Mutagenetix > Incidental Mutation

Incidental Mutation 'R0126:Scube1'

21409

Institutional Source

Beutler Lab

Gene Symbol

Scube1

Ensembl Gene

ENSMUSG00000016763

Gene Name

signal peptide, CUB domain, EGF-like 1

Synonyms

7330410C13Rik, A630023E24Rik

MMRRC Submission

038411-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.132) question?

Stock #

R0126 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

83489200-83609222 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 83505264 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 385 (N385K)

Ref Sequence

ENSEMBL: ENSMUSP00000044835 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000016907] [ENSMUST00000043634] [ENSMUST00000076060] [ENSMUST00000171496]

AlphaFold

Q6NZL8

Predicted Effect

probably damaging
Transcript: ENSMUST00000016907
AA Change: N496K

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

SMART Domains

Protein: ENSMUSP00000016907
Gene: ENSMUSG00000016763
AA Change: N496K

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: N385K

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

SMART Domains

Protein: ENSMUSP00000044835
Gene: ENSMUSG00000016763
AA Change: N385K

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: N466K

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000075434
Gene: ENSMUSG00000016763
AA Change: N466K

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

noncoding transcript
Transcript: ENSMUST00000144773

Predicted Effect

probably damaging
Transcript: ENSMUST00000171496
AA Change: N466K

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000130131
Gene: ENSMUSG00000016763
AA Change: N466K

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

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 98.8%
3x: 97.6%
10x: 93.2%
20x: 81.8%

Validation Efficiency

98% (102/104)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca2	T	C	2: 25,333,742 (GRCm39)	L1730P	possibly damaging	Het
Adam9	T	C	8: 25,460,753 (GRCm39)	N577S	probably damaging	Het
Add1	T	C	5: 34,770,923 (GRCm39)	Y316H	probably benign	Het
Agpat3	T	C	10: 78,113,890 (GRCm39)	D266G	probably null	Het
Aldh3a2	C	A	11: 61,115,384 (GRCm39)	Q524H	probably benign	Het
Alox12b	A	C	11: 69,058,297 (GRCm39)	S550R	probably benign	Het
Ano4	T	A	10: 88,788,154 (GRCm39)	I753F	possibly damaging	Het
AW011738	T	A	4: 156,288,104 (GRCm39)		probably benign	Het
B4galt3	C	T	1: 171,103,738 (GRCm39)	T103M	probably damaging	Het
Cabs1	C	T	5: 88,128,054 (GRCm39)	T235I	probably damaging	Het
Casq2	A	G	3: 102,040,715 (GRCm39)	H272R	probably damaging	Het
Ccdc180	T	C	4: 45,912,866 (GRCm39)		probably null	Het
Cdh12	A	T	15: 21,584,031 (GRCm39)	M624L	probably benign	Het
Cdh5	A	C	8: 104,867,314 (GRCm39)		probably null	Het
Col7a1	A	G	9: 108,798,651 (GRCm39)		probably benign	Het
Cpne2	A	T	8: 95,281,561 (GRCm39)	I199F	probably damaging	Het
Crebbp	A	T	16: 3,901,927 (GRCm39)	F2399L	possibly damaging	Het
Defb36	T	C	2: 152,454,499 (GRCm39)	C53R	probably damaging	Het
Degs1	T	C	1: 182,107,257 (GRCm39)	M1V	probably null	Het
Disp2	T	A	2: 118,620,819 (GRCm39)	F517Y	probably damaging	Het
Dnah5	A	G	15: 28,246,465 (GRCm39)	D601G	probably benign	Het
Dnpep	G	A	1: 75,289,182 (GRCm39)	Q310*	probably null	Het
Dsg1a	A	G	18: 20,473,935 (GRCm39)	T1003A	probably benign	Het
Fbrsl1	C	G	5: 110,543,906 (GRCm39)		probably benign	Het
Foxh1	A	T	15: 76,553,454 (GRCm39)	L116H	probably damaging	Het
Gigyf2	G	A	1: 87,339,597 (GRCm39)		probably benign	Het
Golm2	T	C	2: 121,736,565 (GRCm39)		probably benign	Het
Gp1ba	A	T	11: 70,531,859 (GRCm39)		probably benign	Het
Gucy1b1	A	G	3: 81,945,218 (GRCm39)		probably benign	Het
Gucy2g	T	G	19: 55,229,598 (GRCm39)	D24A	probably benign	Het
Hirip3	A	G	7: 126,462,614 (GRCm39)	K190R	probably damaging	Het
Hmmr	T	C	11: 40,596,781 (GRCm39)	N717D	probably damaging	Het
Il12b	A	T	11: 44,301,045 (GRCm39)	Y187F	probably damaging	Het
Iqgap1	A	G	7: 80,388,070 (GRCm39)	I859T	probably benign	Het
Jmjd1c	T	C	10: 67,055,105 (GRCm39)	L175P	probably damaging	Het
Klc2	T	C	19: 5,162,774 (GRCm39)	M242V	possibly damaging	Het
Klf3	T	C	5: 64,979,446 (GRCm39)	M96T	probably benign	Het
Lrrc66	G	T	5: 73,764,431 (GRCm39)	H871N	probably benign	Het
Ltn1	A	T	16: 87,222,528 (GRCm39)	D168E	probably benign	Het
Mak	T	C	13: 41,186,072 (GRCm39)	D532G	probably damaging	Het
Marchf6	A	G	15: 31,462,151 (GRCm39)	M859T	probably benign	Het
Meak7	T	C	8: 120,489,089 (GRCm39)	D398G	possibly damaging	Het
Mlxipl	C	A	5: 135,161,177 (GRCm39)	N365K	probably damaging	Het
Mplkip	T	C	13: 17,870,337 (GRCm39)	S90P	possibly damaging	Het
Myo5c	A	T	9: 75,176,807 (GRCm39)	H584L	probably benign	Het
Myt1l	A	G	12: 29,901,719 (GRCm39)	T228A	possibly damaging	Het
Nxpe3	A	T	16: 55,686,592 (GRCm39)	Y139N	possibly damaging	Het
Or2z8	C	T	8: 72,812,244 (GRCm39)	T240M	probably damaging	Het
Or51f2	A	G	7: 102,526,347 (GRCm39)	T7A	probably benign	Het
Or8k40	T	A	2: 86,584,981 (GRCm39)	I34L	probably damaging	Het
Pak6	C	T	2: 118,520,813 (GRCm39)	S268F	possibly damaging	Het
Parp10	G	A	15: 76,127,266 (GRCm39)	A57V	probably damaging	Het
Pik3r3	T	A	4: 116,113,465 (GRCm39)	D69E	probably damaging	Het
Polr2a	T	G	11: 69,638,251 (GRCm39)	K105T	probably damaging	Het
Prdm16	A	T	4: 154,413,295 (GRCm39)		probably benign	Het
Prepl	G	A	17: 85,390,670 (GRCm39)	T96I	probably benign	Het
Ret	C	T	6: 118,142,956 (GRCm39)		probably benign	Het
Rgl3	A	T	9: 21,887,108 (GRCm39)	D541E	probably benign	Het
Rpa1	A	C	11: 75,209,355 (GRCm39)	Y143D	probably benign	Het
Rps16	T	A	7: 28,050,508 (GRCm39)	L47Q	probably damaging	Het
Sbno2	A	T	10: 79,904,687 (GRCm39)		probably null	Het
Shank2	A	G	7: 143,585,092 (GRCm39)	E31G	probably damaging	Het
Slc38a9	G	T	13: 112,865,791 (GRCm39)	C496F	possibly damaging	Het
Snap47	A	G	11: 59,328,813 (GRCm39)	V163A	probably damaging	Het
Sntg2	T	C	12: 30,251,260 (GRCm39)		probably benign	Het
Sp7	C	A	15: 102,266,895 (GRCm39)	V322F	probably damaging	Het
Spic	T	C	10: 88,511,924 (GRCm39)	K111E	probably damaging	Het
Sqor	T	C	2: 122,639,947 (GRCm39)		probably benign	Het
St6galnac1	T	A	11: 116,657,410 (GRCm39)	M385L	probably benign	Het
Synpo2	A	T	3: 122,873,511 (GRCm39)	S1211T	possibly damaging	Het
Sytl2	T	A	7: 90,045,797 (GRCm39)	V638E	probably damaging	Het
Taar1	T	A	10: 23,796,445 (GRCm39)	S48T	probably benign	Het
Tbx18	T	A	9: 87,611,706 (GRCm39)	D108V	possibly damaging	Het
Tdh	C	T	14: 63,735,042 (GRCm39)		probably benign	Het
Tlr9	T	A	9: 106,102,881 (GRCm39)	L724Q	probably benign	Het
Tmem270	T	A	5: 134,931,642 (GRCm39)	Y100F	probably benign	Het
Trim65	G	C	11: 116,015,430 (GRCm39)		probably benign	Het
Trrap	A	T	5: 144,742,560 (GRCm39)	K1393*	probably null	Het
Ttc13	A	G	8: 125,410,030 (GRCm39)	V523A	probably damaging	Het
Utrn	T	A	10: 12,587,219 (GRCm39)	D939V	probably benign	Het
Vmn1r46	G	T	6: 89,953,935 (GRCm39)	M261I	probably benign	Het
Vwa5a	A	G	9: 38,649,103 (GRCm39)		probably null	Het
Zfp108	A	T	7: 23,960,149 (GRCm39)	T247S	probably benign	Het
Zfp366	A	T	13: 99,365,129 (GRCm39)	I97F	probably benign	Het
Zfp986	C	T	4: 145,625,513 (GRCm39)	R58C	probably benign	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
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
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'- TGTCACCTCTCCAGAATCCTAAGCC -3'
(R):5'- CCACAGTCTCTTCATGCCAGGTAAC -3'

Sequencing Primer
(F):5'- AGAATCCTAAGCCATGCTGG -3'
(R):5'- ATGGGTTAACATGCTGCTTCC -3'

Posted On

2013-04-11