Mutagenetix > Incidental Mutation

Incidental Mutation 'R9090:Scube1'

690949

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 #

R9090 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

83489200-83609222 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 83494394 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Lysine at position 878 (E878K)

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: E878K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000016907
Gene: ENSMUSG00000016763
AA Change: E878K

Domain	Start	End	E-Value	Type
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: E767K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000044835
Gene: ENSMUSG00000016763
AA Change: E767K

Domain	Start	End	E-Value	Type
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: E848K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000075434
Gene: ENSMUSG00000016763
AA Change: E848K

Domain	Start	End	E-Value	Type
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: E848K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000130131
Gene: ENSMUSG00000016763
AA Change: E848K

Domain	Start	End	E-Value	Type
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: 99.2%

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: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	A	T	11: 119,901,940 (GRCm39)	S819T	probably damaging	Het
Abca13	A	T	11: 9,241,698 (GRCm39)	D1187V	probably damaging	Het
Ak9	C	A	10: 41,300,623 (GRCm39)	T1611K	unknown	Het
Als2	G	T	1: 59,242,189 (GRCm39)	T622K	probably benign	Het
Ankrd40	G	A	11: 94,225,262 (GRCm39)	A98T	probably benign	Het
Ap1b1	T	C	11: 4,973,174 (GRCm39)	L339P	probably damaging	Het
Appl1	A	C	14: 26,669,084 (GRCm39)	H363Q	probably benign	Het
Atf6	T	C	1: 170,622,245 (GRCm39)	N459D	probably damaging	Het
Ccdc6	A	T	10: 70,024,993 (GRCm39)	Q432L	unknown	Het
Ccl21a	T	A	4: 42,773,486 (GRCm39)	Q84L	probably damaging	Het
Cct4	A	G	11: 22,951,389 (GRCm39)	I348V	probably benign	Het
Cd300ld2	A	G	11: 114,904,550 (GRCm39)	Y106H	probably damaging	Het
Cdh19	C	T	1: 110,876,947 (GRCm39)	E131K	probably damaging	Het
Cdon	A	G	9: 35,403,175 (GRCm39)	D1095G	probably damaging	Het
Cep85l	T	A	10: 53,157,670 (GRCm39)	R678*	probably null	Het
Chst3	T	A	10: 60,021,465 (GRCm39)	S461C	probably damaging	Het
Clk1	A	G	1: 58,459,312 (GRCm39)	I149T	possibly damaging	Het
Clvs2	T	A	10: 33,389,301 (GRCm39)	D313V	possibly damaging	Het
Dap3	T	C	3: 88,840,913 (GRCm39)	T75A	probably benign	Het
Dnaaf1	T	A	8: 120,324,392 (GRCm39)	F631L	probably benign	Het
Dnah14	A	T	1: 181,597,325 (GRCm39)	N3549I	probably benign	Het
Dnah17	A	T	11: 117,931,870 (GRCm39)	Y3701N	probably damaging	Het
Dock6	A	G	9: 21,752,796 (GRCm39)	V339A	possibly damaging	Het
Dpp6	T	A	5: 27,803,832 (GRCm39)	C259*	probably null	Het
Dqx1	A	G	6: 83,036,024 (GRCm39)	T119A	probably benign	Het
Dync1h1	G	T	12: 110,583,310 (GRCm39)	R469L	probably benign	Het
Eno4	C	T	19: 58,951,260 (GRCm39)	A424V	probably benign	Het
Entrep1	A	T	19: 23,972,221 (GRCm39)	I161N	possibly damaging	Het
Fads1	T	A	19: 10,163,162 (GRCm39)	D146E	probably damaging	Het
Fam171a1	C	T	2: 3,224,543 (GRCm39)	T303M	probably damaging	Het
Fbxw20	C	T	9: 109,050,423 (GRCm39)	D401N	probably benign	Het
Fcho1	T	A	8: 72,163,068 (GRCm39)	T654S	possibly damaging	Het
Flad1	C	A	3: 89,315,858 (GRCm39)	E235*	probably null	Het
Flrt2	G	T	12: 95,745,907 (GRCm39)	A82S	probably benign	Het
Gabrg3	A	T	7: 56,829,386 (GRCm39)	S124T	probably benign	Het
Galt	C	T	4: 41,756,777 (GRCm39)	T139I	probably benign	Het
Garin4	A	G	1: 190,895,153 (GRCm39)	S497P	probably damaging	Het
Gfod1	T	C	13: 43,456,861 (GRCm39)	E38G	possibly damaging	Het
Gm10330	A	G	12: 23,829,992 (GRCm39)	I63T	possibly damaging	Het
Gm49359	A	G	13: 62,602,867 (GRCm39)	V111A	probably benign	Het
Gpank1	C	T	17: 35,340,734 (GRCm39)		probably benign	Het
Hck	T	C	2: 152,973,185 (GRCm39)	L156P	probably damaging	Het
Hcn3	G	T	3: 89,057,267 (GRCm39)	R444S	probably damaging	Het
Hephl1	T	C	9: 14,988,236 (GRCm39)	N624S	probably damaging	Het
Hmcn1	A	G	1: 150,632,309 (GRCm39)	I876T	probably damaging	Het
Ifi207	CTGTTGATGAAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG	CTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG	1: 173,556,762 (GRCm39)		probably benign	Het
Itga9	T	A	9: 118,500,859 (GRCm39)	D377E	possibly damaging	Het
Itpr3	G	A	17: 27,337,651 (GRCm39)		probably benign	Het
Itprid1	G	T	6: 55,944,051 (GRCm39)	R417L	probably benign	Het
Klk1b11	C	T	7: 43,425,954 (GRCm39)	L32F	probably benign	Het
Lta4h	A	G	10: 93,310,412 (GRCm39)	S427G	probably benign	Het
Lxn	T	A	3: 67,368,651 (GRCm39)	I122F	probably damaging	Het
Lyz1	A	G	10: 117,124,492 (GRCm39)	V148A	possibly damaging	Het
Mael	G	T	1: 166,032,424 (GRCm39)	Q326K	probably benign	Het
Magi3	T	C	3: 103,923,264 (GRCm39)	D1151G	possibly damaging	Het
Map3k9	C	A	12: 81,769,261 (GRCm39)	G929V	probably benign	Het
Mcoln1	A	G	8: 3,555,771 (GRCm39)	Y22C	probably damaging	Het
Mier3	G	T	13: 111,827,870 (GRCm39)	M45I	probably benign	Het
Mrpl1	T	C	5: 96,371,746 (GRCm39)	V91A	probably damaging	Het
Myo7a	T	C	7: 97,740,281 (GRCm39)	H571R	probably benign	Het
Myom1	T	A	17: 71,374,325 (GRCm39)	W601R	probably damaging	Het
Myom3	C	T	4: 135,505,479 (GRCm39)	T456I	probably benign	Het
Nags	A	T	11: 102,037,584 (GRCm39)	H225L	probably benign	Het
Ncaph	C	A	2: 126,958,554 (GRCm39)	K488N	probably damaging	Het
Nkain3	C	T	4: 20,484,897 (GRCm39)	R60H	probably damaging	Het
Nlrp9a	A	T	7: 26,261,944 (GRCm39)	M698L	probably benign	Het
Nmur2	A	C	11: 55,931,308 (GRCm39)	I134M	probably benign	Het
Nrp2	A	C	1: 62,784,670 (GRCm39)	E273A	probably benign	Het
Nup85	A	G	11: 115,468,787 (GRCm39)	D210G	possibly damaging	Het
Obscn	A	G	11: 59,006,643 (GRCm39)	F1173S	probably damaging	Het
Or5ac24	A	T	16: 59,165,145 (GRCm39)	C306*	probably null	Het
Otogl	T	A	10: 107,652,974 (GRCm39)	E1126V	probably null	Het
Pfkl	T	C	10: 77,833,426 (GRCm39)	I259V	probably benign	Het
Phkg1	A	T	5: 129,893,863 (GRCm39)	Y291N	probably benign	Het
Piezo2	T	G	18: 63,163,450 (GRCm39)	H2156P	probably damaging	Het
Piezo2	C	A	18: 63,208,790 (GRCm39)	V1408L	probably damaging	Het
Pira13	T	A	7: 3,819,997 (GRCm39)	E640V	unknown	Het
Plekhg3	A	G	12: 76,622,694 (GRCm39)	T646A	probably benign	Het
Plk5	C	G	10: 80,193,830 (GRCm39)	R40G	probably damaging	Het
Ppp1r12a	T	C	10: 108,098,224 (GRCm39)	S838P	probably damaging	Het
Rarb	A	T	14: 16,435,235 (GRCm38)	Y270*	probably null	Het
Rbm15	T	C	3: 107,239,312 (GRCm39)	E362G	possibly damaging	Het
Rcan1	A	G	16: 92,262,741 (GRCm39)	F76L		Het
Rdh19	T	C	10: 127,696,142 (GRCm39)	L298P	probably damaging	Het
Rims1	T	A	1: 22,498,773 (GRCm39)	H57L		Het
Rlf	T	C	4: 121,004,751 (GRCm39)	T1520A	probably benign	Het
Rnase1	T	A	14: 51,382,964 (GRCm39)	H130L	possibly damaging	Het
Samd8	T	A	14: 21,842,569 (GRCm39)	M360K	probably damaging	Het
Samhd1	A	G	2: 156,956,205 (GRCm39)	L329P	probably damaging	Het
Sema3b	T	C	9: 107,476,154 (GRCm39)	Y689C	probably damaging	Het
Semp2l2a	T	C	8: 13,886,697 (GRCm39)	T465A	possibly damaging	Het
Sh3pxd2b	A	T	11: 32,373,361 (GRCm39)	N843Y	possibly damaging	Het
Slco1a6	C	T	6: 142,035,575 (GRCm39)	C583Y	probably damaging	Het
Smg1	A	C	7: 117,811,786 (GRCm39)	V88G	unknown	Het
Spata24	T	A	18: 35,790,054 (GRCm39)	N146Y	probably damaging	Het
Tcf3	C	A	10: 80,253,191 (GRCm39)	V258L	probably benign	Het
Tiam2	T	C	17: 3,465,011 (GRCm39)	Y247H	probably damaging	Het
Ticrr	T	C	7: 79,310,604 (GRCm39)	F173L	possibly damaging	Het
Tpp2	A	G	1: 43,993,811 (GRCm39)	E232G	probably damaging	Het
Trank1	T	A	9: 111,174,547 (GRCm39)	V138E	probably damaging	Het
Ttll3	T	C	6: 113,369,596 (GRCm39)	S47P	probably benign	Het
Utp4	C	T	8: 107,632,857 (GRCm39)	T280M	probably damaging	Het
Vmn1r123	A	T	7: 20,896,794 (GRCm39)	N229Y	probably benign	Het
Vmn1r85	A	T	7: 12,818,942 (GRCm39)	Y67*	probably null	Het
Zbtb12	T	A	17: 35,114,320 (GRCm39)	V35E	possibly damaging	Het
Zmym6	T	A	4: 127,017,854 (GRCm39)	F1212I	probably damaging	Het

Other mutations in Scube1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- TTCCTATCTCAGGGTAGCCC -3'
(R):5'- AAAGTCCCTTGGCCATGGTAC -3'

Sequencing Primer
(F):5'- GGTAGCCCTAAGCCTTCATGAC -3'
(R):5'- TTGGCCATGGTACCCACAGAC -3'

Posted On

2021-12-30