Incidental Mutation 'R0239:Col4a1'
ID 59231
Institutional Source Beutler Lab
Gene Symbol Col4a1
Ensembl Gene ENSMUSG00000031502
Gene Name collagen, type IV, alpha 1
Synonyms Del(8)Bru44H, Del(8)44H, alpha1(IV) collagen, Col4a-1, Bru, Svc, Raw
MMRRC Submission 038477-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0239 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 11248423-11362826 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) C to T at 11268780 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000147951 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000033898] [ENSMUST00000209661] [ENSMUST00000209735]
AlphaFold P02463
Predicted Effect probably benign
Transcript: ENSMUST00000033898
SMART Domains Protein: ENSMUSP00000033898
Gene: ENSMUSG00000031502

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
low complexity region 28 43 N/A INTRINSIC
internal_repeat_2 49 89 2.1e-8 PROSPERO
Pfam:Collagen 103 163 6.1e-11 PFAM
Pfam:Collagen 167 225 7.8e-10 PFAM
low complexity region 232 248 N/A INTRINSIC
Pfam:Collagen 274 334 1.7e-11 PFAM
low complexity region 356 389 N/A INTRINSIC
low complexity region 404 426 N/A INTRINSIC
low complexity region 435 455 N/A INTRINSIC
Pfam:Collagen 472 533 7.3e-12 PFAM
Pfam:Collagen 539 597 4.8e-9 PFAM
low complexity region 600 636 N/A INTRINSIC
Pfam:Collagen 642 689 4.5e-8 PFAM
Pfam:Collagen 689 746 3.5e-8 PFAM
Pfam:Collagen 736 800 2.2e-9 PFAM
Pfam:Collagen 837 896 5.2e-11 PFAM
Pfam:Collagen 882 940 1.9e-10 PFAM
Pfam:Collagen 943 1007 1.7e-10 PFAM
Pfam:Collagen 996 1058 2e-9 PFAM
Pfam:Collagen 1057 1121 1.5e-10 PFAM
low complexity region 1133 1148 N/A INTRINSIC
Pfam:Collagen 1174 1233 8.6e-11 PFAM
low complexity region 1236 1266 N/A INTRINSIC
Pfam:Collagen 1269 1337 1e-8 PFAM
Pfam:Collagen 1290 1354 2.2e-9 PFAM
Pfam:Collagen 1384 1443 1e-10 PFAM
C4 1445 1554 3.49e-65 SMART
C4 1555 1668 1.53e-79 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130488
Predicted Effect probably benign
Transcript: ENSMUST00000209661
Predicted Effect probably benign
Transcript: ENSMUST00000209735
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 99.0%
  • 10x: 97.9%
  • 20x: 96.2%
Validation Efficiency 98% (81/83)
MGI Phenotype FUNCTION: This gene encodes the alpha-1 subunit of the type IV collagens, an essential component of basement membranes. The encoded protein forms a triple helical heterotrimer comprised of two alpha-1 and one alpha-2 subunits that assembles into a type IV collagen network. This gene is located adjacent to the gene encoding alpha-2 subunit. Mice lacking both the alpha-1 and alpha-2 subunits of collagen IV die in utero due to structural deficiencies in the basement membranes and certain mutations in this gene cause perinatal cerebral hemorrhage and porencephaly. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2015]
PHENOTYPE: Mice with ENU induced alleles have various eye and vision defects and may show bruising at birth. Mice carrying the G498V mutation have renal glomerular defects that resolve within the first weeks of life, but show retinal tortuosity, muscular dystrophy, brain hemorrhages, and renal cysts as adults. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adra1d C A 2: 131,388,134 (GRCm39) V474F probably benign Het
Alg8 A T 7: 97,032,891 (GRCm39) probably null Het
Ash1l A G 3: 88,974,529 (GRCm39) D2618G possibly damaging Het
Atp6v1c2 C A 12: 17,344,676 (GRCm39) probably null Het
Cacna1d A G 14: 29,845,453 (GRCm39) V572A probably benign Het
Camta1 A G 4: 151,228,187 (GRCm39) W882R probably damaging Het
Cd72 A G 4: 43,453,163 (GRCm39) V91A probably benign Het
Cdh12 T C 15: 21,586,493 (GRCm39) W771R probably damaging Het
Cdx2 G T 5: 147,240,097 (GRCm39) T193K probably damaging Het
Cfap70 A C 14: 20,498,673 (GRCm39) S5A probably benign Het
Chmp7 A G 14: 69,958,446 (GRCm39) V241A probably damaging Het
D3Ertd751e A G 3: 41,708,313 (GRCm39) Y150C probably damaging Het
Depdc5 T C 5: 33,100,584 (GRCm39) S832P probably damaging Het
Dnhd1 A G 7: 105,370,738 (GRCm39) S4673G probably benign Het
Dock4 G T 12: 40,787,539 (GRCm39) S818I probably damaging Het
Dysf C T 6: 84,041,461 (GRCm39) Q156* probably null Het
Elp1 C A 4: 56,784,596 (GRCm39) V466L probably benign Het
Espnl T C 1: 91,250,009 (GRCm39) V52A probably damaging Het
Flcn T C 11: 59,691,902 (GRCm39) N249S probably benign Het
Gemin6 C A 17: 80,533,139 (GRCm39) A24D probably damaging Het
Gm5773 A G 3: 93,681,339 (GRCm39) H337R probably benign Het
Greb1l C T 18: 10,458,567 (GRCm39) probably benign Het
Hal T C 10: 93,339,344 (GRCm39) S478P possibly damaging Het
Hectd1 T A 12: 51,816,101 (GRCm39) M1324L possibly damaging Het
Hyal5 T A 6: 24,876,343 (GRCm39) L72Q probably damaging Het
Ift140 C A 17: 25,264,497 (GRCm39) C557* probably null Het
Il4ra T C 7: 125,174,371 (GRCm39) probably benign Het
Ipo9 A G 1: 135,332,074 (GRCm39) probably benign Het
Irag2 G A 6: 145,117,704 (GRCm39) probably benign Het
Kbtbd3 G T 9: 4,330,144 (GRCm39) V173L possibly damaging Het
Kif14 A G 1: 136,455,131 (GRCm39) E1551G probably damaging Het
Klc1 A G 12: 111,751,758 (GRCm39) probably benign Het
Krt17 G A 11: 100,151,704 (GRCm39) R30* probably null Het
Lamb3 A T 1: 193,003,361 (GRCm39) D100V probably damaging Het
Map2 A G 1: 66,455,265 (GRCm39) D1385G probably damaging Het
Mettl25 C T 10: 105,662,386 (GRCm39) V195I probably damaging Het
Micu2 G A 14: 58,154,835 (GRCm39) probably benign Het
Mrrf T C 2: 36,067,293 (GRCm39) probably benign Het
Myh8 A G 11: 67,192,518 (GRCm39) T1466A probably benign Het
Myo3b T A 2: 69,935,769 (GRCm39) C61S probably benign Het
Nacc2 T G 2: 25,952,273 (GRCm39) N361T probably damaging Het
Nf1 A T 11: 79,309,400 (GRCm39) K438M possibly damaging Het
Nipal4 A G 11: 46,041,268 (GRCm39) V309A possibly damaging Het
Nomo1 T C 7: 45,729,018 (GRCm39) probably null Het
Nubp2 T C 17: 25,103,445 (GRCm39) E144G probably damaging Het
Nwd2 A T 5: 63,957,467 (GRCm39) I266F probably benign Het
Or12e7 T C 2: 87,288,381 (GRCm39) F291L probably benign Het
Or2ag1b A G 7: 106,288,462 (GRCm39) Y159H probably benign Het
Or52s1 G A 7: 102,861,933 (GRCm39) V289M possibly damaging Het
Orc1 T C 4: 108,452,843 (GRCm39) probably null Het
Otogl T A 10: 107,642,557 (GRCm39) N1291I probably damaging Het
Pah C T 10: 87,403,143 (GRCm39) P173S possibly damaging Het
Pga5 A G 19: 10,646,817 (GRCm39) Y305H probably damaging Het
Plekha4 A G 7: 45,181,782 (GRCm39) H62R probably damaging Het
Plxnd1 G T 6: 115,945,754 (GRCm39) D906E probably benign Het
Ppfia4 T C 1: 134,256,927 (GRCm39) E98G possibly damaging Het
Ptk2 A T 15: 73,215,132 (GRCm39) probably null Het
Pzp C T 6: 128,466,119 (GRCm39) probably benign Het
Raet1c C A 10: 22,056,761 (GRCm39) H112Q possibly damaging Het
Scai T A 2: 38,965,054 (GRCm39) I597F probably benign Het
Scgb1b2 T A 7: 30,991,155 (GRCm39) probably benign Het
Sec31b G A 19: 44,513,908 (GRCm39) probably benign Het
Sirpd A G 3: 15,361,661 (GRCm39) L163P probably damaging Het
Slc35c2 C T 2: 165,122,757 (GRCm39) G176S probably damaging Het
Slc35f4 A T 14: 49,541,713 (GRCm39) I347N possibly damaging Het
Slc49a3 G T 5: 108,591,882 (GRCm39) probably benign Het
Slc52a3 T C 2: 151,850,076 (GRCm39) *461Q probably null Het
Slc6a1 G A 6: 114,279,761 (GRCm39) V142I probably benign Het
Tbc1d31 C A 15: 57,804,149 (GRCm39) T388N probably benign Het
Tmem131 T C 1: 36,867,131 (GRCm39) probably benign Het
Tmem63c T C 12: 87,122,413 (GRCm39) W404R probably damaging Het
Tmem79 A G 3: 88,240,628 (GRCm39) S107P probably benign Het
Trip11 C T 12: 101,850,987 (GRCm39) E741K probably damaging Het
Trpm5 G T 7: 142,636,695 (GRCm39) T414N probably damaging Het
Tsnaxip1 T A 8: 106,571,120 (GRCm39) I660N possibly damaging Het
Ube2q2 T C 9: 55,070,291 (GRCm39) S78P probably damaging Het
Vac14 A T 8: 111,362,007 (GRCm39) probably null Het
Vps51 G T 19: 6,121,467 (GRCm39) S185* probably null Het
Zfp11 C T 5: 129,735,302 (GRCm39) G53E possibly damaging Het
Zfp532 A T 18: 65,816,056 (GRCm39) I810F possibly damaging Het
Zfp599 C T 9: 22,161,055 (GRCm39) C370Y probably damaging Het
Other mutations in Col4a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00336:Col4a1 APN 8 11,290,077 (GRCm39) splice site probably benign
IGL00503:Col4a1 APN 8 11,290,076 (GRCm39) splice site probably benign
IGL00938:Col4a1 APN 8 11,286,456 (GRCm39) intron probably benign
IGL01295:Col4a1 APN 8 11,286,075 (GRCm39) intron probably benign
IGL01406:Col4a1 APN 8 11,268,898 (GRCm39) missense probably damaging 1.00
IGL01807:Col4a1 APN 8 11,297,056 (GRCm39) utr 5 prime probably benign
IGL01865:Col4a1 APN 8 11,251,790 (GRCm39) utr 3 prime probably benign
IGL02166:Col4a1 APN 8 11,294,509 (GRCm39) unclassified probably benign
IGL02234:Col4a1 APN 8 11,266,713 (GRCm39) missense probably damaging 1.00
IGL02445:Col4a1 APN 8 11,283,911 (GRCm39) intron probably benign
IGL02719:Col4a1 APN 8 11,281,950 (GRCm39) intron probably benign
IGL02817:Col4a1 APN 8 11,270,259 (GRCm39) missense probably damaging 1.00
IGL02821:Col4a1 APN 8 11,271,375 (GRCm39) missense probably benign 0.04
IGL02870:Col4a1 APN 8 11,271,375 (GRCm39) missense probably benign 0.04
IGL02935:Col4a1 APN 8 11,269,166 (GRCm39) missense probably damaging 1.00
IGL03085:Col4a1 APN 8 11,272,198 (GRCm39) nonsense probably null
Wayne UTSW 8 11,259,650 (GRCm39) missense probably damaging 1.00
IGL03134:Col4a1 UTSW 8 11,290,069 (GRCm39) critical splice acceptor site probably null
R0076:Col4a1 UTSW 8 11,268,713 (GRCm39) missense probably damaging 1.00
R0076:Col4a1 UTSW 8 11,268,713 (GRCm39) missense probably damaging 1.00
R0238:Col4a1 UTSW 8 11,268,780 (GRCm39) splice site probably benign
R0268:Col4a1 UTSW 8 11,317,588 (GRCm39) splice site probably benign
R0320:Col4a1 UTSW 8 11,292,782 (GRCm39) splice site probably null
R0402:Col4a1 UTSW 8 11,249,838 (GRCm39) utr 3 prime probably benign
R0483:Col4a1 UTSW 8 11,286,423 (GRCm39) splice site probably benign
R0511:Col4a1 UTSW 8 11,258,333 (GRCm39) critical splice acceptor site probably null
R0544:Col4a1 UTSW 8 11,276,487 (GRCm39) intron probably benign
R0630:Col4a1 UTSW 8 11,249,889 (GRCm39) splice site probably benign
R0648:Col4a1 UTSW 8 11,296,892 (GRCm39) missense unknown
R0733:Col4a1 UTSW 8 11,268,934 (GRCm39) missense possibly damaging 0.46
R0839:Col4a1 UTSW 8 11,271,015 (GRCm39) missense probably damaging 0.96
R0900:Col4a1 UTSW 8 11,268,014 (GRCm39) small deletion probably benign
R0941:Col4a1 UTSW 8 11,258,296 (GRCm39) missense unknown
R1456:Col4a1 UTSW 8 11,292,829 (GRCm39) splice site probably benign
R1728:Col4a1 UTSW 8 11,262,712 (GRCm39) missense possibly damaging 0.81
R1832:Col4a1 UTSW 8 11,264,644 (GRCm39) splice site probably benign
R1862:Col4a1 UTSW 8 11,276,439 (GRCm39) intron probably benign
R1955:Col4a1 UTSW 8 11,258,228 (GRCm39) splice site probably null
R2058:Col4a1 UTSW 8 11,260,792 (GRCm39) missense probably damaging 0.96
R2263:Col4a1 UTSW 8 11,362,586 (GRCm39) unclassified probably benign
R2696:Col4a1 UTSW 8 11,285,092 (GRCm39) splice site probably null
R3826:Col4a1 UTSW 8 11,259,650 (GRCm39) missense probably damaging 1.00
R3828:Col4a1 UTSW 8 11,259,650 (GRCm39) missense probably damaging 1.00
R3829:Col4a1 UTSW 8 11,259,650 (GRCm39) missense probably damaging 1.00
R3830:Col4a1 UTSW 8 11,259,650 (GRCm39) missense probably damaging 1.00
R3923:Col4a1 UTSW 8 11,251,665 (GRCm39) utr 3 prime probably benign
R3980:Col4a1 UTSW 8 11,289,155 (GRCm39) intron probably benign
R4120:Col4a1 UTSW 8 11,256,263 (GRCm39) missense unknown
R4152:Col4a1 UTSW 8 11,267,227 (GRCm39) splice site probably null
R4437:Col4a1 UTSW 8 11,256,387 (GRCm39) nonsense probably null
R5237:Col4a1 UTSW 8 11,295,068 (GRCm39) unclassified probably benign
R5362:Col4a1 UTSW 8 11,295,760 (GRCm39) unclassified probably benign
R5488:Col4a1 UTSW 8 11,362,550 (GRCm39) unclassified probably benign
R5489:Col4a1 UTSW 8 11,362,550 (GRCm39) unclassified probably benign
R5864:Col4a1 UTSW 8 11,252,973 (GRCm39) utr 3 prime probably benign
R5929:Col4a1 UTSW 8 11,266,788 (GRCm39) missense probably benign 0.17
R6159:Col4a1 UTSW 8 11,270,007 (GRCm39) missense probably damaging 1.00
R6261:Col4a1 UTSW 8 11,257,409 (GRCm39) splice site probably null
R6404:Col4a1 UTSW 8 11,257,409 (GRCm39) splice site probably null
R6520:Col4a1 UTSW 8 11,269,152 (GRCm39) missense probably damaging 1.00
R6862:Col4a1 UTSW 8 11,252,926 (GRCm39) utr 3 prime probably benign
R6974:Col4a1 UTSW 8 11,362,538 (GRCm39) unclassified probably benign
R7329:Col4a1 UTSW 8 11,276,494 (GRCm39) critical splice acceptor site probably null
R7893:Col4a1 UTSW 8 11,270,243 (GRCm39) missense unknown
R8392:Col4a1 UTSW 8 11,258,333 (GRCm39) critical splice acceptor site probably null
R8809:Col4a1 UTSW 8 11,295,916 (GRCm39) missense unknown
R8957:Col4a1 UTSW 8 11,295,906 (GRCm39) unclassified probably benign
R9013:Col4a1 UTSW 8 11,272,270 (GRCm39) missense probably benign 0.02
R9048:Col4a1 UTSW 8 11,281,944 (GRCm39) splice site probably benign
R9102:Col4a1 UTSW 8 11,253,007 (GRCm39) missense possibly damaging 0.67
R9154:Col4a1 UTSW 8 11,267,446 (GRCm39) missense probably damaging 0.99
R9379:Col4a1 UTSW 8 11,249,838 (GRCm39) missense unknown
Z1088:Col4a1 UTSW 8 11,296,859 (GRCm39) splice site probably benign
Z1177:Col4a1 UTSW 8 11,289,024 (GRCm39) missense unknown
Z1177:Col4a1 UTSW 8 11,285,218 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- TCGAAAGCCATCCACCCTAGATGAG -3'
(R):5'- ATAAAGGTTCCCGAGGAGACCCTG -3'

Sequencing Primer
(F):5'- GCCCTGGATCTTCCAAGTG -3'
(R):5'- CGAGGAGACCCTGGAACAC -3'
Posted On 2013-07-11