Mutagenetix > Incidental Mutation

Incidental Mutation 'R7404:Scube1'

574460

Institutional Source

Beutler Lab

Gene Symbol

Scube1

Ensembl Gene

ENSMUSG00000016763

Gene Name

signal peptide, CUB domain, EGF-like 1

Synonyms

7330410C13Rik, A630023E24Rik

MMRRC Submission

045486-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.135) question?

Stock #

R7404 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

83489200-83609222 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 83499211 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 668 (Y668C)

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: Y668C

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000016907
Gene: ENSMUSG00000016763
AA Change: Y668C

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: Y557C

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000044835
Gene: ENSMUSG00000016763
AA Change: Y557C

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: Y638C

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000075434
Gene: ENSMUSG00000016763
AA Change: Y638C

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: Y638C

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000130131
Gene: ENSMUSG00000016763
AA Change: Y638C

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: 99.1%

Validation Efficiency

99% (92/93)

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ablim3	C	T	18: 61,955,099 (GRCm39)	A297T	probably damaging	Het
Adprhl1	T	A	8: 13,275,118 (GRCm39)	S547C	probably damaging	Het
Ankrd63	G	C	2: 118,533,793 (GRCm39)	R43G	unknown	Het
Asah2	T	C	19: 32,035,254 (GRCm39)	T24A	probably benign	Het
Asb17	G	A	3: 153,550,447 (GRCm39)		probably null	Het
Atp8b5	C	T	4: 43,342,640 (GRCm39)	T437I	probably benign	Het
Bbs2	T	C	8: 94,808,992 (GRCm39)	D311G	probably damaging	Het
Birc6	C	T	17: 74,946,789 (GRCm39)	T2851I	possibly damaging	Het
Bnip5	G	A	17: 29,124,298 (GRCm39)	R335W	probably damaging	Het
Cchcr1	T	C	17: 35,835,693 (GRCm39)	W266R	probably benign	Het
Col14a1	C	A	15: 55,252,024 (GRCm39)	S560*	probably null	Het
Crocc	G	A	4: 140,753,497 (GRCm39)	T1317M	possibly damaging	Het
Cxxc1	T	A	18: 74,352,278 (GRCm39)	V334E	possibly damaging	Het
Cyp3a25	T	A	5: 145,923,635 (GRCm39)	D336V	probably damaging	Het
Dapk1	A	G	13: 60,867,455 (GRCm39)	T221A	probably benign	Het
Dnah11	G	T	12: 118,068,543 (GRCm39)	T1605K	probably benign	Het
Dnah7c	T	C	1: 46,705,223 (GRCm39)	V2412A	possibly damaging	Het
Ect2l	T	A	10: 18,035,529 (GRCm39)	D524V	probably damaging	Het
Ehbp1l1	T	C	19: 5,770,872 (GRCm39)	E223G	possibly damaging	Het
Ephb2	A	T	4: 136,498,524 (GRCm39)	M185K	probably damaging	Het
Fcer1a	T	C	1: 173,049,083 (GRCm39)	K243E	probably damaging	Het
Fcgbp	T	A	7: 27,800,932 (GRCm39)	I1326N	probably damaging	Het
Fgfr1	T	C	8: 26,045,566 (GRCm39)	V45A	probably benign	Het
Filip1	T	A	9: 79,727,380 (GRCm39)	E413V	possibly damaging	Het
Frs3	T	C	17: 48,013,651 (GRCm39)		probably null	Het
Fstl4	A	G	11: 53,024,898 (GRCm39)	T257A	probably benign	Het
Golga5	A	T	12: 102,450,778 (GRCm39)	K477M	probably damaging	Het
Gpr171	A	T	3: 59,005,622 (GRCm39)	I51K	probably damaging	Het
H1f0	T	A	15: 78,913,080 (GRCm39)	Y53*	probably null	Het
Hephl1	A	G	9: 14,981,047 (GRCm39)	V795A	possibly damaging	Het
Hmcn1	A	T	1: 150,596,510 (GRCm39)	D1775E	probably benign	Het
Hs3st2	A	G	7: 121,100,168 (GRCm39)	D338G	possibly damaging	Het
Hsd3b6	T	A	3: 98,713,534 (GRCm39)	Y255F	probably benign	Het
Hspa9	T	C	18: 35,076,329 (GRCm39)	N328D	possibly damaging	Het
Hvcn1	T	A	5: 122,375,748 (GRCm39)	I100N	probably damaging	Het
Ifi207	C	T	1: 173,556,494 (GRCm39)	S748N	possibly damaging	Het
Katnip	A	T	7: 125,464,434 (GRCm39)	N1267I	probably damaging	Het
Kcnma1	G	T	14: 24,052,902 (GRCm39)	T180K	unknown	Het
Kctd16	A	G	18: 40,391,826 (GRCm39)	D138G	probably damaging	Het
Kifc3	A	G	8: 95,830,092 (GRCm39)	Y605H	probably benign	Het
Kmt2d	T	A	15: 98,743,376 (GRCm39)	Q3928L	unknown	Het
Lamb2	C	T	9: 108,364,782 (GRCm39)	R1179C	probably damaging	Het
Layn	T	A	9: 50,968,670 (GRCm39)	I358F	possibly damaging	Het
Lrig1	G	A	6: 94,603,452 (GRCm39)	T232M	probably damaging	Het
Lrp1	T	C	10: 127,418,577 (GRCm39)	T38A		Het
Map3k14	A	G	11: 103,129,918 (GRCm39)	V333A	probably benign	Het
Med13	T	C	11: 86,177,272 (GRCm39)	D1608G	possibly damaging	Het
Mrps31	T	G	8: 22,911,429 (GRCm39)	S224A	probably benign	Het
Msh6	G	T	17: 88,282,548 (GRCm39)			Het
Ncapd3	A	G	9: 26,978,315 (GRCm39)	D838G	probably benign	Het
Nlrp1a	C	A	11: 70,987,919 (GRCm39)	E1184*	probably null	Het
Npat	T	A	9: 53,466,233 (GRCm39)		probably null	Het
Nup210	A	T	6: 91,050,227 (GRCm39)	I414N	probably benign	Het
Or1e19	A	T	11: 73,316,419 (GRCm39)	L130H	probably damaging	Het
Or52n2	A	T	7: 104,542,181 (GRCm39)	V218E	possibly damaging	Het
Or5b122	T	A	19: 13,562,752 (GRCm39)	I28N	possibly damaging	Het
Or5h19	T	C	16: 58,856,603 (GRCm39)	T166A	possibly damaging	Het
Or6z5	T	C	7: 6,477,163 (GRCm39)	L18P	probably damaging	Het
Or8b12c	A	T	9: 37,715,257 (GRCm39)	T17S	possibly damaging	Het
Or8h7	A	C	2: 86,721,217 (GRCm39)	L101V	probably benign	Het
Otud7b	G	C	3: 96,043,936 (GRCm39)		probably null	Het
Phf11d	A	C	14: 59,596,942 (GRCm39)	W86G	probably benign	Het
Pik3c2b	T	A	1: 133,018,444 (GRCm39)	S964T	probably damaging	Het
Pira1	T	C	7: 3,742,344 (GRCm39)	Y61C	probably damaging	Het
Plod3	G	A	5: 137,023,901 (GRCm39)	V687I	probably benign	Het
Poglut1	T	G	16: 38,358,284 (GRCm39)	Y208S	possibly damaging	Het
Pou1f1	T	A	16: 65,330,749 (GRCm39)	L253H	probably damaging	Het
Pou2f1	C	T	1: 165,738,955 (GRCm39)	A166T	unknown	Het
Rhbdl3	C	T	11: 80,237,659 (GRCm39)	S297L	probably damaging	Het
Rxra	A	T	2: 27,631,866 (GRCm39)	N179I	probably damaging	Het
Ryr2	C	T	13: 11,750,506 (GRCm39)	E1922K	probably damaging	Het
Sec16b	A	G	1: 157,358,927 (GRCm39)	Y120C	probably damaging	Het
Sec61b	G	T	4: 47,483,047 (GRCm39)	K92N	probably damaging	Het
Skic3	T	A	13: 76,296,866 (GRCm39)	Y1074*	probably null	Het
Slc13a3	T	C	2: 165,275,984 (GRCm39)	N254S	possibly damaging	Het
Slc17a7	T	A	7: 44,822,354 (GRCm39)	Y397N	probably benign	Het
Slc25a3	A	G	10: 90,952,902 (GRCm39)	V333A	possibly damaging	Het
Slc7a8	A	T	14: 54,964,283 (GRCm39)	V390E	probably damaging	Het
Sorbs2	G	A	8: 46,212,233 (GRCm39)		probably null	Het
Srgap1	T	C	10: 121,621,650 (GRCm39)	N948D	probably benign	Het
Tacc2	A	T	7: 130,225,066 (GRCm39)	T584S	probably benign	Het
Tec	A	T	5: 72,920,961 (GRCm39)	D471E	probably damaging	Het
Tecpr2	C	T	12: 110,898,038 (GRCm39)	A430V	probably benign	Het
Tmcc2	A	T	1: 132,288,759 (GRCm39)	D309E	probably damaging	Het
Tmem82	G	A	4: 141,344,742 (GRCm39)	A67V	possibly damaging	Het
Ttc23l	T	C	15: 10,551,663 (GRCm39)	Q21R	probably damaging	Het
Ubl3	A	G	5: 148,448,764 (GRCm39)	F26L	probably damaging	Het
Upf2	A	G	2: 6,045,014 (GRCm39)	E1088G	unknown	Het
Usp9y	T	A	Y: 1,341,780 (GRCm39)	I1362F	probably benign	Het
Wnk4	T	A	11: 101,159,318 (GRCm39)		probably null	Het
Wrn	C	G	8: 33,738,994 (GRCm39)	W1278S	probably benign	Het
Zfc3h1	T	A	10: 115,251,153 (GRCm39)	V1248D	probably damaging	Het
Zfp12	T	A	5: 143,226,099 (GRCm39)	V56D	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
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'- ACATGCTTTGGCTCAGGGAG -3'
(R):5'- GGTCAGAGACACAGAAGTCC -3'

Sequencing Primer
(F):5'- GGAACTTGTCCCCACCTGAC -3'
(R):5'- CCAGCTATGGGTAAGGGCTG -3'

Posted On

2019-09-13