Mutagenetix > Incidental Mutation

Incidental Mutation 'R4809:Scube3'

370948

Institutional Source

Beutler Lab

Gene Symbol

Scube3

Ensembl Gene

ENSMUSG00000038677

Gene Name

signal peptide, CUB domain, EGF-like 3

Synonyms

MMRRC Submission

042428-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.435) question?

Stock #

R4809 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

28142316-28174852 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 28165173 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 549 (R549W)

Ref Sequence

ENSEMBL: ENSMUSP00000038366 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043503]

AlphaFold

Q66PY1

Predicted Effect

probably damaging
Transcript: ENSMUST00000043503
AA Change: R549W

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

SMART Domains

Protein: ENSMUSP00000038366
Gene: ENSMUSG00000038677
AA Change: R549W

Domain	Start	End	E-Value	Type
low complexity region	9	15	N/A	INTRINSIC
EGF_CA	29	69	5.23e-9	SMART
EGF_CA	70	111	1.2e-8	SMART
EGF_CA	112	152	1.14e-9	SMART
EGF	160	198	6.65e-2	SMART
EGF	200	237	7.95e0	SMART
EGF	239	276	7.76e-3	SMART
EGF_CA	277	317	7.63e-11	SMART
EGF_CA	318	356	7.01e-10	SMART
EGF_CA	357	398	6.8e-8	SMART
Pfam:GCC2_GCC3	642	689	8.6e-15	PFAM
Pfam:GCC2_GCC3	696	743	4.2e-17	PFAM
Pfam:GCC2_GCC3	752	799	5.8e-17	PFAM
CUB	804	916	1.09e-16	SMART
Blast:CUB	942	988	8e-15	BLAST

Predicted Effect

unknown
Transcript: ENSMUST00000132670
AA Change: R465W

SMART Domains

Protein: ENSMUSP00000117490
Gene: ENSMUSG00000038677
AA Change: R465W

Domain	Start	End	E-Value	Type
EGF_like	1	28	1.2e-1	SMART
EGF_CA	29	69	1.14e-9	SMART
EGF	77	115	6.65e-2	SMART
EGF	117	154	7.95e0	SMART
EGF	156	193	7.76e-3	SMART
EGF_CA	194	234	7.63e-11	SMART
EGF_CA	235	273	7.01e-10	SMART
EGF_CA	274	315	6.8e-8	SMART
Pfam:GCC2_GCC3	559	606	1.8e-17	PFAM
Pfam:GCC2_GCC3	615	662	4.2e-17	PFAM
CUB	667	779	1.09e-16	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137147

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142170

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148342

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.0%

Validation Efficiency

96% (96/100)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the signal peptide, complement subcomponents C1r/C1s, Uegf, bone morphogenetic protein-1 and epidermal growth factor-like domain containing protein family. Overexpression of this gene in human embryonic kidney cells results in secretion of a glycosylated form of the protein that forms oligomers and tethers to the cell surface. This gene is upregulated in lung cancer tumor tissue compared to healthy tissue and is associated with loss of the epithelial marker E-cadherin and with increased expression of vimentin, a mesenchymal marker. In addition, the protein encoded by this gene is a transforming growth factor beta receptor ligand, and when secreted by cancer cells, it can be cleaved in vitro to release the N-terminal epidermal growth factor-like repeat domain and the C-terminal complement subcomponents C1r/C1s domain. Both the full length protein and C-terminal fragment can bind to the transforming growth factor beta type II receptor to promote the epithelial-mesenchymal transition and tumor angiogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
PHENOTYPE: Mice homozygous for a targeted allele encoding a truncated protein exhibit normal morphology. Mice with a point mutation show skeletal abnormalities, bone metabolism alterations, changes in renal function, behavioral alternations and hearing loss. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	A	G	14: 32,662,631 (GRCm38)	V459A	probably benign	Het
Abca12	C	T	1: 71,278,856 (GRCm38)	A1840T	probably benign	Het
Abhd6	T	G	14: 8,039,771 (GRCm38)	M1R	probably null	Het
Abl1	T	C	2: 31,800,242 (GRCm38)	L572P	probably damaging	Het
Adamts2	C	A	11: 50,803,690 (GRCm38)	S1101R	probably benign	Het
Adgra2	G	A	8: 27,110,479 (GRCm38)	W200*	probably null	Het
AI661453	C	A	17: 47,467,187 (GRCm38)		probably benign	Het
Aldh1l2	A	G	10: 83,506,632 (GRCm38)	F438S	probably damaging	Het
Ankrd49	G	A	9: 14,781,214 (GRCm38)	T218I	possibly damaging	Het
Ano7	T	C	1: 93,394,566 (GRCm38)	F410L	probably benign	Het
Aox4	T	A	1: 58,266,649 (GRCm38)	F1271I	probably damaging	Het
Aqr	T	C	2: 114,175,214 (GRCm38)		probably benign	Het
Arhgap42	A	G	9: 9,180,117 (GRCm38)	S54P	probably damaging	Het
Aunip	C	A	4: 134,511,139 (GRCm38)	D16E	possibly damaging	Het
Btbd7	A	G	12: 102,793,744 (GRCm38)		probably null	Het
Cabp4	T	C	19: 4,139,291 (GRCm38)	H89R	probably benign	Het
Ccni	AAA	AAACTAA	5: 93,187,570 (GRCm38)		probably benign	Het
Chfr	C	T	5: 110,158,834 (GRCm38)	H410Y	probably damaging	Het
Churc1	C	A	12: 76,782,897 (GRCm38)	L111M	probably damaging	Het
Clasp1	C	T	1: 118,461,250 (GRCm38)	T113I	probably benign	Het
Col12a1	T	A	9: 79,693,567 (GRCm38)	Q745L	probably benign	Het
Col20a1	T	C	2: 180,998,661 (GRCm38)	L537P	probably damaging	Het
Creb5	A	T	6: 53,610,426 (GRCm38)	E47V	probably null	Het
Csnk1d	A	T	11: 120,963,842 (GRCm38)		probably benign	Het
Cts6	A	T	13: 61,202,181 (GRCm38)	W29R	probably damaging	Het
Dbt	T	A	3: 116,546,343 (GRCm38)	I420N	probably damaging	Het
Det1	C	A	7: 78,843,807 (GRCm38)	D150Y	probably damaging	Het
Dlk2	A	G	17: 46,299,014 (GRCm38)		probably null	Het
Dnmt3a	A	T	12: 3,900,352 (GRCm38)	I639F	probably damaging	Het
Dock9	A	T	14: 121,546,596 (GRCm38)	Y1989N	probably benign	Het
Dsg4	A	T	18: 20,466,621 (GRCm38)	T765S	possibly damaging	Het
Epha5	C	T	5: 84,105,891 (GRCm38)	D548N	possibly damaging	Het
Fam189a1	G	A	7: 64,776,740 (GRCm38)	T159I	probably damaging	Het
Fam227b	T	A	2: 126,116,125 (GRCm38)	Y240F	possibly damaging	Het
Fbxw21	C	T	9: 109,143,390 (GRCm38)	V395I	probably damaging	Het
Fn1	C	A	1: 71,652,800 (GRCm38)		probably benign	Het
Fpr-rs3	A	T	17: 20,624,421 (GRCm38)	S153T	probably benign	Het
Frem2	A	G	3: 53,653,895 (GRCm38)	F1064L	probably benign	Het
Gas2l3	CACTCGTCATACT	CACT	10: 89,430,958 (GRCm38)		probably benign	Het
Gjd2	C	T	2: 114,011,541 (GRCm38)	G152R	probably damaging	Het
Gpr75	T	C	11: 30,892,154 (GRCm38)	I353T	possibly damaging	Het
Grb7	T	C	11: 98,451,436 (GRCm38)	V145A	possibly damaging	Het
Igkv4-73	G	A	6: 69,197,823 (GRCm38)	R40W	unknown	Het
Kif1c	C	T	11: 70,726,357 (GRCm38)	A839V	probably benign	Het
Krt31	G	A	11: 100,049,922 (GRCm38)	A125V	possibly damaging	Het
Lamb1	A	G	12: 31,278,526 (GRCm38)	Y163C	probably damaging	Het
Mars	G	T	10: 127,300,215 (GRCm38)	T535K	probably damaging	Het
Mdc1	T	C	17: 35,849,101 (GRCm38)		probably null	Het
Micu1	C	T	10: 59,740,822 (GRCm38)	H167Y	probably benign	Het
Minos1	C	G	4: 139,130,957 (GRCm38)	W10S	probably damaging	Het
Mrgprb1	C	T	7: 48,447,991 (GRCm38)	V58I	possibly damaging	Het
Ncoa7	T	A	10: 30,771,762 (GRCm38)	E6V	possibly damaging	Het
Nectin3	A	C	16: 46,448,160 (GRCm38)		probably benign	Het
Olfr1085	T	A	2: 86,657,685 (GRCm38)	M258L	possibly damaging	Het
Olfr1294	C	T	2: 111,537,611 (GRCm38)	C226Y	probably benign	Het
Olfr46	A	G	7: 140,611,074 (GRCm38)	K295E	probably damaging	Het
Olfr598	T	A	7: 103,328,523 (GRCm38)	Y12*	probably null	Het
Pex16	T	C	2: 92,376,638 (GRCm38)	S54P	probably damaging	Het
Pik3cg	A	T	12: 32,204,081 (GRCm38)	S636T	possibly damaging	Het
Plin5	A	G	17: 56,116,855 (GRCm38)	S27P	probably benign	Het
Ptch1	A	T	13: 63,513,708 (GRCm38)	D1068E	probably damaging	Het
Ptprq	T	C	10: 107,563,175 (GRCm38)	T1960A	probably damaging	Het
Rap1gap2	T	C	11: 74,407,974 (GRCm38)		probably benign	Het
Rcc2	G	A	4: 140,717,042 (GRCm38)	R348Q	probably damaging	Het
Rhbdd3	C	A	11: 5,105,949 (GRCm38)	A377D	probably damaging	Het
Rpl7	T	G	1: 16,101,965 (GRCm38)		probably benign	Het
Scn11a	G	T	9: 119,819,870 (GRCm38)	D42E	probably benign	Het
Sil1	A	T	18: 35,325,375 (GRCm38)	M189K	probably damaging	Het
Slc39a6	G	A	18: 24,585,474 (GRCm38)	Q225*	probably null	Het
Slc7a15	A	T	12: 8,539,002 (GRCm38)	C182S	probably benign	Het
Spata21	G	A	4: 141,097,120 (GRCm38)		probably null	Het
Stim2	T	C	5: 54,110,613 (GRCm38)	V417A	probably damaging	Het
Szt2	T	C	4: 118,388,985 (GRCm38)	D993G	probably damaging	Het
Tet3	A	G	6: 83,402,946 (GRCm38)	S747P	probably benign	Het
Tmem86a	C	G	7: 47,052,930 (GRCm38)	S34R	possibly damaging	Het
Top2b	T	A	14: 16,383,125 (GRCm38)	S38T	probably benign	Het
Trim33	A	T	3: 103,329,256 (GRCm38)	T561S	possibly damaging	Het
Ttc39a	C	T	4: 109,416,021 (GRCm38)	Q25*	probably null	Het
Urb1	A	G	16: 90,759,842 (GRCm38)	I1816T	possibly damaging	Het
Usp24	T	C	4: 106,413,676 (GRCm38)		probably null	Het
Usp36	A	C	11: 118,263,070 (GRCm38)	L840R	probably damaging	Het
Usp50	C	A	2: 126,777,853 (GRCm38)		probably benign	Het
Vangl2	A	G	1: 172,009,663 (GRCm38)	V193A	possibly damaging	Het
Vmn1r62	T	A	7: 5,675,867 (GRCm38)	H182Q	probably benign	Het
Vmn2r124	A	T	17: 18,073,745 (GRCm38)	Y698F	probably benign	Het
Wls	C	T	3: 159,897,445 (GRCm38)	T165I	probably benign	Het
Zfp808	G	T	13: 62,171,292 (GRCm38)	E112*	probably null	Het

Other mutations in Scube3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02019:Scube3	APN	17	28,167,684 (GRCm38)	missense	probably damaging	1.00
IGL02189:Scube3	APN	17	28,162,996 (GRCm38)	missense	probably benign
IGL02416:Scube3	APN	17	28,164,136 (GRCm38)	missense	probably damaging	1.00
IGL02904:Scube3	APN	17	28,167,600 (GRCm38)	missense	probably benign	0.01
IGL03153:Scube3	APN	17	28,167,058 (GRCm38)	missense	possibly damaging	0.54
IGL03309:Scube3	APN	17	28,164,357 (GRCm38)	nonsense	probably null
dinklage	UTSW	17	28,162,388 (GRCm38)	missense	probably damaging	1.00
R0027:Scube3	UTSW	17	28,164,357 (GRCm38)	nonsense	probably null
R0084:Scube3	UTSW	17	28,162,961 (GRCm38)	missense	probably benign	0.12
R0122:Scube3	UTSW	17	28,166,528 (GRCm38)	splice site	probably benign
R0544:Scube3	UTSW	17	28,164,153 (GRCm38)	missense	probably damaging	1.00
R1779:Scube3	UTSW	17	28,168,379 (GRCm38)	splice site	probably benign
R1842:Scube3	UTSW	17	28,165,089 (GRCm38)	missense	probably damaging	1.00
R1878:Scube3	UTSW	17	28,152,413 (GRCm38)	missense	probably benign	0.10
R1950:Scube3	UTSW	17	28,164,300 (GRCm38)	missense	possibly damaging	0.66
R2011:Scube3	UTSW	17	28,168,158 (GRCm38)	missense	probably damaging	0.99
R2164:Scube3	UTSW	17	28,166,134 (GRCm38)	missense	possibly damaging	0.64
R4356:Scube3	UTSW	17	28,164,309 (GRCm38)	missense	probably benign	0.01
R4392:Scube3	UTSW	17	28,164,788 (GRCm38)	missense	probably null
R4528:Scube3	UTSW	17	28,162,999 (GRCm38)	missense	possibly damaging	0.82
R4709:Scube3	UTSW	17	28,167,192 (GRCm38)	splice site	probably null
R4832:Scube3	UTSW	17	28,166,015 (GRCm38)	missense	probably damaging	0.98
R4841:Scube3	UTSW	17	28,164,123 (GRCm38)	missense	probably damaging	1.00
R4842:Scube3	UTSW	17	28,164,123 (GRCm38)	missense	probably damaging	1.00
R5372:Scube3	UTSW	17	28,152,482 (GRCm38)	missense	probably damaging	0.99
R5889:Scube3	UTSW	17	28,160,913 (GRCm38)	missense	possibly damaging	0.84
R5936:Scube3	UTSW	17	28,165,487 (GRCm38)	missense	probably damaging	1.00
R6523:Scube3	UTSW	17	28,162,388 (GRCm38)	missense	probably damaging	1.00
R7051:Scube3	UTSW	17	28,167,599 (GRCm38)	missense	probably benign
R7337:Scube3	UTSW	17	28,168,182 (GRCm38)	missense	probably damaging	1.00
R7699:Scube3	UTSW	17	28,167,049 (GRCm38)	missense	probably damaging	1.00
R7700:Scube3	UTSW	17	28,167,049 (GRCm38)	missense	probably damaging	1.00
R7848:Scube3	UTSW	17	28,165,595 (GRCm38)	missense	probably benign
R7950:Scube3	UTSW	17	28,171,226 (GRCm38)	missense	probably benign	0.11
R8991:Scube3	UTSW	17	28,164,053 (GRCm38)	missense	probably damaging	0.98
R9376:Scube3	UTSW	17	28,164,696 (GRCm38)	missense	possibly damaging	0.92
R9469:Scube3	UTSW	17	28,167,164 (GRCm38)	nonsense	probably null
R9653:Scube3	UTSW	17	28,156,798 (GRCm38)	missense	probably damaging	1.00
R9660:Scube3	UTSW	17	28,152,440 (GRCm38)	missense	probably benign	0.05
RF009:Scube3	UTSW	17	28,168,397 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATTCCCTCCTACCGAGAAGAG -3'
(R):5'- TGCTGCTCGCCATTACACAG -3'

Sequencing Primer
(F):5'- CTCCTACCGAGAAGAGGGTTG -3'
(R):5'- ATTACACAGGCCCAGAGTTG -3'

Posted On

2016-02-04