Incidental Mutation 'R0230:Col6a4'
ID 34059
Institutional Source Beutler Lab
Gene Symbol Col6a4
Ensembl Gene ENSMUSG00000032572
Gene Name collagen, type VI, alpha 4
Synonyms Vwa6, EG235580, 1110001D15Rik, Dvwa
MMRRC Submission 038473-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0230 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 105866653-105973982 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 105949565 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Arginine at position 690 (M690R)
Ref Sequence ENSEMBL: ENSMUSP00000112472 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000121963]
AlphaFold A2AX52
Predicted Effect probably benign
Transcript: ENSMUST00000121963
AA Change: M690R

PolyPhen 2 Score 0.107 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000112472
Gene: ENSMUSG00000032572
AA Change: M690R

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
VWA 32 211 2.44e-35 SMART
VWA 233 410 8.67e-50 SMART
VWA 428 604 2.74e-29 SMART
VWA 632 816 4.78e-20 SMART
VWA 847 1019 3.02e-40 SMART
VWA 1028 1204 3.17e-43 SMART
VWA 1210 1391 4.73e-1 SMART
low complexity region 1444 1462 N/A INTRINSIC
PDB:3HR2|B 1469 1593 3e-7 PDB
low complexity region 1594 1622 N/A INTRINSIC
low complexity region 1625 1643 N/A INTRINSIC
low complexity region 1649 1671 N/A INTRINSIC
Pfam:Collagen 1684 1748 1.4e-9 PFAM
VWA 1774 1953 2.18e-14 SMART
VWA 1980 2174 1.89e-9 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137847
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.7%
Validation Efficiency 100% (83/83)
Allele List at MGI
Other mutations in this stock
Total: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Amy1 T C 3: 113,352,079 (GRCm39) D371G probably benign Het
Asrgl1 T A 19: 9,095,883 (GRCm39) probably benign Het
Asxl3 T A 18: 22,585,383 (GRCm39) probably benign Het
B3galnt1 T C 3: 69,482,673 (GRCm39) N196S possibly damaging Het
Bbof1 A G 12: 84,471,978 (GRCm39) H74R probably damaging Het
Bpifb9b C T 2: 154,158,995 (GRCm39) T504M probably damaging Het
Cdk12 T G 11: 98,094,817 (GRCm39) S208R probably damaging Het
Cdk5r1 T C 11: 80,368,576 (GRCm39) L81P probably damaging Het
Chrd T C 16: 20,552,025 (GRCm39) L43P probably benign Het
Cyp39a1 A T 17: 44,042,903 (GRCm39) R418W probably damaging Het
Dars2 C T 1: 160,890,357 (GRCm39) V162M probably benign Het
Dixdc1 C T 9: 50,606,807 (GRCm39) V270M possibly damaging Het
Dnah11 C A 12: 117,946,791 (GRCm39) E1194* probably null Het
Dnah7b T C 1: 46,258,508 (GRCm39) S1900P probably damaging Het
Dnah9 C T 11: 65,746,141 (GRCm39) E3991K probably damaging Het
Dsp A T 13: 38,381,681 (GRCm39) I2210F probably benign Het
Ebf1 A G 11: 44,886,949 (GRCm39) S556G probably damaging Het
Enam G A 5: 88,637,514 (GRCm39) probably benign Het
Eno1b T C 18: 48,180,806 (GRCm39) I328T probably benign Het
Epc1 T C 18: 6,440,168 (GRCm39) D579G probably damaging Het
Ephb3 A T 16: 21,039,525 (GRCm39) I426F probably damaging Het
Fam135b T G 15: 71,317,886 (GRCm39) I1359L probably benign Het
Fcgbpl1 T A 7: 27,856,250 (GRCm39) H2012Q probably damaging Het
Gm16519 T C 17: 71,236,128 (GRCm39) S26P probably benign Het
Gm17622 T A 13: 96,627,594 (GRCm39) probably null Het
Gpat2 G A 2: 127,277,765 (GRCm39) V764I possibly damaging Het
Gpx4 G A 10: 79,890,838 (GRCm39) A81T probably benign Het
Gss C A 2: 155,420,326 (GRCm39) R83L probably damaging Het
Hcls1 C A 16: 36,758,216 (GRCm39) Q36K probably damaging Het
Hepacam2 A G 6: 3,463,336 (GRCm39) V438A probably benign Het
Hnf4a T C 2: 163,401,005 (GRCm39) F184S probably damaging Het
Katnal1 T A 5: 148,855,460 (GRCm39) D90V possibly damaging Het
Kcnt2 A G 1: 140,174,083 (GRCm39) D30G probably benign Het
Kyat1 T C 2: 30,084,087 (GRCm39) E11G probably benign Het
Lefty1 T A 1: 180,764,579 (GRCm39) V168E probably damaging Het
Map2k6 C T 11: 110,387,281 (GRCm39) P218S probably damaging Het
Mlkl C G 8: 112,041,694 (GRCm39) K415N probably benign Het
Myh7 A T 14: 55,211,390 (GRCm39) M1593K probably benign Het
Myo19 T A 11: 84,784,159 (GRCm39) C186S possibly damaging Het
Ngp T C 9: 110,249,069 (GRCm39) L47P probably damaging Het
Nkiras1 A G 14: 18,280,185 (GRCm38) N192S probably benign Het
Or1j17 G A 2: 36,578,628 (GRCm39) V205M probably benign Het
Or2n1 A G 17: 38,486,841 (GRCm39) I289V probably damaging Het
Or2z8 C T 8: 72,812,244 (GRCm39) T240M probably damaging Het
Or8u9 T C 2: 86,001,886 (GRCm39) I92V probably benign Het
Pdcd6ip A G 9: 113,514,361 (GRCm39) probably benign Het
Pde4b T C 4: 102,454,707 (GRCm39) Y186H probably benign Het
Pex7 A G 10: 19,780,331 (GRCm39) V101A possibly damaging Het
Phldb3 G A 7: 24,312,004 (GRCm39) R106Q probably benign Het
Plxnc1 A G 10: 94,635,209 (GRCm39) V1339A probably benign Het
Proser1 A G 3: 53,386,383 (GRCm39) N755S probably damaging Het
Ptpn13 A G 5: 103,674,997 (GRCm39) D658G probably damaging Het
Rassf8 A C 6: 145,765,700 (GRCm39) probably benign Het
Rfc4 G A 16: 22,932,849 (GRCm39) Q363* probably null Het
Rxfp1 T C 3: 79,552,282 (GRCm39) N673S probably damaging Het
Scn7a T C 2: 66,556,628 (GRCm39) E319G probably damaging Het
Scnn1g A G 7: 121,345,984 (GRCm39) probably benign Het
Scube2 C T 7: 109,423,971 (GRCm39) probably null Het
Slc4a4 A C 5: 89,304,195 (GRCm39) H502P possibly damaging Het
Slc6a13 A G 6: 121,301,262 (GRCm39) N184D probably benign Het
Slco1a5 T A 6: 142,182,054 (GRCm39) probably benign Het
Slf1 T A 13: 77,260,867 (GRCm39) probably benign Het
Smarca4 G A 9: 21,612,168 (GRCm39) V1518I probably damaging Het
Smyd3 A G 1: 179,250,993 (GRCm39) probably benign Het
Sox5 A G 6: 144,155,064 (GRCm39) F11L probably benign Het
Spag17 T C 3: 100,014,143 (GRCm39) S2139P probably benign Het
Spice1 A T 16: 44,185,939 (GRCm39) probably benign Het
Sptan1 T A 2: 29,900,704 (GRCm39) probably benign Het
Srebf2 T A 15: 82,066,286 (GRCm39) N571K probably damaging Het
Tbl3 A G 17: 24,920,307 (GRCm39) L670P probably damaging Het
Tmem45a2 A G 16: 56,867,359 (GRCm39) V114A possibly damaging Het
Tmigd3 A G 3: 105,826,053 (GRCm39) N132D possibly damaging Het
Ttn T C 2: 76,567,778 (GRCm39) D19378G probably damaging Het
Ugcg C A 4: 59,189,739 (GRCm39) Y32* probably null Het
Ush2a C T 1: 188,582,301 (GRCm39) P3788L probably damaging Het
Usp22 T A 11: 61,050,023 (GRCm39) probably benign Het
Xaf1 T C 11: 72,197,381 (GRCm39) probably benign Het
Zbtb41 C T 1: 139,374,673 (GRCm39) T711I probably damaging Het
Zfp457 T C 13: 67,442,180 (GRCm39) T132A possibly damaging Het
Zfp64 T G 2: 168,754,150 (GRCm39) probably benign Het
Other mutations in Col6a4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00573:Col6a4 APN 9 105,900,095 (GRCm39) missense probably benign 0.00
IGL00691:Col6a4 APN 9 105,934,606 (GRCm39) missense probably damaging 1.00
IGL01508:Col6a4 APN 9 105,890,804 (GRCm39) missense possibly damaging 0.95
IGL01580:Col6a4 APN 9 105,945,397 (GRCm39) missense probably damaging 1.00
IGL01610:Col6a4 APN 9 105,924,906 (GRCm39) splice site probably benign
IGL01813:Col6a4 APN 9 105,954,452 (GRCm39) missense probably damaging 1.00
IGL01933:Col6a4 APN 9 105,937,313 (GRCm39) missense probably benign 0.04
IGL01973:Col6a4 APN 9 105,940,093 (GRCm39) missense probably damaging 1.00
IGL02053:Col6a4 APN 9 105,940,294 (GRCm39) missense possibly damaging 0.92
IGL02063:Col6a4 APN 9 105,934,617 (GRCm39) missense probably benign 0.01
IGL02065:Col6a4 APN 9 105,954,302 (GRCm39) missense probably damaging 0.99
IGL02106:Col6a4 APN 9 105,940,304 (GRCm39) missense possibly damaging 0.95
IGL02220:Col6a4 APN 9 105,940,141 (GRCm39) missense possibly damaging 0.91
IGL02228:Col6a4 APN 9 105,945,277 (GRCm39) missense probably benign
IGL02234:Col6a4 APN 9 105,890,631 (GRCm39) missense possibly damaging 0.92
IGL02294:Col6a4 APN 9 105,943,931 (GRCm39) missense probably benign 0.04
IGL02314:Col6a4 APN 9 105,874,355 (GRCm39) missense probably damaging 0.99
IGL03065:Col6a4 APN 9 105,918,363 (GRCm39) splice site probably benign
IGL03086:Col6a4 APN 9 105,960,061 (GRCm39) splice site probably benign
IGL03185:Col6a4 APN 9 105,896,653 (GRCm39) missense probably damaging 0.97
R0092:Col6a4 UTSW 9 105,890,513 (GRCm39) missense probably benign 0.04
R0095:Col6a4 UTSW 9 105,952,555 (GRCm39) missense probably benign 0.03
R0359:Col6a4 UTSW 9 105,874,345 (GRCm39) missense probably benign
R0415:Col6a4 UTSW 9 105,952,279 (GRCm39) missense probably damaging 0.99
R0433:Col6a4 UTSW 9 105,945,193 (GRCm39) missense probably damaging 0.99
R0450:Col6a4 UTSW 9 105,957,746 (GRCm39) missense probably damaging 1.00
R0469:Col6a4 UTSW 9 105,957,746 (GRCm39) missense probably damaging 1.00
R0490:Col6a4 UTSW 9 105,890,969 (GRCm39) missense probably damaging 0.99
R0621:Col6a4 UTSW 9 105,943,990 (GRCm39) missense probably damaging 0.97
R0667:Col6a4 UTSW 9 105,907,158 (GRCm39) splice site probably benign
R0681:Col6a4 UTSW 9 105,944,343 (GRCm39) nonsense probably null
R0690:Col6a4 UTSW 9 105,905,386 (GRCm39) splice site probably benign
R0714:Col6a4 UTSW 9 105,895,102 (GRCm39) unclassified probably benign
R0788:Col6a4 UTSW 9 105,949,197 (GRCm39) missense probably benign 0.15
R1036:Col6a4 UTSW 9 105,945,397 (GRCm39) missense probably damaging 1.00
R1296:Col6a4 UTSW 9 105,940,052 (GRCm39) missense possibly damaging 0.47
R1386:Col6a4 UTSW 9 105,940,144 (GRCm39) missense probably benign 0.15
R1484:Col6a4 UTSW 9 105,890,501 (GRCm39) critical splice donor site probably null
R1528:Col6a4 UTSW 9 105,952,419 (GRCm39) missense probably damaging 0.99
R1555:Col6a4 UTSW 9 105,878,085 (GRCm39) missense possibly damaging 0.93
R1622:Col6a4 UTSW 9 105,874,334 (GRCm39) missense probably benign 0.01
R1653:Col6a4 UTSW 9 105,949,608 (GRCm39) missense probably damaging 0.99
R1720:Col6a4 UTSW 9 105,903,671 (GRCm39) missense probably damaging 1.00
R1768:Col6a4 UTSW 9 105,957,299 (GRCm39) missense probably benign
R1941:Col6a4 UTSW 9 105,952,209 (GRCm39) missense probably benign 0.00
R2092:Col6a4 UTSW 9 105,937,530 (GRCm39) missense probably damaging 1.00
R2134:Col6a4 UTSW 9 105,943,860 (GRCm39) missense probably benign 0.09
R2149:Col6a4 UTSW 9 105,954,128 (GRCm39) missense probably benign 0.00
R2174:Col6a4 UTSW 9 105,937,331 (GRCm39) missense probably damaging 0.98
R2204:Col6a4 UTSW 9 105,937,331 (GRCm39) missense probably damaging 0.98
R2248:Col6a4 UTSW 9 105,957,158 (GRCm39) missense probably benign 0.15
R2568:Col6a4 UTSW 9 105,940,275 (GRCm39) missense possibly damaging 0.90
R3750:Col6a4 UTSW 9 105,897,864 (GRCm39) critical splice acceptor site probably null
R3751:Col6a4 UTSW 9 105,949,313 (GRCm39) missense probably damaging 0.98
R3776:Col6a4 UTSW 9 105,928,900 (GRCm39) nonsense probably null
R3872:Col6a4 UTSW 9 105,890,858 (GRCm39) missense possibly damaging 0.95
R4043:Col6a4 UTSW 9 105,949,610 (GRCm39) nonsense probably null
R4056:Col6a4 UTSW 9 105,903,665 (GRCm39) missense probably damaging 0.98
R4212:Col6a4 UTSW 9 105,952,569 (GRCm39) missense probably benign 0.28
R4417:Col6a4 UTSW 9 105,949,215 (GRCm39) missense probably damaging 0.99
R4683:Col6a4 UTSW 9 105,957,329 (GRCm39) missense probably benign 0.00
R4719:Col6a4 UTSW 9 105,945,451 (GRCm39) missense probably damaging 0.99
R4791:Col6a4 UTSW 9 105,957,401 (GRCm39) missense possibly damaging 0.68
R4833:Col6a4 UTSW 9 105,949,178 (GRCm39) missense probably benign 0.00
R4886:Col6a4 UTSW 9 105,937,271 (GRCm39) missense probably benign 0.00
R4998:Col6a4 UTSW 9 105,867,977 (GRCm39) utr 3 prime probably benign
R5091:Col6a4 UTSW 9 105,952,262 (GRCm39) missense probably damaging 1.00
R5113:Col6a4 UTSW 9 105,944,159 (GRCm39) missense possibly damaging 0.89
R5129:Col6a4 UTSW 9 105,890,576 (GRCm39) missense probably damaging 0.98
R5231:Col6a4 UTSW 9 105,902,730 (GRCm39) missense probably damaging 0.96
R5297:Col6a4 UTSW 9 105,952,066 (GRCm39) missense probably benign 0.02
R5352:Col6a4 UTSW 9 105,938,743 (GRCm39) missense probably damaging 1.00
R5438:Col6a4 UTSW 9 105,890,895 (GRCm39) missense possibly damaging 0.95
R5518:Col6a4 UTSW 9 105,949,387 (GRCm39) missense possibly damaging 0.68
R5657:Col6a4 UTSW 9 105,949,397 (GRCm39) missense probably damaging 0.99
R5660:Col6a4 UTSW 9 105,873,315 (GRCm39) missense probably benign 0.01
R5662:Col6a4 UTSW 9 105,945,200 (GRCm39) missense probably damaging 0.99
R5777:Col6a4 UTSW 9 105,890,895 (GRCm39) missense possibly damaging 0.95
R5800:Col6a4 UTSW 9 105,957,474 (GRCm39) missense probably damaging 0.99
R5929:Col6a4 UTSW 9 105,940,243 (GRCm39) missense probably benign 0.15
R5999:Col6a4 UTSW 9 105,945,120 (GRCm39) missense probably benign 0.11
R6243:Col6a4 UTSW 9 105,890,589 (GRCm39) missense possibly damaging 0.95
R6285:Col6a4 UTSW 9 105,952,185 (GRCm39) missense probably damaging 0.96
R6288:Col6a4 UTSW 9 105,945,462 (GRCm39) missense probably damaging 0.99
R6361:Col6a4 UTSW 9 105,943,902 (GRCm39) missense probably benign 0.28
R6485:Col6a4 UTSW 9 105,954,069 (GRCm39) critical splice donor site probably null
R6490:Col6a4 UTSW 9 105,952,191 (GRCm39) nonsense probably null
R6537:Col6a4 UTSW 9 105,945,153 (GRCm39) missense possibly damaging 0.87
R6598:Col6a4 UTSW 9 105,877,611 (GRCm39) missense probably damaging 0.99
R6643:Col6a4 UTSW 9 105,877,830 (GRCm39) missense probably damaging 0.96
R6905:Col6a4 UTSW 9 105,937,517 (GRCm39) splice site probably null
R6944:Col6a4 UTSW 9 105,949,370 (GRCm39) missense probably damaging 0.98
R7015:Col6a4 UTSW 9 105,910,954 (GRCm39) critical splice donor site probably null
R7027:Col6a4 UTSW 9 105,944,213 (GRCm39) missense probably damaging 1.00
R7088:Col6a4 UTSW 9 105,877,885 (GRCm39) missense possibly damaging 0.56
R7200:Col6a4 UTSW 9 105,949,448 (GRCm39) missense possibly damaging 0.68
R7238:Col6a4 UTSW 9 105,877,519 (GRCm39) missense probably damaging 0.99
R7273:Col6a4 UTSW 9 105,877,656 (GRCm39) missense possibly damaging 0.92
R7335:Col6a4 UTSW 9 105,954,091 (GRCm39) missense possibly damaging 0.90
R7418:Col6a4 UTSW 9 105,900,114 (GRCm39) missense probably damaging 1.00
R7421:Col6a4 UTSW 9 105,897,994 (GRCm39) missense probably damaging 0.99
R7530:Col6a4 UTSW 9 105,945,589 (GRCm39) missense probably damaging 0.99
R7600:Col6a4 UTSW 9 105,944,198 (GRCm39) missense possibly damaging 0.86
R7701:Col6a4 UTSW 9 105,960,087 (GRCm39) missense probably benign 0.17
R7830:Col6a4 UTSW 9 105,952,589 (GRCm39) missense probably damaging 0.99
R7881:Col6a4 UTSW 9 105,957,497 (GRCm39) missense probably benign 0.14
R8157:Col6a4 UTSW 9 105,945,097 (GRCm39) missense possibly damaging 0.92
R8292:Col6a4 UTSW 9 105,954,076 (GRCm39) missense probably benign 0.01
R8309:Col6a4 UTSW 9 105,952,414 (GRCm39) missense probably benign 0.08
R8336:Col6a4 UTSW 9 105,952,528 (GRCm39) missense possibly damaging 0.65
R8359:Col6a4 UTSW 9 105,945,583 (GRCm39) missense probably benign 0.00
R8530:Col6a4 UTSW 9 105,957,704 (GRCm39) missense probably benign 0.31
R8556:Col6a4 UTSW 9 105,944,252 (GRCm39) missense probably damaging 0.96
R8832:Col6a4 UTSW 9 105,949,353 (GRCm39) missense probably benign
R9001:Col6a4 UTSW 9 105,944,370 (GRCm39) missense probably benign 0.26
R9009:Col6a4 UTSW 9 105,954,404 (GRCm39) missense probably benign 0.38
R9069:Col6a4 UTSW 9 105,952,138 (GRCm39) missense possibly damaging 0.85
R9155:Col6a4 UTSW 9 105,952,209 (GRCm39) missense probably benign
R9175:Col6a4 UTSW 9 105,957,560 (GRCm39) missense probably benign
R9176:Col6a4 UTSW 9 105,938,755 (GRCm39) missense probably damaging 1.00
R9295:Col6a4 UTSW 9 105,957,734 (GRCm39) missense probably damaging 1.00
R9298:Col6a4 UTSW 9 105,945,534 (GRCm39) missense probably damaging 0.96
R9389:Col6a4 UTSW 9 105,877,983 (GRCm39) missense probably damaging 1.00
R9424:Col6a4 UTSW 9 105,945,271 (GRCm39) missense probably benign 0.30
R9576:Col6a4 UTSW 9 105,945,271 (GRCm39) missense probably benign 0.30
RF022:Col6a4 UTSW 9 105,954,207 (GRCm39) missense probably damaging 0.99
X0025:Col6a4 UTSW 9 105,877,654 (GRCm39) missense probably damaging 0.99
Z1176:Col6a4 UTSW 9 105,878,069 (GRCm39) missense probably damaging 0.99
Z1176:Col6a4 UTSW 9 105,877,996 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- ATTCCGCTCAACATCTCAGGGCAG -3'
(R):5'- AGGACTTTAGCAGTGCCAGGCAAC -3'

Sequencing Primer
(F):5'- AGGGTATGTGACAATCTTCTCCAG -3'
(R):5'- GTGCCAGGCAACCCAATTTC -3'
Posted On 2013-05-09