Incidental Mutation 'R6259:Col11a1'
ID 523289
Institutional Source Beutler Lab
Gene Symbol Col11a1
Ensembl Gene ENSMUSG00000027966
Gene Name collagen, type XI, alpha 1
Synonyms C530001D20Rik
MMRRC Submission 044376-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.939) question?
Stock # R6259 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 113824189-114014367 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 113932096 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Arginine at position 89 (C89R)
Ref Sequence ENSEMBL: ENSMUSP00000148798 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000092155] [ENSMUST00000211802]
AlphaFold Q61245
Predicted Effect silent
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: ENSMUST00000211802
AA Change: C89R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.5%
  • 20x: 96.0%
Validation Efficiency 99% (74/75)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5730507C01Rik C A 12: 18,584,120 (GRCm39) N393K probably benign Het
Acap3 A T 4: 155,980,575 (GRCm39) I19F possibly damaging Het
Acsbg3 A G 17: 57,184,513 (GRCm39) Y96C probably benign Het
Adamts5 C T 16: 85,696,641 (GRCm39) R172H probably benign Het
Adgra3 A G 5: 50,156,483 (GRCm39) F416L possibly damaging Het
Amy1 T C 3: 113,363,059 (GRCm39) D96G possibly damaging Het
Ank2 A G 3: 126,810,635 (GRCm39) S484P probably benign Het
Arsa A G 15: 89,359,724 (GRCm39) C68R probably damaging Het
Asprv1 A G 6: 86,605,361 (GRCm39) Y69C probably benign Het
Ass1 A G 2: 31,378,654 (GRCm39) E162G possibly damaging Het
Atf7 G T 15: 102,455,673 (GRCm39) N230K probably damaging Het
Atp10b A G 11: 43,092,065 (GRCm39) M367V probably benign Het
Atp11b A G 3: 35,861,050 (GRCm39) Y179C probably damaging Het
BC004004 A T 17: 29,517,686 (GRCm39) Q300L possibly damaging Het
Bglap3 A T 3: 88,276,067 (GRCm39) I95N probably damaging Het
Cacna1h T C 17: 25,616,630 (GRCm39) probably null Het
Caskin2 C T 11: 115,691,279 (GRCm39) G1141D probably damaging Het
Clcn4 G A 7: 7,294,529 (GRCm39) R351W possibly damaging Het
Csrp1 T G 1: 135,667,252 (GRCm39) probably null Het
Cwf19l2 T C 9: 3,458,879 (GRCm39) I776T probably damaging Het
Cyp2b19 A T 7: 26,470,817 (GRCm39) Q486L possibly damaging Het
Cyp2j9 T A 4: 96,472,243 (GRCm39) Y165F probably benign Het
Dab1 C T 4: 104,588,948 (GRCm39) A524V probably benign Het
Dennd1c G A 17: 57,374,104 (GRCm39) R522C probably damaging Het
Dmgdh T C 13: 93,888,816 (GRCm39) V818A probably benign Het
Dst T A 1: 34,221,477 (GRCm39) V2427E probably benign Het
Duox1 C T 2: 122,175,264 (GRCm39) T1354M probably benign Het
Ehbp1 A G 11: 22,235,684 (GRCm39) probably benign Het
Epc2 T A 2: 49,378,866 (GRCm39) probably null Het
Eya2 T C 2: 165,558,019 (GRCm39) V205A probably benign Het
Fat4 A G 3: 39,061,395 (GRCm39) H4326R probably benign Het
Gaa C A 11: 119,171,997 (GRCm39) A700D probably benign Het
Gm10100 G T 10: 77,562,498 (GRCm39) C60F possibly damaging Het
Hhip T A 8: 80,699,033 (GRCm39) R678W probably damaging Het
Il21r T A 7: 125,229,891 (GRCm39) I266K possibly damaging Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Kif26b T C 1: 178,744,970 (GRCm39) S1689P probably damaging Het
L3mbtl2 A G 15: 81,566,128 (GRCm39) E317G probably damaging Het
Lgr6 C T 1: 134,921,748 (GRCm39) A199T probably damaging Het
Lratd1 T A 12: 14,200,646 (GRCm39) D27V probably damaging Het
Lrr1 A G 12: 69,221,589 (GRCm39) N244D probably damaging Het
Lrrk2 A T 15: 91,586,450 (GRCm39) H422L probably benign Het
Map4k5 A G 12: 69,899,514 (GRCm39) S46P probably damaging Het
Ngf A G 3: 102,417,113 (GRCm39) probably benign Het
Nploc4 T C 11: 120,276,691 (GRCm39) I452V probably benign Het
Oas1d T A 5: 121,057,244 (GRCm39) Y283* probably null Het
Or52h1 A T 7: 103,829,261 (GRCm39) M118K possibly damaging Het
Or56b35 A T 7: 104,963,264 (GRCm39) I18F probably benign Het
Or5b109 A G 19: 13,211,785 (GRCm39) H57R probably damaging Het
Or5l13 T C 2: 87,779,779 (GRCm39) N266S probably benign Het
Pdzrn4 A T 15: 92,655,562 (GRCm39) E485V probably damaging Het
Peg3 A G 7: 6,712,810 (GRCm39) V804A probably damaging Het
Piezo2 T A 18: 63,250,749 (GRCm39) Y450F possibly damaging Het
Pprc1 T A 19: 46,052,849 (GRCm39) V789E probably damaging Het
Prcc A G 3: 87,769,454 (GRCm39) M436T possibly damaging Het
Prepl A T 17: 85,377,859 (GRCm39) V507D probably damaging Het
Rag1 T A 2: 101,474,797 (GRCm39) N115I possibly damaging Het
Rap1gap T C 4: 137,409,068 (GRCm39) probably null Het
Reln A C 5: 22,265,331 (GRCm39) F454V probably damaging Het
Slc39a11 A T 11: 113,354,780 (GRCm39) S150T probably benign Het
Slc45a1 T A 4: 150,722,817 (GRCm39) I356F possibly damaging Het
Snrnp200 G A 2: 127,060,343 (GRCm39) G529D possibly damaging Het
Stkld1 A T 2: 26,839,393 (GRCm39) D353V possibly damaging Het
Susd2 T C 10: 75,473,880 (GRCm39) S572G probably damaging Het
Synrg T A 11: 83,899,484 (GRCm39) D563E probably damaging Het
Tmem131 C T 1: 36,858,209 (GRCm39) V713I probably benign Het
Tnfrsf8 A G 4: 145,004,094 (GRCm39) probably null Het
Trim26 C T 17: 37,167,110 (GRCm39) A267V probably benign Het
Trpm1 T G 7: 63,918,226 (GRCm39) F522C possibly damaging Het
Uggt1 T C 1: 36,273,997 (GRCm39) I29V probably benign Het
Unc5d C T 8: 29,156,820 (GRCm39) M808I probably benign Het
Vmn2r108 T A 17: 20,683,371 (GRCm39) D611V possibly damaging Het
Vps13a A C 19: 16,664,534 (GRCm39) Y1436* probably null Het
Wdfy3 C T 5: 102,020,831 (GRCm39) R2491Q possibly damaging Het
Zfp518a G T 19: 40,901,225 (GRCm39) V385F probably benign Het
Zfp541 C T 7: 15,829,451 (GRCm39) A1222V probably benign Het
Zfp709 TCGACG TCG 8: 72,644,552 (GRCm39) probably benign 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
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
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'- GCAAGAACGGACCTTATGTAGTG -3'
(R):5'- AAACTAAGTACCCACCGTTGG -3'

Sequencing Primer
(F):5'- CGGACCTTATGTAGTGACTAAAATAC -3'
(R):5'- ACCGTTGGACCACGCTGTC -3'
Posted On 2018-06-18