROSPERO
low complexity region 872 944 N/A INTRINSIC
low complexity region 952 1001 N/A INTRINSIC
low complexity region 1031 1059 N/A INTRINSIC
low complexity region 1066 1100 N/A INTRINSIC
low complexity region 1103 1121 N/A INTRINSIC
internal_repeat_2 1124 1188 2.4e-12 PROSPERO
low complexity region 1189 1205 N/A INTRINSIC
low complexity region 1211 1232 N/A INTRINSIC
low complexity region 1235 1250 N/A INTRINSIC
low complexity region 1252 1368 N/A INTRINSIC
low complexity region 1373 1392 N/A INTRINSIC
low complexity region 1417 1448 N/A INTRINSIC
low complexity region 1453 1463 N/A INTRINSIC
Pfam:Collagen 1481 1543 8.3e-9 PFAM
COLFI 1574 1803 7.28e-127 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000184978
SMART Domains Protein: ENSMUSP00000138879
Gene: ENSMUSG00000027966

DomainStartEndE-ValueType
Pfam:Collagen 1 57 6.3e-10 PFAM
Pfam:Collagen 49 110 3.2e-10 PFAM
Pfam:Collagen 95 165 6.2e-8 PFAM
Pfam:Collagen 242 318 2.2e-9 PFAM
Pfam:Collagen 289 362 1.6e-7 PFAM
Pfam:Collagen 341 403 2e-9 PFAM
COLFI 434 536 8.88e-12 SMART
Meta Mutation Damage Score 0.9488 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.7%
Validation Efficiency 99% (67/68)
MGI Phenotype FUNCTION: This gene encodes the alpha-1 subunit of type XI collagen, one of the low abundance fibrillar collagens that is essential for normal embryonic skeletal development and the cohesive properties of cartilage. The encoded protein, in association with the alpha-1 subunit of type II collagen, forms a heterotrimeric type XI procollagen that undergoes proteolytic processing. Mice lacking the encoded protein develop severe chondrodysplasia and die at birth. [provided by RefSeq, Dec 2015]
PHENOTYPE: Homozygous mutation of this gene results in perinatal lethality by asphyxia. Mutants animals display weak tracheal cartilage, short snout, short mandible, cleft palate, short limbs, and externally rotated distal portion of the hindlimbs. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik T G 12: 71,289,801 (GRCm39) C1499G probably benign Het
Aldoart1 A G 4: 72,770,352 (GRCm39) V152A possibly damaging Het
Alms1 T C 6: 85,673,771 (GRCm39) L3591P probably benign Het
Ankrd12 A T 17: 66,356,843 (GRCm39) M58K probably damaging Het
Asb3 A C 11: 31,051,114 (GRCm39) I523L probably benign Het
Ascl2 T C 7: 142,522,436 (GRCm39) H4R possibly damaging Het
Asic2 T C 11: 80,862,413 (GRCm39) M246V probably damaging Het
Btc A T 5: 91,524,779 (GRCm39) C53S possibly damaging Het
Cdhr5 T C 7: 140,856,437 (GRCm39) I39M probably damaging Het
Cdkn3 T A 14: 47,004,807 (GRCm39) M123K possibly damaging Het
Cebpz A G 17: 79,233,542 (GRCm39) Y762H possibly damaging Het
Ces1g T A 8: 94,063,821 (GRCm39) probably benign Het
Cfap44 T C 16: 44,236,763 (GRCm39) probably null Het
Chd7 G T 4: 8,844,417 (GRCm39) G1537W probably damaging Het
Clca3a2 A T 3: 144,793,703 (GRCm39) D317E probably damaging Het
Clec3a C A 8: 115,149,712 (GRCm39) N56K probably damaging Het
Cox20 G A 1: 178,149,598 (GRCm39) probably benign Het
Cyp2d22 A G 15: 82,255,839 (GRCm39) V471A possibly damaging Het
D630045J12Rik A G 6: 38,135,163 (GRCm39) V1339A probably damaging Het
Duox2 T C 2: 122,112,352 (GRCm39) D1278G probably benign Het
Epc1 G A 18: 6,450,614 (GRCm39) P284L probably benign Het
Evi5l G T 8: 4,235,990 (GRCm39) R61L possibly damaging Het
Fbln2 T C 6: 91,243,365 (GRCm39) Y914H probably damaging Het
Fbxo44 A G 4: 148,238,030 (GRCm39) S191P probably damaging Het
Fign A G 2: 63,809,569 (GRCm39) I567T probably benign Het
Fryl C T 5: 73,262,117 (GRCm39) R550K probably damaging Het
Gpcpd1 G A 2: 132,400,597 (GRCm39) probably benign Het
Hectd4 T C 5: 121,481,739 (GRCm39) I3096T probably benign Het
Hic2 T A 16: 17,075,712 (GRCm39) D180E probably benign Het
Ibtk A G 9: 85,617,057 (GRCm39) F172L possibly damaging Het
Itga1 A G 13: 115,138,845 (GRCm39) S369P possibly damaging Het
Itgb4 G A 11: 115,880,575 (GRCm39) R675Q probably null Het
Lrrc3b T C 14: 15,358,591 (GRCm38) D5G probably damaging Het
Maml3 T A 3: 52,011,146 (GRCm39) D140V probably damaging Het
Med21 A G 6: 146,550,683 (GRCm39) T65A probably benign Het
Mta1 T C 12: 113,095,186 (GRCm39) probably benign Het
Mybpc1 T C 10: 88,406,430 (GRCm39) D152G probably damaging Het
Oas1b C A 5: 120,960,269 (GRCm39) Q325K probably benign Het
Or10j27 A G 1: 172,958,673 (GRCm39) L37P probably benign Het
Or2n1c C A 17: 38,519,995 (GRCm39) N286K probably damaging Het
Or5d44 A C 2: 88,141,334 (GRCm39) C269G probably benign Het
Pclo A G 5: 14,726,626 (GRCm39) probably benign Het
Phactr2 C T 10: 13,129,360 (GRCm39) V233I possibly damaging Het
Plekha2 A T 8: 25,533,063 (GRCm39) probably null Het
Reg3b A G 6: 78,349,843 (GRCm39) M128V probably benign Het
Rnaseh2a A G 8: 85,684,735 (GRCm39) probably benign Het
Scn5a T C 9: 119,363,073 (GRCm39) S516G probably benign Het
Serpina12 T A 12: 104,001,807 (GRCm39) probably null Het
Slc10a1 T C 12: 81,000,540 (GRCm39) T320A possibly damaging Het
Slc26a7 A T 4: 14,519,402 (GRCm39) D539E probably benign Het
Specc1l C A 10: 75,082,007 (GRCm39) R485S possibly damaging Het
Srp54b T G 12: 55,302,366 (GRCm39) I339S probably damaging Het
Tada1 G A 1: 166,207,081 (GRCm39) probably benign Het
Trim16 T C 11: 62,711,751 (GRCm39) C54R probably damaging Het
Trio C T 15: 27,735,618 (GRCm39) R2824Q probably benign Het
Ttpa A G 4: 20,021,245 (GRCm39) I138V probably damaging Het
Ubap2 A C 4: 41,251,578 (GRCm39) M18R possibly damaging Het
Usp38 A G 8: 81,712,392 (GRCm39) S548P possibly damaging Het
Vmn2r73 T C 7: 85,525,046 (GRCm39) D34G probably benign Het
Vps13d T A 4: 144,904,904 (GRCm39) H74L probably damaging Het
Zfp408 C T 2: 91,475,588 (GRCm39) C622Y probably benign Het
Zfp616 T C 11: 73,975,321 (GRCm39) I530T possibly damaging Het
Zfp9 C A 6: 118,442,140 (GRCm39) C174F probably damaging Het
Zfyve16 A G 13: 92,658,096 (GRCm39) I605T possibly damaging Het
Zmym5 T C 14: 57,031,519 (GRCm39) T530A probably damaging Het
Other mutations in Col11a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00474:Col11a1 APN 3 113,860,182 (GRCm39) missense unknown
IGL00578:Col11a1 APN 3 113,987,755 (GRCm39) missense possibly damaging 0.95
IGL00742:Col11a1 APN 3 113,917,964 (GRCm39) missense unknown
IGL01014:Col11a1 APN 3 113,917,458 (GRCm39) splice site probably benign
IGL01099:Col11a1 APN 3 113,905,690 (GRCm39) nonsense probably null
IGL01129:Col11a1 APN 3 113,979,522 (GRCm39) splice site probably benign
IGL01474:Col11a1 APN 3 114,010,783 (GRCm39) utr 3 prime probably benign
IGL01884:Col11a1 APN 3 113,860,191 (GRCm39) missense unknown
IGL02104:Col11a1 APN 3 113,975,046 (GRCm39) critical splice donor site probably null
IGL02715:Col11a1 APN 3 113,923,058 (GRCm39) missense probably benign 0.06
IGL02978:Col11a1 APN 3 113,855,211 (GRCm39) missense unknown
IGL03203:Col11a1 APN 3 114,005,733 (GRCm39) missense possibly damaging 0.91
IGL03240:Col11a1 APN 3 114,010,859 (GRCm39) splice site probably null
IGL03357:Col11a1 APN 3 113,987,740 (GRCm39) missense probably damaging 1.00
IGL03390:Col11a1 APN 3 113,883,902 (GRCm39) missense unknown
gluon UTSW 3 114,010,819 (GRCm39) utr 3 prime probably benign
uncovered UTSW 3 113,906,116 (GRCm39) unclassified probably benign
weakforce UTSW 3 113,907,249 (GRCm39) missense unknown
R0110:Col11a1 UTSW 3 113,899,105 (GRCm39) splice site probably benign
R0144:Col11a1 UTSW 3 113,907,243 (GRCm39) missense unknown
R0432:Col11a1 UTSW 3 113,999,550 (GRCm39) splice site probably benign
R0468:Col11a1 UTSW 3 114,010,707 (GRCm39) utr 3 prime probably benign
R0510:Col11a1 UTSW 3 113,899,105 (GRCm39) splice site probably benign
R0535:Col11a1 UTSW 3 113,855,184 (GRCm39) missense unknown
R0608:Col11a1 UTSW 3 114,012,364 (GRCm39) utr 3 prime probably benign
R0826:Col11a1 UTSW 3 113,932,414 (GRCm39) missense unknown
R0827:Col11a1 UTSW 3 113,932,414 (GRCm39) missense unknown
R0862:Col11a1 UTSW 3 113,932,414 (GRCm39) missense unknown
R0863:Col11a1 UTSW 3 113,932,414 (GRCm39) missense unknown
R0926:Col11a1 UTSW 3 113,883,829 (GRCm39) missense unknown
R0980:Col11a1 UTSW 3 113,932,414 (GRCm39) missense unknown
R0981:Col11a1 UTSW 3 113,932,414 (GRCm39) missense unknown
R1004:Col11a1 UTSW 3 113,888,671 (GRCm39) splice site probably benign
R1037:Col11a1 UTSW 3 113,987,801 (GRCm39) missense probably damaging 1.00
R1171:Col11a1 UTSW 3 113,860,213 (GRCm39) missense unknown
R1316:Col11a1 UTSW 3 113,932,619 (GRCm39) splice site probably null
R1324:Col11a1 UTSW 3 113,824,565 (GRCm39) missense unknown
R1338:Col11a1 UTSW 3 114,010,644 (GRCm39) utr 3 prime probably benign
R1513:Col11a1 UTSW 3 113,890,803 (GRCm39) missense unknown
R1528:Col11a1 UTSW 3 114,010,644 (GRCm39) utr 3 prime probably benign
R1567:Col11a1 UTSW 3 113,932,261 (GRCm39) missense unknown
R1596:Col11a1 UTSW 3 113,946,262 (GRCm39) utr 3 prime probably benign
R1605:Col11a1 UTSW 3 113,925,290 (GRCm39) missense probably damaging 1.00
R1624:Col11a1 UTSW 3 113,951,804 (GRCm39) missense probably damaging 0.97
R1626:Col11a1 UTSW 3 113,925,218 (GRCm39) missense probably damaging 1.00
R1666:Col11a1 UTSW 3 113,855,184 (GRCm39) missense unknown
R1806:Col11a1 UTSW 3 113,951,791 (GRCm39) missense probably damaging 1.00
R2001:Col11a1 UTSW 3 113,958,942 (GRCm39) splice site probably null
R2084:Col11a1 UTSW 3 113,951,791 (GRCm39) missense probably damaging 1.00
R2085:Col11a1 UTSW 3 113,951,791 (GRCm39) missense probably damaging 1.00
R3926:Col11a1 UTSW 3 113,883,773 (GRCm39) splice site probably benign
R3950:Col11a1 UTSW 3 113,915,094 (GRCm39) critical splice donor site probably null
R3970:Col11a1 UTSW 3 113,890,838 (GRCm39) missense unknown
R4171:Col11a1 UTSW 3 114,001,863 (GRCm39) missense probably damaging 0.99
R4175:Col11a1 UTSW 3 114,001,872 (GRCm39) missense possibly damaging 0.83
R4176:Col11a1 UTSW 3 114,001,872 (GRCm39) missense possibly damaging 0.83
R4413:Col11a1 UTSW 3 113,901,965 (GRCm39) missense unknown
R4540:Col11a1 UTSW 3 113,890,815 (GRCm39) missense unknown
R5210:Col11a1 UTSW 3 113,946,806 (GRCm39) missense probably damaging 1.00
R5250:Col11a1 UTSW 3 114,010,819 (GRCm39) utr 3 prime probably benign
R5335:Col11a1 UTSW 3 113,888,889 (GRCm39) missense unknown
R5394:Col11a1 UTSW 3 113,987,833 (GRCm39) splice site probably null
R5687:Col11a1 UTSW 3 114,010,752 (GRCm39) utr 3 prime probably benign
R5708:Col11a1 UTSW 3 113,890,743 (GRCm39) missense unknown
R5763:Col11a1 UTSW 3 113,888,245 (GRCm39) intron probably benign
R5792:Col11a1 UTSW 3 113,925,242 (GRCm39) missense probably damaging 1.00
R6259:Col11a1 UTSW 3 113,932,096 (GRCm39) missense probably benign
R6679:Col11a1 UTSW 3 113,946,368 (GRCm39) splice site probably null
R6738:Col11a1 UTSW 3 113,906,116 (GRCm39) unclassified probably benign
R6747:Col11a1 UTSW 3 114,006,099 (GRCm39) nonsense probably null
R6808:Col11a1 UTSW 3 113,888,593 (GRCm39) missense possibly damaging 0.87
R6861:Col11a1 UTSW 3 113,961,141 (GRCm39) missense probably damaging 1.00
R7201:Col11a1 UTSW 3 113,883,806 (GRCm39) missense unknown
R7264:Col11a1 UTSW 3 113,979,248 (GRCm39) missense unknown
R7393:Col11a1 UTSW 3 113,890,755 (GRCm39) missense unknown
R7445:Col11a1 UTSW 3 113,987,578 (GRCm39) missense unknown
R7479:Col11a1 UTSW 3 113,896,218 (GRCm39) missense unknown
R7548:Col11a1 UTSW 3 113,917,409 (GRCm39) missense unknown
R7683:Col11a1 UTSW 3 113,907,385 (GRCm39) missense unknown
R7747:Col11a1 UTSW 3 113,896,221 (GRCm39) missense unknown
R7809:Col11a1 UTSW 3 113,890,835 (GRCm39) missense unknown
R7951:Col11a1 UTSW 3 113,888,864 (GRCm39) missense unknown
R8057:Col11a1 UTSW 3 113,925,263 (GRCm39) missense unknown
R8134:Col11a1 UTSW 3 114,012,435 (GRCm39) missense unknown
R8139:Col11a1 UTSW 3 113,890,698 (GRCm39) missense unknown
R8243:Col11a1 UTSW 3 113,855,141 (GRCm39) missense unknown
R8324:Col11a1 UTSW 3 113,958,059 (GRCm39) missense probably damaging 1.00
R8346:Col11a1 UTSW 3 114,005,818 (GRCm39) missense unknown
R8480:Col11a1 UTSW 3 113,975,043 (GRCm39) missense probably benign 0.04
R9113:Col11a1 UTSW 3 113,888,192 (GRCm39) nonsense probably null
R9122:Col11a1 UTSW 3 113,907,249 (GRCm39) missense unknown
R9137:Col11a1 UTSW 3 113,855,172 (GRCm39) missense unknown
R9224:Col11a1 UTSW 3 114,001,929 (GRCm39) missense unknown
R9264:Col11a1 UTSW 3 114,005,809 (GRCm39) missense unknown
R9272:Col11a1 UTSW 3 113,901,948 (GRCm39) nonsense probably null
R9382:Col11a1 UTSW 3 113,899,046 (GRCm39) missense unknown
R9492:Col11a1 UTSW 3 114,005,752 (GRCm39) missense probably benign 0.39
RF002:Col11a1 UTSW 3 114,010,650 (GRCm39) missense unknown
X0018:Col11a1 UTSW 3 113,905,882 (GRCm39) unclassified probably benign
Z1177:Col11a1 UTSW 3 113,958,884 (GRCm39) critical splice acceptor site probably null
Z1177:Col11a1 UTSW 3 113,932,570 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- AAAGCATCCAGGGTGATGC -3'
(R):5'- CCCTATCTACAAGGCTAACAGTAATAG -3'

Sequencing Primer
(F):5'- CCAGGGTGATGCAGGAGATAATATTC -3'
(R):5'- CCTATCTACAAGGCTAACAGTA -3'
Posted On 2016-08-04