Incidental Mutation 'R7267:Scube1'
ID 565028
Institutional Source Beutler Lab
Gene Symbol Scube1
Ensembl Gene ENSMUSG00000016763
Gene Name signal peptide, CUB domain, EGF-like 1
Synonyms 7330410C13Rik, A630023E24Rik
Accession Numbers
Essential gene? Probably non essential (E-score: 0.135) question?
Stock # R7267 (G1)
Quality Score 225.009
Status Not validated
Chromosome 15
Chromosomal Location 83489200-83609222 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 83505266 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Tyrosine at position 496 (N496Y)
Ref Sequence ENSEMBL: ENSMUSP00000016907 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000016907] [ENSMUST00000043634] [ENSMUST00000076060] [ENSMUST00000171496]
AlphaFold Q6NZL8
Predicted Effect probably damaging
Transcript: ENSMUST00000016907
AA Change: N496Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000016907
Gene: ENSMUSG00000016763
AA Change: N496Y

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
EGF_CA 33 73 1.5e-9 SMART
EGF_CA 74 116 7.29e-8 SMART
EGF_CA 117 157 1.4e-9 SMART
EGF 165 203 1.43e-1 SMART
EGF 205 242 1.09e1 SMART
EGF 274 311 1.69e-3 SMART
EGF_CA 312 352 2.13e-9 SMART
EGF_CA 353 391 4.7e-11 SMART
EGF_CA 392 432 3.91e-8 SMART
low complexity region 560 573 N/A INTRINSIC
Pfam:GCC2_GCC3 666 713 4.5e-13 PFAM
EGF_like 766 804 6.81e1 SMART
CUB 828 940 1.51e-19 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000043634
AA Change: N385Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000044835
Gene: ENSMUSG00000016763
AA Change: N385Y

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
EGF_CA 33 73 1.5e-9 SMART
EGF_CA 74 116 7.29e-8 SMART
EGF_CA 117 157 1.4e-9 SMART
EGF 163 200 1.69e-3 SMART
EGF_CA 201 241 2.13e-9 SMART
EGF_CA 242 280 4.7e-11 SMART
EGF_CA 281 321 3.91e-8 SMART
low complexity region 449 462 N/A INTRINSIC
Pfam:GCC2_GCC3 555 602 3.2e-11 PFAM
EGF_like 655 693 6.81e1 SMART
CUB 717 829 1.51e-19 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000076060
AA Change: N466Y

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000075434
Gene: ENSMUSG00000016763
AA Change: N466Y

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
EGF_CA 33 73 1.5e-9 SMART
EGF_CA 74 116 7.29e-8 SMART
EGF_CA 117 157 1.4e-9 SMART
EGF 165 203 1.43e-1 SMART
EGF 205 242 1.09e1 SMART
EGF 244 281 1.69e-3 SMART
EGF_CA 282 322 2.13e-9 SMART
EGF_CA 323 361 4.7e-11 SMART
EGF_CA 362 402 3.91e-8 SMART
low complexity region 530 543 N/A INTRINSIC
Pfam:GCC2_GCC3 636 683 1.3e-11 PFAM
EGF_like 736 774 6.81e1 SMART
CUB 798 910 1.51e-19 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000171496
AA Change: N466Y

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000130131
Gene: ENSMUSG00000016763
AA Change: N466Y

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
EGF_CA 33 73 1.5e-9 SMART
EGF_CA 74 116 7.29e-8 SMART
EGF_CA 117 157 1.4e-9 SMART
EGF 165 203 1.43e-1 SMART
EGF 205 242 1.09e1 SMART
EGF 244 281 1.69e-3 SMART
EGF_CA 282 322 2.13e-9 SMART
EGF_CA 323 361 4.7e-11 SMART
EGF_CA 362 402 3.91e-8 SMART
low complexity region 530 543 N/A INTRINSIC
Pfam:GCC2_GCC3 636 683 1.7e-11 PFAM
EGF_like 736 774 6.81e1 SMART
CUB 798 910 1.51e-19 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a cell surface glycoprotein that is a member of the SCUBE (signal peptide, CUB domain, EGF (epidermal growth factor)-like protein) family. Family members have an amino-terminal signal peptide, nine copies of EGF-like repeats and a CUB domain at the carboxyl terminus. This protein is expressed in platelets and endothelial cells and may play an important role in vascular biology. [provided by RefSeq, Oct 2011]
PHENOTYPE: A fraction of homozygotes die neonatally with acrania and loss of brain tissue. Early skull bone defects include lack of the interparietal and supraoccipital bones and cranial vault. Affected mutant embryos show exencephaly, a thick-walled forebrain neuroepithelium and hyperplastic cranial ganglia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 A G 12: 118,916,205 (GRCm39) I37T probably damaging Het
Ackr2 A G 9: 121,737,874 (GRCm39) Y83C probably damaging Het
Adam19 C T 11: 46,012,403 (GRCm39) Q300* probably null Het
Anxa7 C T 14: 20,519,474 (GRCm39) A115T probably benign Het
Aoc1l3 AGGCCCAGCCTGATCCTAAATTTCCTATCCCCATCAGCAAAGGTGGCCCTCAAGTGGCCCAGCC AGGCCCAGCC 6: 48,964,952 (GRCm39) probably benign Het
Atad2b A T 12: 5,077,105 (GRCm39) R1109* probably null Het
Batf2 A G 19: 6,221,396 (GRCm39) T69A probably benign Het
Best1 A G 19: 9,964,177 (GRCm39) C428R probably benign Het
Birc6 A G 17: 74,892,980 (GRCm39) T973A probably benign Het
Bmp2k C T 5: 97,216,293 (GRCm39) T597I unknown Het
Bmpr1a G A 14: 34,165,836 (GRCm39) P57L possibly damaging Het
Camk2d A T 3: 126,591,379 (GRCm39) H283L possibly damaging Het
Cd86 CA CAA 16: 36,426,917 (GRCm39) probably null Het
Ces1b C A 8: 93,806,132 (GRCm39) K36N possibly damaging Het
Ces2a T A 8: 105,465,672 (GRCm39) M308K probably benign Het
Ctnnd2 C A 15: 30,683,501 (GRCm39) Q501K probably benign Het
Cyb561d1 T C 3: 108,106,629 (GRCm39) T197A probably benign Het
Dedd2 C A 7: 24,918,391 (GRCm39) A55S probably damaging Het
Dnah2 C T 11: 69,391,643 (GRCm39) R684Q probably damaging Het
Elovl3 A G 19: 46,122,979 (GRCm39) Y185C probably damaging Het
Fgf3 C T 7: 144,392,569 (GRCm39) A42V probably damaging Het
Gabra5 A G 7: 57,140,529 (GRCm39) L56P probably damaging Het
Gm19410 T G 8: 36,281,997 (GRCm39) V1860G possibly damaging Het
Gm21663 G T 5: 26,143,751 (GRCm39) N190K probably damaging Het
Grm3 T A 5: 9,639,581 (GRCm39) I155L probably benign Het
Hadha A G 5: 30,327,755 (GRCm39) I495T probably damaging Het
Herc4 C T 10: 63,109,365 (GRCm39) A200V possibly damaging Het
Itga3 C A 11: 94,967,188 (GRCm39) probably benign Het
Krt6a C T 15: 101,602,289 (GRCm39) S132N probably benign Het
Lpar1 T C 4: 58,486,857 (GRCm39) N138S possibly damaging Het
Lrrc42 T A 4: 107,096,983 (GRCm39) T247S probably damaging Het
Man2b1 T A 8: 85,813,804 (GRCm39) V256E probably damaging Het
Map3k4 G T 17: 12,490,536 (GRCm39) Y298* probably null Het
Mars1 A G 10: 127,144,455 (GRCm39) V195A probably benign Het
Mdm4 A T 1: 132,922,311 (GRCm39) V278E probably benign Het
Mdp1 A G 14: 55,897,544 (GRCm39) V37A probably damaging Het
Med13 A G 11: 86,199,652 (GRCm39) I685T probably benign Het
Mobp A G 9: 119,996,914 (GRCm39) N15S probably damaging Het
Nbn T A 4: 15,979,320 (GRCm39) M435K probably benign Het
Nfs1 A G 2: 155,965,703 (GRCm39) V126A probably benign Het
Npepl1 T A 2: 173,963,909 (GRCm39) V480E probably damaging Het
Nr2e3 G A 9: 59,855,972 (GRCm39) S155F possibly damaging Het
Oplah T C 15: 76,189,209 (GRCm39) D278G probably benign Het
Or4c124 A T 2: 89,156,157 (GRCm39) Y122* probably null Het
Or51q1c A G 7: 103,653,046 (GRCm39) H188R probably benign Het
Pard3 T C 8: 128,098,056 (GRCm39) Y366H probably damaging Het
Pcdhb11 A G 18: 37,555,006 (GRCm39) N112S possibly damaging Het
Pde11a A G 2: 76,168,189 (GRCm39) S255P probably damaging Het
Piezo1 T C 8: 123,224,268 (GRCm39) H745R Het
Pkn2 A T 3: 142,517,776 (GRCm39) S441T possibly damaging Het
Pld1 A C 3: 28,130,550 (GRCm39) H450P probably damaging Het
Plekhs1 T A 19: 56,459,209 (GRCm39) H22Q probably damaging Het
Prss44 A C 9: 110,645,611 (GRCm39) Y285S probably damaging Het
Qpctl T C 7: 18,878,852 (GRCm39) E249G probably benign Het
Rcsd1 A T 1: 165,491,185 (GRCm39) S50T probably damaging Het
Runx2 G A 17: 45,125,079 (GRCm39) P80L probably damaging Het
Skic3 A G 13: 76,328,196 (GRCm39) M1415V probably benign Het
Slc16a8 AGGCC A 15: 79,136,125 (GRCm39) probably null Het
Slc38a4 T A 15: 96,903,781 (GRCm39) T407S probably benign Het
Slc51a T G 16: 32,298,590 (GRCm39) I56L probably benign Het
Slc6a18 T G 13: 73,819,755 (GRCm39) I272L probably damaging Het
Sorl1 A G 9: 42,035,375 (GRCm39) L12P possibly damaging Het
Sycp2l A T 13: 41,300,070 (GRCm39) D428V possibly damaging Het
Syne1 C T 10: 5,178,218 (GRCm39) R4752Q probably damaging Het
Tbc1d9 C A 8: 83,997,957 (GRCm39) H1171Q probably damaging Het
Thsd1 G A 8: 22,733,597 (GRCm39) V215I probably benign Het
Tmem143 T A 7: 45,557,598 (GRCm39) M208K probably benign Het
Tmem63b C T 17: 45,977,048 (GRCm39) V440I probably benign Het
Tnik A T 3: 28,700,776 (GRCm39) S918C probably damaging Het
Ttn A G 2: 76,733,751 (GRCm39) I4508T unknown Het
Vav2 A G 2: 27,173,334 (GRCm39) F497L probably damaging Het
Zc3h14 G A 12: 98,751,988 (GRCm39) R730Q probably damaging Het
Zfp560 G A 9: 20,259,384 (GRCm39) H493Y probably damaging Het
Other mutations in Scube1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00903:Scube1 APN 15 83,587,702 (GRCm39) missense probably damaging 0.98
IGL01152:Scube1 APN 15 83,497,771 (GRCm39) missense probably damaging 1.00
IGL01388:Scube1 APN 15 83,504,332 (GRCm39) missense probably benign 0.00
IGL01589:Scube1 APN 15 83,496,754 (GRCm39) missense probably damaging 1.00
IGL02208:Scube1 APN 15 83,587,741 (GRCm39) missense probably damaging 1.00
IGL02305:Scube1 APN 15 83,491,591 (GRCm39) missense probably damaging 1.00
IGL02728:Scube1 APN 15 83,543,217 (GRCm39) splice site probably benign
IGL02737:Scube1 APN 15 83,606,044 (GRCm39) splice site probably benign
IGL03326:Scube1 APN 15 83,491,617 (GRCm39) missense probably damaging 1.00
R0055:Scube1 UTSW 15 83,518,937 (GRCm39) missense probably damaging 1.00
R0055:Scube1 UTSW 15 83,518,937 (GRCm39) missense probably damaging 1.00
R0126:Scube1 UTSW 15 83,505,264 (GRCm39) missense probably damaging 1.00
R0792:Scube1 UTSW 15 83,512,277 (GRCm39) critical splice acceptor site probably null
R1438:Scube1 UTSW 15 83,499,227 (GRCm39) missense possibly damaging 0.93
R1522:Scube1 UTSW 15 83,512,277 (GRCm39) critical splice acceptor site probably null
R1735:Scube1 UTSW 15 83,491,638 (GRCm39) missense probably damaging 1.00
R1766:Scube1 UTSW 15 83,606,146 (GRCm39) missense probably damaging 1.00
R1778:Scube1 UTSW 15 83,494,405 (GRCm39) missense probably damaging 1.00
R2975:Scube1 UTSW 15 83,543,299 (GRCm39) missense probably damaging 0.99
R4080:Scube1 UTSW 15 83,492,948 (GRCm39) missense probably damaging 1.00
R4434:Scube1 UTSW 15 83,606,125 (GRCm39) missense probably damaging 1.00
R5585:Scube1 UTSW 15 83,561,124 (GRCm39) missense probably damaging 1.00
R5857:Scube1 UTSW 15 83,491,461 (GRCm39) unclassified probably benign
R5977:Scube1 UTSW 15 83,513,689 (GRCm39) missense probably damaging 1.00
R6054:Scube1 UTSW 15 83,535,877 (GRCm39) missense probably benign 0.43
R6461:Scube1 UTSW 15 83,496,628 (GRCm39) missense probably damaging 1.00
R6956:Scube1 UTSW 15 83,606,077 (GRCm39) missense probably damaging 1.00
R6959:Scube1 UTSW 15 83,513,636 (GRCm39) missense probably benign 0.42
R7124:Scube1 UTSW 15 83,513,712 (GRCm39) splice site probably null
R7404:Scube1 UTSW 15 83,499,211 (GRCm39) missense probably damaging 0.98
R7584:Scube1 UTSW 15 83,606,088 (GRCm39) nonsense probably null
R7585:Scube1 UTSW 15 83,522,988 (GRCm39) missense possibly damaging 0.83
R7599:Scube1 UTSW 15 83,497,653 (GRCm39) missense probably damaging 1.00
R8055:Scube1 UTSW 15 83,543,226 (GRCm39) critical splice donor site probably null
R8098:Scube1 UTSW 15 83,543,289 (GRCm39) missense probably damaging 1.00
R8192:Scube1 UTSW 15 83,513,583 (GRCm39) critical splice donor site probably null
R8394:Scube1 UTSW 15 83,492,492 (GRCm39) missense probably damaging 1.00
R8441:Scube1 UTSW 15 83,494,423 (GRCm39) missense probably damaging 0.99
R8713:Scube1 UTSW 15 83,494,471 (GRCm39) missense possibly damaging 0.58
R8844:Scube1 UTSW 15 83,561,164 (GRCm39) missense probably damaging 1.00
R9090:Scube1 UTSW 15 83,494,394 (GRCm39) missense probably damaging 1.00
R9169:Scube1 UTSW 15 83,543,298 (GRCm39) missense possibly damaging 0.88
R9271:Scube1 UTSW 15 83,494,394 (GRCm39) missense probably damaging 1.00
R9334:Scube1 UTSW 15 83,512,264 (GRCm39) missense possibly damaging 0.72
R9363:Scube1 UTSW 15 83,499,080 (GRCm39) nonsense probably null
R9534:Scube1 UTSW 15 83,606,102 (GRCm39) missense probably damaging 1.00
R9569:Scube1 UTSW 15 83,513,605 (GRCm39) missense probably damaging 1.00
R9574:Scube1 UTSW 15 83,501,000 (GRCm39) missense
R9759:Scube1 UTSW 15 83,492,465 (GRCm39) missense probably benign 0.02
R9788:Scube1 UTSW 15 83,535,901 (GRCm39) missense possibly damaging 0.73
X0022:Scube1 UTSW 15 83,518,870 (GRCm39) critical splice donor site probably null
Z1177:Scube1 UTSW 15 83,496,617 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- ACTGTACGACTGTGACAGC -3'
(R):5'- AGTCTTGATCTTCATTCGGGAG -3'

Sequencing Primer
(F):5'- AGTCAGAAAGGCCCTCTGCTG -3'
(R):5'- TTCATTCGGGAGCCCCTTGG -3'
Posted On 2019-06-26