Mutagenetix > Incidental Mutation

Incidental Mutation 'R7599:Scube1'

587935

Institutional Source

Beutler Lab

Gene Symbol

Scube1

Ensembl Gene

ENSMUSG00000016763

Gene Name

signal peptide, CUB domain, EGF-like 1

Synonyms

7330410C13Rik, A630023E24Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.108) question?

Stock #

R7599 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

83604999-83725021 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 83613452 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 766 (D766V)

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: D766V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000016907
Gene: ENSMUSG00000016763
AA Change: D766V

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

possibly damaging
Transcript: ENSMUST00000043634
AA Change: D655V

PolyPhen 2 Score 0.847 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000044835
Gene: ENSMUSG00000016763
AA Change: D655V

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: D736V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000075434
Gene: ENSMUSG00000016763
AA Change: D736V

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: D736V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000130131
Gene: ENSMUSG00000016763
AA Change: D736V

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: 100.0%
10x: 99.7%
20x: 99.1%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210016F16Rik	T	A	13: 58,381,835	H321L	probably damaging	Het
Adamts3	T	C	5: 89,861,397	S136G	probably benign	Het
Apba3	T	A	10: 81,272,346	N445K	probably damaging	Het
Aqp6	A	G	15: 99,603,771	K237E	possibly damaging	Het
Arhgap23	A	G	11: 97,500,343	T1229A	probably benign	Het
Bpifb1	T	C	2: 154,214,151	I379T	probably damaging	Het
Ccdc169	A	G	3: 55,140,109	D7G	probably damaging	Het
Cyp2f2	T	A	7: 27,131,359		probably null	Het
Daam2	T	A	17: 49,480,727	K453*	probably null	Het
Dennd4c	T	C	4: 86,811,612	L817P	probably damaging	Het
Efcab6	T	A	15: 83,870,988	R1376W	probably damaging	Het
Esrra	G	T	19: 6,913,846	A182E	possibly damaging	Het
Fam234b	T	A	6: 135,226,876	V392E	probably damaging	Het
Fanca	A	G	8: 123,271,260	V1229A	probably benign	Het
Fdps	G	T	3: 89,099,386	Q66K	probably benign	Het
Fer1l6	T	A	15: 58,627,589	D1269E	probably benign	Het
Foxred1	G	A	9: 35,205,636	R353W	probably damaging	Het
Gabrg2	C	T	11: 41,967,624	V226I	possibly damaging	Het
Gcnt2	C	A	13: 40,860,867	C171*	probably null	Het
Glyat	C	A	19: 12,639,808	A8E	probably damaging	Het
Golgb1	C	A	16: 36,875,396	R86S	unknown	Het
Hc	T	A	2: 35,050,419	T136S	probably damaging	Het
Hdac1	G	T	4: 129,517,466	S421*	probably null	Het
Hmcn2	G	T	2: 31,356,286	A756S	possibly damaging	Het
Igkv8-26	A	G	6: 70,193,587	N54S	probably benign	Het
Impad1	G	A	4: 4,778,207	T177I	probably damaging	Het
Itgae	T	A	11: 73,121,960	V706E	possibly damaging	Het
Itgax	G	A	7: 128,148,090	V992M	probably damaging	Het
Klk10	A	G	7: 43,784,427	D221G	probably benign	Het
Klkb1	T	C	8: 45,278,113	I205V	probably benign	Het
Kpna2	T	C	11: 106,998,757	N8S	probably null	Het
L3mbtl1	A	C	2: 162,964,514	T442P	possibly damaging	Het
Lrp1b	C	T	2: 40,661,549	C4181Y		Het
Mcat	T	C	15: 83,547,671	Y332C	probably damaging	Het
Mecom	T	C	3: 29,956,385	D648G	probably damaging	Het
Mesp2	A	T	7: 79,810,969	D14V	probably damaging	Het
Mlh3	A	T	12: 85,268,199	Y404*	probably null	Het
Mterf3	A	T	13: 66,917,148	F230I	probably damaging	Het
Nrxn3	T	C	12: 89,512,062	V602A	probably benign	Het
Olfr1247	T	A	2: 89,609,227	I292F	possibly damaging	Het
Plekhg6	A	G	6: 125,374,660	F209L	probably damaging	Het
Pmp22	C	A	11: 63,158,348	A139D	probably damaging	Het
Polr2e	T	C	10: 80,038,570	D34G	possibly damaging	Het
Ppard	T	A	17: 28,297,117	L105H	probably damaging	Het
Ptpn14	T	A	1: 189,850,745	D596E	probably benign	Het
Ptprz1	C	T	6: 23,002,519	A1536V	not run	Het
Rabgap1	TGGGG	TGGG	2: 37,502,896		probably null	Het
Retreg1	T	A	15: 25,971,641	D222E	probably benign	Het
Rmnd1	T	C	10: 4,413,404	K282R	probably benign	Het
Rsf1	ATGGCG	ATGGCGACGGTGGCG	7: 97,579,904		probably benign	Het
Sall3	C	T	18: 80,972,052	R887H	possibly damaging	Het
Samd3	A	G	10: 26,263,813	D281G	probably benign	Het
Sec24b	TGC	TGCAGC	3: 130,040,811		probably benign	Het
Slc2a2	A	G	3: 28,698,017	M1V	probably null	Het
Slc39a2	A	T	14: 51,895,031	T144S	probably benign	Het
Slc5a9	T	C	4: 111,877,740	H619R	probably benign	Het
Slco4a1	T	C	2: 180,471,255	F427L	probably benign	Het
Snapc3	C	A	4: 83,417,836	Y28*	probably null	Het
St3gal6	C	T	16: 58,473,437	R243H	probably benign	Het
Stat2	T	A	10: 128,277,197	N119K	possibly damaging	Het
Syne2	G	C	12: 75,966,371	V2779L	probably benign	Het
Tacc1	T	A	8: 25,201,285	M1L	probably damaging	Het
Tbc1d32	A	T	10: 56,151,833	F724L	possibly damaging	Het
Ttc23l	A	G	15: 10,533,680	I259T	possibly damaging	Het
Ucn2	T	C	9: 108,986,224	I18T	probably benign	Het
Wdr35	G	C	12: 9,024,886	A1000P	probably benign	Het
Wnk1	C	A	6: 119,929,828	C244F	possibly damaging	Het
Zeb2	T	G	2: 44,994,613	D1022A	probably damaging	Het
Zfp26	A	T	9: 20,437,833	H478Q	probably damaging	Het
Zfp410	A	G	12: 84,331,856	K265R	probably benign	Het
Zfp575	T	C	7: 24,586,668	D21G	probably benign	Het

Other mutations in Scube1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00903:Scube1	APN	15	83703501	missense	probably damaging	0.98
IGL01152:Scube1	APN	15	83613570	missense	probably damaging	1.00
IGL01388:Scube1	APN	15	83620131	missense	probably benign	0.00
IGL01589:Scube1	APN	15	83612553	missense	probably damaging	1.00
IGL02208:Scube1	APN	15	83703540	missense	probably damaging	1.00
IGL02305:Scube1	APN	15	83607390	missense	probably damaging	1.00
IGL02728:Scube1	APN	15	83659016	splice site	probably benign
IGL02737:Scube1	APN	15	83721843	splice site	probably benign
IGL03326:Scube1	APN	15	83607416	missense	probably damaging	1.00
R0055:Scube1	UTSW	15	83634736	missense	probably damaging	1.00
R0055:Scube1	UTSW	15	83634736	missense	probably damaging	1.00
R0126:Scube1	UTSW	15	83621063	missense	probably damaging	1.00
R0792:Scube1	UTSW	15	83628076	critical splice acceptor site	probably null
R1438:Scube1	UTSW	15	83615026	missense	possibly damaging	0.93
R1522:Scube1	UTSW	15	83628076	critical splice acceptor site	probably null
R1735:Scube1	UTSW	15	83607437	missense	probably damaging	1.00
R1766:Scube1	UTSW	15	83721945	missense	probably damaging	1.00
R1778:Scube1	UTSW	15	83610204	missense	probably damaging	1.00
R2975:Scube1	UTSW	15	83659098	missense	probably damaging	0.99
R4080:Scube1	UTSW	15	83608747	missense	probably damaging	1.00
R4434:Scube1	UTSW	15	83721924	missense	probably damaging	1.00
R5585:Scube1	UTSW	15	83676923	missense	probably damaging	1.00
R5857:Scube1	UTSW	15	83607260	unclassified	probably benign
R5977:Scube1	UTSW	15	83629488	missense	probably damaging	1.00
R6054:Scube1	UTSW	15	83651676	missense	probably benign	0.43
R6461:Scube1	UTSW	15	83612427	missense	probably damaging	1.00
R6956:Scube1	UTSW	15	83721876	missense	probably damaging	1.00
R6959:Scube1	UTSW	15	83629435	missense	probably benign	0.42
R7124:Scube1	UTSW	15	83629511	splice site	probably null
R7267:Scube1	UTSW	15	83621065	missense	probably damaging	1.00
R7404:Scube1	UTSW	15	83615010	missense	probably damaging	0.98
R7584:Scube1	UTSW	15	83721887	nonsense	probably null
R7585:Scube1	UTSW	15	83638787	missense	possibly damaging	0.83
R8055:Scube1	UTSW	15	83659025	critical splice donor site	probably null
R8098:Scube1	UTSW	15	83659088	missense	probably damaging	1.00
R8192:Scube1	UTSW	15	83629382	critical splice donor site	probably null
R8394:Scube1	UTSW	15	83608291	missense	probably damaging	1.00
R8441:Scube1	UTSW	15	83610222	missense	probably damaging	0.99
R8713:Scube1	UTSW	15	83610270	missense	possibly damaging	0.58
R8844:Scube1	UTSW	15	83676963	missense	probably damaging	1.00
R9090:Scube1	UTSW	15	83610193	missense	probably damaging	1.00
R9169:Scube1	UTSW	15	83659097	missense	possibly damaging	0.88
R9271:Scube1	UTSW	15	83610193	missense	probably damaging	1.00
R9334:Scube1	UTSW	15	83628063	missense	possibly damaging	0.72
R9363:Scube1	UTSW	15	83614879	nonsense	probably null
R9534:Scube1	UTSW	15	83721901	missense	probably damaging	1.00
R9569:Scube1	UTSW	15	83629404	missense	probably damaging	1.00
R9574:Scube1	UTSW	15	83616799	missense
R9759:Scube1	UTSW	15	83608264	missense	probably benign	0.02
R9788:Scube1	UTSW	15	83651700	missense	possibly damaging	0.73
X0022:Scube1	UTSW	15	83634669	critical splice donor site	probably null
Z1177:Scube1	UTSW	15	83612416	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- ACTCCCTTGAGGTGCTGGTATC -3'
(R):5'- TTCTGACTTCCAGGCCAGTG -3'

Sequencing Primer
(F):5'- GCTCAGAGTCTAGCTGCTGTC -3'
(R):5'- GACTTCCAGGCCAGTGCTCTC -3'

Posted On

2019-10-24