Incidental Mutation 'R5394:Col11a1'
ID 426012
Institutional Source Beutler Lab
Gene Symbol Col11a1
Ensembl Gene ENSMUSG00000027966
Gene Name collagen, type XI, alpha 1
Synonyms C530001D20Rik
MMRRC Submission 042966-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.939) question?
Stock # R5394 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 113824189-114014367 bp(+) (GRCm39)
Type of Mutation splice site (4 bp from exon)
DNA Base Change (assembly) A to G at 113987833 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 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 97% (96/99)
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: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930503B20Rik A G 3: 146,356,363 (GRCm39) F182L probably damaging Het
4930503B20Rik T C 3: 146,356,713 (GRCm39) Y65C probably damaging Het
4930590J08Rik A G 6: 91,896,174 (GRCm39) T341A probably benign Het
Adamts13 G A 2: 26,876,570 (GRCm39) V495I probably benign Het
Alms1 C A 6: 85,600,070 (GRCm39) T2101K probably benign Het
Als2 T C 1: 59,214,105 (GRCm39) D1361G probably benign Het
Ankdd1a A T 9: 65,412,496 (GRCm39) M275K probably benign Het
Arfip2 A T 7: 105,286,183 (GRCm39) Y161* probably null Het
Asap3 A T 4: 135,968,570 (GRCm39) E707D probably benign Het
Atm C T 9: 53,419,077 (GRCm39) probably null Het
Atp9b A T 18: 80,820,052 (GRCm39) S577R probably benign Het
Bltp1 G T 3: 36,971,817 (GRCm39) V517F probably damaging Het
Camk1d G C 2: 5,308,177 (GRCm39) D274E probably benign Het
Cebpz C T 17: 79,229,634 (GRCm39) D907N probably benign Het
Cmtm1 CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT 8: 105,036,102 (GRCm39) probably benign Het
Cnst T A 1: 179,429,301 (GRCm39) probably benign Het
Cog2 G T 8: 125,259,268 (GRCm39) V196L probably benign Het
Cops6 T A 5: 138,161,762 (GRCm39) probably null Het
Cspg4 A G 9: 56,797,484 (GRCm39) E1316G probably damaging Het
Cwc22 G C 2: 77,759,683 (GRCm39) D122E possibly damaging Het
Dapk2 G A 9: 66,176,000 (GRCm39) V300M probably benign Het
Dcp1b C A 6: 119,152,328 (GRCm39) D25E probably damaging Het
Ddx10 A T 9: 53,145,157 (GRCm39) Y273* probably null Het
Dhx58 T C 11: 100,589,034 (GRCm39) E504G probably benign Het
Dync2h1 C T 9: 7,120,899 (GRCm39) W2129* probably null Het
Egr4 A T 6: 85,489,442 (GRCm39) L206Q probably damaging Het
Eif4g3 A G 4: 137,830,709 (GRCm39) probably null Het
Fbxo46 A G 7: 18,870,541 (GRCm39) N387D possibly damaging Het
Fpr-rs3 T G 17: 20,844,470 (GRCm39) M224L probably benign Het
Gm14325 G A 2: 177,474,777 (GRCm39) H102Y possibly damaging Het
Gxylt2 A G 6: 100,682,075 (GRCm39) K91E probably benign Het
Hecw1 A T 13: 14,497,174 (GRCm39) V278E probably damaging Het
Hydin A G 8: 111,266,474 (GRCm39) probably null Het
Iars1 T C 13: 49,875,641 (GRCm39) L776P probably damaging Het
Kcnh2 T A 5: 24,537,039 (GRCm39) T182S probably benign Het
Kplce T C 3: 92,776,005 (GRCm39) E226G probably damaging Het
Lats2 T G 14: 57,928,810 (GRCm39) S1022R probably benign Het
Lef1 C T 3: 130,988,308 (GRCm39) P264S probably damaging Het
Lyrm1 A C 7: 119,513,471 (GRCm39) I79L possibly damaging Het
Macroh2a2 G A 10: 61,587,466 (GRCm39) T156M possibly damaging Het
Man2b2 T G 5: 36,971,862 (GRCm39) Q618P probably benign Het
Mei1 T C 15: 81,976,957 (GRCm39) V180A possibly damaging Het
Mmp15 A T 8: 96,093,032 (GRCm39) N137I probably damaging Het
Mms22l A G 4: 24,517,115 (GRCm39) D222G possibly damaging Het
Mmut T A 17: 41,258,075 (GRCm39) S414T probably benign Het
Myo18a T C 11: 77,744,176 (GRCm39) M1846T probably benign Het
Neo1 A T 9: 58,897,517 (GRCm39) N146K probably benign Het
Nos3 A G 5: 24,588,888 (GRCm39) T1174A probably benign Het
Or10d4b A T 9: 39,534,430 (GRCm39) T4S probably benign Het
Or10x1 T C 1: 174,196,836 (GRCm39) Y118H probably damaging Het
Or4c125 A T 2: 89,169,806 (GRCm39) I280N probably damaging Het
Or51f1 A T 7: 102,505,686 (GRCm39) S268T probably damaging Het
Pax8 A T 2: 24,332,922 (GRCm39) probably benign Het
Pde5a G A 3: 122,611,658 (GRCm39) C532Y probably damaging Het
Pigq T C 17: 26,150,446 (GRCm39) D442G possibly damaging Het
Pik3c2g T C 6: 139,665,808 (GRCm39) V43A probably benign Het
Pik3cb T C 9: 98,970,716 (GRCm39) N325S probably benign Het
Pot1b T C 17: 56,007,063 (GRCm39) K18R probably benign Het
Ppp1r42 A T 1: 10,069,630 (GRCm39) L144Q probably damaging Het
Prdm13 T A 4: 21,679,455 (GRCm39) Q345L unknown Het
Pyroxd2 T A 19: 42,728,898 (GRCm39) K167N probably benign Het
Rnf123 T C 9: 107,947,930 (GRCm39) Y131C probably damaging Het
Rnf25 T C 1: 74,634,411 (GRCm39) D204G probably damaging Het
Rpf2 G A 10: 40,109,181 (GRCm39) T60I possibly damaging Het
Scaf11 T C 15: 96,317,339 (GRCm39) N742D probably benign Het
Shank1 G A 7: 44,002,075 (GRCm39) D1257N possibly damaging Het
Shc2 A G 10: 79,465,933 (GRCm39) V168A probably damaging Het
Slc16a4 G A 3: 107,199,758 (GRCm39) V2M probably benign Het
Slc24a3 T C 2: 145,455,494 (GRCm39) V461A probably benign Het
Slc45a2 C T 15: 11,027,871 (GRCm39) T480I probably damaging Het
Slc4a4 T A 5: 89,345,623 (GRCm39) probably null Het
Snx30 T A 4: 59,879,329 (GRCm39) D189E probably benign Het
Sspo A G 6: 48,472,194 (GRCm39) Q4653R possibly damaging Het
Tpte G T 8: 22,817,806 (GRCm39) R264I probably damaging Het
Tsc22d4 T A 5: 137,757,036 (GRCm39) probably benign Het
Ubn1 T C 16: 4,892,233 (GRCm39) L585P possibly damaging Het
Usp24 A T 4: 106,265,210 (GRCm39) D1781V probably damaging Het
Utp20 A T 10: 88,608,777 (GRCm39) Y1514* probably null Het
Vmn1r55 A T 7: 5,149,995 (GRCm39) Y143N probably damaging Het
Vmn2r65 A G 7: 84,595,862 (GRCm39) V274A probably benign Het
Wdr17 A G 8: 55,092,524 (GRCm39) S1087P possibly damaging Het
Wnt5b C A 6: 119,417,283 (GRCm39) R156L probably damaging Het
Zan T C 5: 137,433,896 (GRCm39) D2279G unknown Het
Zan T C 5: 137,462,336 (GRCm39) T948A unknown Het
Zfp758 T C 17: 22,591,049 (GRCm39) S4P probably damaging Het
Zfp839 A G 12: 110,822,020 (GRCm39) E278G probably benign Het
Zfp994 T A 17: 22,419,506 (GRCm39) H481L probably damaging Het
Zswim9 G A 7: 12,994,909 (GRCm39) R416C 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
R5344:Col11a1 UTSW 3 114,002,011 (GRCm39) critical splice donor 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'- GCACCAAAGGCATGTGTTTCAAC -3'
(R):5'- GCTGTCATATTAGGACCTAGTTTTC -3'

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