Incidental Mutation 'R0573:Col4a3'
ID 46502
Institutional Source Beutler Lab
Gene Symbol Col4a3
Ensembl Gene ENSMUSG00000079465
Gene Name collagen, type IV, alpha 3
Synonyms tumstatin, alpha3(IV)
MMRRC Submission 038763-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0573 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 82564647-82699778 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 82694084 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Glutamine at position 1568 (P1568Q)
Ref Sequence ENSEMBL: ENSMUSP00000109084 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000113457] [ENSMUST00000125563] [ENSMUST00000152664]
AlphaFold Q9QZS0
Predicted Effect possibly damaging
Transcript: ENSMUST00000113457
AA Change: P1568Q

PolyPhen 2 Score 0.829 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000109084
Gene: ENSMUSG00000079465
AA Change: P1568Q

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
Pfam:Collagen 41 102 9.6e-11 PFAM
Pfam:Collagen 97 164 3.6e-11 PFAM
Pfam:Collagen 164 223 3.6e-9 PFAM
low complexity region 233 243 N/A INTRINSIC
Pfam:Collagen 284 344 2.4e-10 PFAM
low complexity region 368 393 N/A INTRINSIC
Pfam:Collagen 415 477 5e-10 PFAM
Pfam:Collagen 481 545 1e-9 PFAM
low complexity region 550 585 N/A INTRINSIC
Pfam:Collagen 588 653 8.9e-9 PFAM
Pfam:Collagen 682 744 1.1e-8 PFAM
Pfam:Collagen 743 807 6.9e-10 PFAM
Pfam:Collagen 786 847 1.5e-8 PFAM
Pfam:Collagen 845 904 1.5e-10 PFAM
Pfam:Collagen 887 946 4.1e-10 PFAM
Pfam:Collagen 948 1006 8.1e-11 PFAM
Pfam:Collagen 997 1061 2.8e-10 PFAM
Pfam:Collagen 1057 1120 2.5e-10 PFAM
Pfam:Collagen 1114 1176 1.7e-9 PFAM
Pfam:Collagen 1174 1233 1.1e-9 PFAM
Pfam:Collagen 1232 1295 6.9e-9 PFAM
low complexity region 1326 1347 N/A INTRINSIC
Pfam:Collagen 1377 1439 4.9e-11 PFAM
C4 1444 1553 3.77e-70 SMART
C4 1554 1667 3.28e-70 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000125563
SMART Domains Protein: ENSMUSP00000137944
Gene: ENSMUSG00000079465

DomainStartEndE-ValueType
Pfam:C4 8 60 4.7e-18 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000152664
AA Change: P132Q

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000119094
Gene: ENSMUSG00000079465
AA Change: P132Q

DomainStartEndE-ValueType
C4 8 117 3.77e-70 SMART
Pfam:C4 118 169 4.1e-14 PFAM
low complexity region 185 196 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000181720
Predicted Effect noncoding transcript
Transcript: ENSMUST00000186858
Meta Mutation Damage Score 0.1343 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.5%
Validation Efficiency 97% (60/62)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Type IV collagen, the major structural component of basement membranes, is a multimeric protein composed of 3 alpha subunits. These subunits are encoded by 6 different genes, alpha 1 through alpha 6, each of which can form a triple helix structure with 2 other subunits to form type IV collagen. This gene encodes alpha 3. In the Goodpasture syndrome, autoantibodies bind to the collagen molecules in the basement membranes of alveoli and glomeruli. The epitopes that elicit these autoantibodies are localized largely to the non-collagenous C-terminal domain of the protein. A specific kinase phosphorylates amino acids in this same C-terminal region and the expression of this kinase is upregulated during pathogenesis. This gene is also linked to an autosomal recessive form of Alport syndrome. The mutations contributing to this syndrome are also located within the exons that encode this C-terminal region. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jun 2010]
PHENOTYPE: Homozygotes for targeted null mutations exhibit renal pathology including reduced glomerular filtration, impaired glomerular integrity, and glomerulonephrosis, resulting in uremia, proteinuria, and high mortality in young adults. Auditory thresholds aremildly increased across all test frequencies. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam6b A T 12: 113,455,278 (GRCm39) K698N possibly damaging Het
Adcy8 A T 15: 64,694,044 (GRCm39) V411D probably damaging Het
Arfgef3 T A 10: 18,475,036 (GRCm39) E1550V probably damaging Het
Asb3 T A 11: 31,011,406 (GRCm39) I306K probably damaging Het
Asic4 T A 1: 75,445,746 (GRCm39) probably benign Het
Basp1 G T 15: 25,364,948 (GRCm39) D16E unknown Het
Cbll1 A T 12: 31,540,539 (GRCm39) I123N probably damaging Het
Ccdc141 A T 2: 76,869,837 (GRCm39) H889Q probably benign Het
Ccdc65 T C 15: 98,618,930 (GRCm39) V303A probably benign Het
Ceacam20 T A 7: 19,720,593 (GRCm39) M60K probably damaging Het
Chd9 T A 8: 91,725,223 (GRCm39) V711D probably damaging Het
Clcn1 T A 6: 42,289,979 (GRCm39) probably null Het
Col16a1 A T 4: 129,962,268 (GRCm39) probably benign Het
Colec12 C A 18: 9,858,650 (GRCm39) P478T probably damaging Het
Dchs1 T C 7: 105,407,985 (GRCm39) H1949R probably damaging Het
Dgka A G 10: 128,572,876 (GRCm39) probably null Het
Dlgap4 A G 2: 156,588,111 (GRCm39) I669V probably benign Het
Dsg1c T A 18: 20,412,298 (GRCm39) D543E probably benign Het
Egflam A T 15: 7,271,906 (GRCm39) C677* probably null Het
Eml5 A C 12: 98,791,031 (GRCm39) probably null Het
Fbn1 G A 2: 125,231,169 (GRCm39) R466C probably damaging Het
Fnbp1 C A 2: 30,948,990 (GRCm39) D198Y probably damaging Het
Gfra3 T A 18: 34,824,668 (GRCm39) M272L probably benign Het
Gm5422 T A 10: 31,126,156 (GRCm39) noncoding transcript Het
Gpr21 T A 2: 37,407,556 (GRCm39) I34N probably damaging Het
Hspb2 G T 9: 50,662,664 (GRCm39) T155K probably benign Het
Il21r A G 7: 125,224,457 (GRCm39) T24A probably benign Het
Mmadhc T A 2: 50,182,847 (GRCm39) H43L possibly damaging Het
Morn1 T A 4: 155,195,473 (GRCm39) D278E possibly damaging Het
Myoc T C 1: 162,476,243 (GRCm39) Y316H probably damaging Het
Nags A G 11: 102,037,805 (GRCm39) D266G probably damaging Het
Nlrp4b A G 7: 10,448,142 (GRCm39) N115S probably benign Het
Nlrp5 T A 7: 23,117,056 (GRCm39) I260N probably damaging Het
Obscn G A 11: 58,926,905 (GRCm39) R6190C probably damaging Het
Or5b24 T C 19: 12,912,624 (GRCm39) V174A possibly damaging Het
Or5be3 A G 2: 86,863,812 (GRCm39) F251S probably damaging Het
Orc4 C T 2: 48,807,285 (GRCm39) M215I probably benign Het
Osbpl6 A T 2: 76,420,735 (GRCm39) H770L probably damaging Het
Otogl A C 10: 107,616,849 (GRCm39) N1809K probably benign Het
Pde3a G T 6: 141,437,957 (GRCm39) V1009L probably damaging Het
Pign T C 1: 105,580,902 (GRCm39) Y159C probably damaging Het
Pik3cg C A 12: 32,247,196 (GRCm39) M842I probably damaging Het
Pnliprp1 C T 19: 58,723,314 (GRCm39) T235I possibly damaging Het
Pramel17 A C 4: 101,692,611 (GRCm39) V463G probably damaging Het
Prpf8 A G 11: 75,381,480 (GRCm39) N239D probably damaging Het
Psd2 T A 18: 36,113,546 (GRCm39) probably benign Het
Ptprt T C 2: 161,393,668 (GRCm39) D1251G probably damaging Het
Pwp2 G A 10: 78,018,520 (GRCm39) S88L probably benign Het
Rassf4 C T 6: 116,624,516 (GRCm39) probably benign Het
Rexo1 A G 10: 80,380,684 (GRCm39) S884P probably damaging Het
Rgs20 C A 1: 5,091,037 (GRCm39) R131L possibly damaging Het
Setd4 A G 16: 93,386,834 (GRCm39) V288A probably benign Het
Stx3 G T 19: 11,763,110 (GRCm39) T160K probably damaging Het
Tas2r102 T A 6: 132,739,636 (GRCm39) S181R probably damaging Het
Tenm3 T C 8: 49,127,434 (GRCm39) probably benign Het
Tmem33 T C 5: 67,421,603 (GRCm39) probably benign Het
Trim33 A G 3: 103,259,306 (GRCm39) probably benign Het
Trip11 A G 12: 101,853,119 (GRCm39) I491T probably benign Het
Trp53bp1 A G 2: 121,058,653 (GRCm39) probably benign Het
Tuba4a T C 1: 75,193,017 (GRCm39) D199G probably benign Het
Zcchc4 A G 5: 52,953,321 (GRCm39) Y110C probably damaging Het
Zp2 C T 7: 119,734,693 (GRCm39) probably benign Het
Other mutations in Col4a3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00693:Col4a3 APN 1 82,675,475 (GRCm39) missense unknown
IGL00847:Col4a3 APN 1 82,695,590 (GRCm39) missense probably damaging 1.00
IGL01011:Col4a3 APN 1 82,660,022 (GRCm39) missense unknown
IGL01102:Col4a3 APN 1 82,647,976 (GRCm39) missense unknown
IGL01102:Col4a3 APN 1 82,647,441 (GRCm39) missense unknown
IGL02071:Col4a3 APN 1 82,638,608 (GRCm39) critical splice donor site probably null
IGL02244:Col4a3 APN 1 82,647,492 (GRCm39) splice site probably benign
IGL02380:Col4a3 APN 1 82,650,509 (GRCm39) splice site probably benign
IGL02431:Col4a3 APN 1 82,657,344 (GRCm39) nonsense probably null
IGL02466:Col4a3 APN 1 82,647,913 (GRCm39) missense unknown
IGL02694:Col4a3 APN 1 82,688,515 (GRCm39) unclassified probably benign
IGL02709:Col4a3 APN 1 82,656,833 (GRCm39) missense unknown
IGL02752:Col4a3 APN 1 82,637,946 (GRCm39) missense unknown
IGL02792:Col4a3 APN 1 82,696,524 (GRCm39) missense probably damaging 1.00
IGL03203:Col4a3 APN 1 82,650,360 (GRCm39) nonsense probably null
IGL03218:Col4a3 APN 1 82,620,927 (GRCm39) splice site probably benign
FR4976:Col4a3 UTSW 1 82,696,627 (GRCm39) frame shift probably null
PIT4260001:Col4a3 UTSW 1 82,660,482 (GRCm39) missense unknown
PIT4515001:Col4a3 UTSW 1 82,660,024 (GRCm39) missense unknown
R0035:Col4a3 UTSW 1 82,650,474 (GRCm39) missense unknown
R0099:Col4a3 UTSW 1 82,695,714 (GRCm39) missense probably benign 0.41
R0433:Col4a3 UTSW 1 82,647,940 (GRCm39) missense unknown
R0606:Col4a3 UTSW 1 82,650,307 (GRCm39) splice site probably benign
R0715:Col4a3 UTSW 1 82,629,879 (GRCm39) splice site probably benign
R0961:Col4a3 UTSW 1 82,686,297 (GRCm39) splice site probably benign
R1257:Col4a3 UTSW 1 82,694,086 (GRCm39) missense probably damaging 1.00
R1264:Col4a3 UTSW 1 82,621,022 (GRCm39) splice site probably benign
R1373:Col4a3 UTSW 1 82,667,808 (GRCm39) splice site probably benign
R1694:Col4a3 UTSW 1 82,668,384 (GRCm39) splice site probably null
R1895:Col4a3 UTSW 1 82,656,829 (GRCm39) missense unknown
R1925:Col4a3 UTSW 1 82,689,595 (GRCm39) unclassified probably benign
R1925:Col4a3 UTSW 1 82,678,094 (GRCm39) missense unknown
R2033:Col4a3 UTSW 1 82,695,732 (GRCm39) intron probably benign
R2044:Col4a3 UTSW 1 82,674,040 (GRCm39) missense unknown
R2122:Col4a3 UTSW 1 82,632,678 (GRCm39) missense unknown
R2282:Col4a3 UTSW 1 82,686,359 (GRCm39) missense unknown
R2318:Col4a3 UTSW 1 82,626,290 (GRCm39) splice site probably null
R2421:Col4a3 UTSW 1 82,647,996 (GRCm39) splice site probably benign
R2517:Col4a3 UTSW 1 82,658,431 (GRCm39) missense unknown
R2965:Col4a3 UTSW 1 82,626,321 (GRCm39) missense unknown
R3085:Col4a3 UTSW 1 82,628,979 (GRCm39) missense unknown
R3150:Col4a3 UTSW 1 82,634,858 (GRCm39) splice site probably null
R3947:Col4a3 UTSW 1 82,693,053 (GRCm39) missense probably damaging 1.00
R4756:Col4a3 UTSW 1 82,694,018 (GRCm39) critical splice acceptor site probably null
R4910:Col4a3 UTSW 1 82,650,400 (GRCm39) missense unknown
R4928:Col4a3 UTSW 1 82,688,698 (GRCm39) unclassified probably benign
R5044:Col4a3 UTSW 1 82,644,267 (GRCm39) missense unknown
R5557:Col4a3 UTSW 1 82,692,968 (GRCm39) unclassified probably benign
R5761:Col4a3 UTSW 1 82,693,778 (GRCm39) nonsense probably null
R5970:Col4a3 UTSW 1 82,694,050 (GRCm39) missense possibly damaging 0.76
R6576:Col4a3 UTSW 1 82,686,295 (GRCm39) splice site probably null
R6583:Col4a3 UTSW 1 82,619,197 (GRCm39) missense unknown
R6675:Col4a3 UTSW 1 82,646,646 (GRCm39) missense unknown
R7170:Col4a3 UTSW 1 82,693,630 (GRCm39) splice site probably null
R7592:Col4a3 UTSW 1 82,626,338 (GRCm39) missense unknown
R7624:Col4a3 UTSW 1 82,696,605 (GRCm39) missense probably benign
R7994:Col4a3 UTSW 1 82,640,627 (GRCm39) missense unknown
R8127:Col4a3 UTSW 1 82,627,481 (GRCm39) missense unknown
R8702:Col4a3 UTSW 1 82,688,700 (GRCm39) missense unknown
R8865:Col4a3 UTSW 1 82,647,483 (GRCm39) critical splice donor site probably null
R8973:Col4a3 UTSW 1 82,693,052 (GRCm39) missense probably benign 0.11
R9611:Col4a3 UTSW 1 82,678,018 (GRCm39) missense unknown
R9665:Col4a3 UTSW 1 82,668,301 (GRCm39) missense unknown
R9765:Col4a3 UTSW 1 82,646,678 (GRCm39) nonsense probably null
X0067:Col4a3 UTSW 1 82,693,880 (GRCm39) missense probably damaging 0.99
Z1177:Col4a3 UTSW 1 82,667,760 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- GGACATGGCTCCAATTAGTGGCAGA -3'
(R):5'- AGGTGTATTTTCAGATCGCCAAGCA -3'

Sequencing Primer
(F):5'- GCTCTCGAACCCTATATTAGCAGG -3'
(R):5'- CGCCAAGCATCTATATATTAACAGG -3'
Posted On 2013-06-11