Incidental Mutation 'R9569:Scube1'
ID 721871
Institutional Source Beutler Lab
Gene Symbol Scube1
Ensembl Gene ENSMUSG00000016763
Gene Name signal peptide, CUB domain, EGF-like 1
Synonyms 7330410C13Rik, A630023E24Rik
MMRRC Submission 068966-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.135) question?
Stock # R9569 (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 C at 83513605 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 385 (Y385C)
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: Y385C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000016907
Gene: ENSMUSG00000016763
AA Change: Y385C

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: Y274C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000044835
Gene: ENSMUSG00000016763
AA Change: Y274C

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: Y355C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000075434
Gene: ENSMUSG00000016763
AA Change: Y355C

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: Y355C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000130131
Gene: ENSMUSG00000016763
AA Change: Y355C

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: 99.7%
  • 20x: 98.9%
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi2 T A 1: 60,503,763 (GRCm39) V356D probably damaging Het
Adgrd1 T C 5: 129,256,701 (GRCm39) V690A possibly damaging Het
Apba2 T C 7: 64,393,138 (GRCm39) M553T possibly damaging Het
Apeh C T 9: 107,971,609 (GRCm39) V13M unknown Het
Apol11b C T 15: 77,524,771 (GRCm39) E5K possibly damaging Het
Apol7e C T 15: 77,601,933 (GRCm39) T177I probably damaging Het
Bltp1 T C 3: 37,066,770 (GRCm39) M211T Het
Bub1b T C 2: 118,468,884 (GRCm39) I883T probably damaging Het
C9 T C 15: 6,489,062 (GRCm39) S140P probably damaging Het
Cbfa2t2 T A 2: 154,346,485 (GRCm39) I64N probably benign Het
Cd180 A T 13: 102,842,486 (GRCm39) I511F possibly damaging Het
Cic T C 7: 24,972,120 (GRCm39) V617A possibly damaging Het
Clca3a2 A C 3: 144,513,075 (GRCm39) probably null Het
D5Ertd579e T C 5: 36,759,979 (GRCm39) T1394A probably damaging Het
Dclk1 A T 3: 55,387,852 (GRCm39) E422D probably benign Het
Depdc5 A T 5: 33,025,321 (GRCm39) D21V probably damaging Het
Dis3l A G 9: 64,236,829 (GRCm39) F40S unknown Het
Duox1 T C 2: 122,148,971 (GRCm39) V82A probably benign Het
Dus2 T C 8: 106,771,507 (GRCm39) V211A probably damaging Het
Eif2ak4 G A 2: 118,251,316 (GRCm39) S326N probably benign Het
Fat3 A C 9: 15,830,495 (GRCm39) L153R Het
Gpx8 C T 13: 113,182,125 (GRCm39) V103I probably damaging Het
Gtf2a1l A G 17: 89,001,948 (GRCm39) D268G probably benign Het
Hc T C 2: 34,926,359 (GRCm39) I342V probably benign Het
Hsp90ab1 T A 17: 45,879,878 (GRCm39) D546V possibly damaging Het
Ifi206 T G 1: 173,314,209 (GRCm39) D77A Het
Igfbp1 A G 11: 7,147,881 (GRCm39) probably benign Het
Kdm3a T C 6: 71,584,434 (GRCm39) D559G probably benign Het
Kif2a A G 13: 107,105,246 (GRCm39) I565T probably benign Het
Krt1c T C 15: 101,724,924 (GRCm39) T229A probably damaging Het
Lcmt2 G A 2: 120,970,522 (GRCm39) A187V probably damaging Het
Mapk8ip1 A G 2: 92,217,599 (GRCm39) M241T probably benign Het
Mup15 T C 4: 61,357,875 (GRCm39) probably benign Het
Myo9b T C 8: 71,811,629 (GRCm39) V1912A probably benign Het
Naip5 T A 13: 100,356,338 (GRCm39) E1092D probably benign Het
Naip5 T C 13: 100,359,821 (GRCm39) T472A probably benign Het
Net1 A G 13: 3,938,518 (GRCm39) F123S probably benign Het
Or1j8 T C 2: 36,191,946 (GRCm39) Y132H probably damaging Het
Or52n2 C T 7: 104,542,525 (GRCm39) M103I possibly damaging Het
Or5h17 A G 16: 58,820,228 (GRCm39) Y60C probably damaging Het
Pcdhb13 T C 18: 37,576,153 (GRCm39) F177S probably damaging Het
Pclo T C 5: 14,907,065 (GRCm39) probably null Het
Perm1 A G 4: 156,303,039 (GRCm39) T528A probably benign Het
Pik3c2a C T 7: 115,957,939 (GRCm39) A1116T possibly damaging Het
Prox2 G A 12: 85,141,766 (GRCm39) Q146* probably null Het
Psd A T 19: 46,308,717 (GRCm39) C639S possibly damaging Het
Rffl T A 11: 82,703,264 (GRCm39) T220S probably benign Het
Scn2a A G 2: 65,560,622 (GRCm39) D1284G probably damaging Het
Sec14l3 A T 11: 4,026,324 (GRCm39) D388V probably damaging Het
Slc26a1 G T 5: 108,819,460 (GRCm39) Q596K probably benign Het
Slc6a19 T C 13: 73,834,030 (GRCm39) T343A probably benign Het
Slc7a4 A G 16: 17,393,262 (GRCm39) V179A Het
Sox14 T G 9: 99,757,562 (GRCm39) D49A Het
Spata31g1 G C 4: 42,971,740 (GRCm39) V358L probably benign Het
Timm22 A G 11: 76,298,196 (GRCm39) S56G probably benign Het
Tmub2 G A 11: 102,179,153 (GRCm39) W322* probably null Het
Tsc22d4 A G 5: 137,756,428 (GRCm39) T8A probably benign Het
Ttn T C 2: 76,539,652 (GRCm39) I34445V probably benign Het
Tyms A T 5: 30,268,360 (GRCm39) Y196* probably null Het
Ube2o G A 11: 116,434,823 (GRCm39) T546M probably damaging Het
Umodl1 A G 17: 31,217,143 (GRCm39) Y1125C probably damaging Het
Unc13b CGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGC CGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGC 4: 43,177,312 (GRCm39) probably benign Het
Unk A T 11: 115,950,035 (GRCm39) Q747L probably damaging Het
Vmn1r170 A G 7: 23,306,294 (GRCm39) E232G probably benign Het
Vps41 A G 13: 19,013,396 (GRCm39) Y338C possibly damaging Het
Washc5 T C 15: 59,215,980 (GRCm39) M800V probably benign Het
Wt1 T A 2: 104,993,711 (GRCm39) I348N possibly damaging Het
Xirp2 A G 2: 67,341,242 (GRCm39) Y1161C probably damaging Het
Xpo7 A G 14: 70,906,140 (GRCm39) M1001T possibly damaging Het
Yeats2 A T 16: 19,972,902 (GRCm39) R19W probably damaging Het
Zfp142 T C 1: 74,615,386 (GRCm39) T476A probably damaging Het
Zfp229 T C 17: 21,964,573 (GRCm39) W268R possibly damaging Het
Zfp473 A G 7: 44,388,971 (GRCm39) F50S probably damaging Het
Zfp975 A T 7: 42,311,413 (GRCm39) M400K probably benign Het
Zkscan5 A G 5: 145,144,419 (GRCm39) M150V probably benign Het
Znfx1 T A 2: 166,897,875 (GRCm39) I350F 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
R7267:Scube1 UTSW 15 83,505,266 (GRCm39) missense probably damaging 1.00
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
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'- GTTCTGGGTTTATGTTTCCAAACC -3'
(R):5'- TCCAGACAGGATGTTCCGTG -3'

Sequencing Primer
(F):5'- GGGTTTATGTTTCCAAACCTGCTAAG -3'
(R):5'- ACAGGATGTTCCGTGGGTGAC -3'
Posted On 2022-08-09