Mutagenetix > Incidental Mutation

Incidental Mutation 'R4999:Rufy3'

389716

Institutional Source

Beutler Lab

Gene Symbol

Rufy3

Ensembl Gene

ENSMUSG00000029291

Gene Name

RUN and FYVE domain containing 3

Synonyms

Rpipx, D5Bwg0860e, 6330416M07Rik, 2810428M05Rik

MMRRC Submission

042593-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4999 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

88712899-88799251 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 88785085 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 387 (M387K)

Ref Sequence

ENSEMBL: ENSMUSP00000143115 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031229] [ENSMUST00000196686] [ENSMUST00000196894] [ENSMUST00000198965] [ENSMUST00000199312]

AlphaFold

Q9D394

Predicted Effect

possibly damaging
Transcript: ENSMUST00000031229
AA Change: M369K

PolyPhen 2 Score 0.673 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000031229
Gene: ENSMUSG00000029291
AA Change: M369K

Domain	Start	End	E-Value	Type
low complexity region	5	16	N/A	INTRINSIC
RUN	163	225	8.08e-23	SMART
coiled coil region	267	329	N/A	INTRINSIC
coiled coil region	357	464	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000196686
AA Change: M387K

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

SMART Domains

Protein: ENSMUSP00000143209
Gene: ENSMUSG00000029291
AA Change: M387K

Domain	Start	End	E-Value	Type
low complexity region	5	16	N/A	INTRINSIC
RUN	181	243	8.08e-23	SMART
coiled coil region	285	347	N/A	INTRINSIC
coiled coil region	375	482	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000196894
AA Change: M419K

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000143770
Gene: ENSMUSG00000029291
AA Change: M419K

Domain	Start	End	E-Value	Type
low complexity region	2	34	N/A	INTRINSIC
low complexity region	84	107	N/A	INTRINSIC
RUN	213	275	8.08e-23	SMART
coiled coil region	317	379	N/A	INTRINSIC
coiled coil region	407	514	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000198965
AA Change: M419K

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000143302
Gene: ENSMUSG00000029291
AA Change: M419K

Domain	Start	End	E-Value	Type
low complexity region	2	34	N/A	INTRINSIC
low complexity region	84	107	N/A	INTRINSIC
RUN	213	275	2.8e-25	SMART
coiled coil region	317	379	N/A	INTRINSIC
coiled coil region	407	555	N/A	INTRINSIC
FYVE	597	662	2.9e-6	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000199312
AA Change: M387K

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

SMART Domains

Protein: ENSMUSP00000143115
Gene: ENSMUSG00000029291
AA Change: M387K

Domain	Start	End	E-Value	Type
low complexity region	5	16	N/A	INTRINSIC
RUN	181	243	8.08e-23	SMART
coiled coil region	285	347	N/A	INTRINSIC
coiled coil region	375	482	N/A	INTRINSIC

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a RPIP8, UNC-14, and NESCA domain-containing protein that is required for maintenance of neuronal polarity. In addition, it has been implicated in mediation of gastric cancer cell migration and invasion via interaction with P21-activated kinase-1, which promotes its expression. The encoded protein localizes to F-actin-enriched invadopodia to induce formation of protrusions, thereby facilitating cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
PHENOTYPE: The gene product is involved in regulating neuronal polarity and axon growth. Homozygous KO leads to loss of neuronal polarity and causes neonatal lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930444P10Rik	A	G	1: 16,139,022 (GRCm39)		probably null	Het
Abca4	T	A	3: 121,899,019 (GRCm39)	V667D	probably damaging	Het
Aco1	A	G	4: 40,176,507 (GRCm39)	I224V	probably damaging	Het
Arel1	C	T	12: 84,978,541 (GRCm39)	V364M	probably damaging	Het
Arhgap42	A	G	9: 9,009,435 (GRCm39)	V484A	probably damaging	Het
Asap2	T	C	12: 21,302,766 (GRCm39)	F681L	probably benign	Het
Atrn	C	A	2: 130,817,874 (GRCm39)	D809E	probably damaging	Het
Ccdc70	G	A	8: 22,463,266 (GRCm39)	V19M	possibly damaging	Het
Ccp110	G	T	7: 118,329,235 (GRCm39)	E73*	probably null	Het
Cfap57	A	C	4: 118,453,045 (GRCm39)	S553A	probably benign	Het
Cftr	A	G	6: 18,221,613 (GRCm39)	K212E	probably benign	Het
Chkb	A	T	15: 89,312,368 (GRCm39)	Y216N	probably damaging	Het
Cntnap2	G	T	6: 45,897,768 (GRCm39)	D149Y	probably damaging	Het
Cpd	A	G	11: 76,737,048 (GRCm39)		probably null	Het
Creb3l1	C	T	2: 91,813,571 (GRCm39)	D489N	probably benign	Het
Crhbp	A	G	13: 95,578,753 (GRCm39)	F123L	probably damaging	Het
Cryab	T	C	9: 50,665,909 (GRCm39)	V100A	possibly damaging	Het
Csmd2	T	C	4: 128,415,723 (GRCm39)	I2684T	probably benign	Het
Ctbp2	G	T	7: 132,616,378 (GRCm39)	P186T	possibly damaging	Het
Ctnna2	T	C	6: 76,892,745 (GRCm39)	N814S	possibly damaging	Het
Dntt	T	C	19: 41,028,295 (GRCm39)	V197A	probably damaging	Het
Fam135a	G	A	1: 24,059,758 (GRCm39)	A1187V	possibly damaging	Het
Filip1l	A	T	16: 57,390,778 (GRCm39)	Q455H	probably benign	Het
Grm2	T	C	9: 106,531,189 (GRCm39)	E100G	probably damaging	Het
Gtf2ird2	G	A	5: 134,246,306 (GRCm39)	V855M	probably damaging	Het
Heatr9	A	T	11: 83,409,618 (GRCm39)	I118N	possibly damaging	Het
Htra3	T	C	5: 35,828,469 (GRCm39)	H137R	probably benign	Het
Iars1	A	G	13: 49,863,137 (GRCm39)	S530G	probably damaging	Het
Klhdc4	T	A	8: 122,523,342 (GRCm39)	M510L	probably benign	Het
Lipc	T	C	9: 70,724,013 (GRCm39)	T204A	probably benign	Het
Lrp1	A	G	10: 127,389,648 (GRCm39)	V3129A	probably damaging	Het
Macf1	G	A	4: 123,388,702 (GRCm39)	T1120I	probably benign	Het
Maco1	A	G	4: 134,555,444 (GRCm39)	I343T	probably benign	Het
Map4	T	C	9: 109,867,445 (GRCm39)		probably benign	Het
Mbtps1	A	T	8: 120,260,087 (GRCm39)	V420D	probably damaging	Het
Mta2	G	T	19: 8,927,747 (GRCm39)	D523Y	probably benign	Het
Mtcl2	C	T	2: 156,864,776 (GRCm39)	G1144D	probably benign	Het
Muc4	A	G	16: 32,576,670 (GRCm39)		probably benign	Het
Mug1	C	T	6: 121,855,902 (GRCm39)	Q965*	probably null	Het
Myo1e	T	A	9: 70,260,594 (GRCm39)	I584N	probably damaging	Het
Nolc1	T	C	19: 46,067,359 (GRCm39)	V80A	probably damaging	Het
Nop56	G	T	2: 130,117,645 (GRCm39)	V91L	probably benign	Het
Or5b99	A	T	19: 12,976,583 (GRCm39)	M78L	probably benign	Het
Or5h23	A	T	16: 58,906,765 (GRCm39)	L27Q	probably damaging	Het
Or6f2	T	C	7: 139,756,933 (GRCm39)	V300A	probably damaging	Het
Osbpl3	T	C	6: 50,313,277 (GRCm39)	E107G	probably damaging	Het
Pde3a	T	A	6: 141,195,751 (GRCm39)	C146S	probably benign	Het
Pfkm	A	G	15: 98,026,123 (GRCm39)	M573V	probably damaging	Het
Pkd1l2	C	T	8: 117,774,113 (GRCm39)		probably null	Het
Plekhg3	T	C	12: 76,612,021 (GRCm39)	I374T	possibly damaging	Het
Ppig	T	A	2: 69,571,830 (GRCm39)	V183D	unknown	Het
Prom1	T	G	5: 44,194,876 (GRCm39)	I290L	probably benign	Het
Selenoo	G	A	15: 88,978,387 (GRCm39)	R270H	probably damaging	Het
Sema3d	T	A	5: 12,558,054 (GRCm39)		probably null	Het
Sema6c	C	T	3: 95,075,674 (GRCm39)	T175I	probably damaging	Het
Serpina3k	T	C	12: 104,307,305 (GRCm39)	I179T	probably damaging	Het
Sf3b3	T	C	8: 111,567,835 (GRCm39)	T207A	probably benign	Het
Slc22a26	C	A	19: 7,779,546 (GRCm39)	R90L	probably damaging	Het
Slitrk5	T	C	14: 111,917,648 (GRCm39)	V424A	probably damaging	Het
Smarca2	G	T	19: 26,698,255 (GRCm39)	E89*	probably null	Het
Stab2	T	A	10: 86,773,773 (GRCm39)	S853C	probably damaging	Het
Stk17b	A	T	1: 53,800,306 (GRCm39)		probably null	Het
Taar5	T	A	10: 23,847,445 (GRCm39)	I281N	possibly damaging	Het
Tars3	A	T	7: 65,308,683 (GRCm39)	E284D	probably damaging	Het
Tbx15	C	A	3: 99,223,649 (GRCm39)	T279K	probably damaging	Het
Tfr2	G	A	5: 137,585,187 (GRCm39)	V740I	probably benign	Het
Tlr12	T	C	4: 128,511,473 (GRCm39)	E259G	probably benign	Het
Tmem145	A	G	7: 25,008,459 (GRCm39)	T302A	probably benign	Het
Trappc14	T	A	5: 138,259,884 (GRCm39)	T391S	probably damaging	Het
Trpa1	G	T	1: 14,946,085 (GRCm39)	H1015Q	probably benign	Het
Tspan8	A	G	10: 115,653,534 (GRCm39)	Y10C	possibly damaging	Het
Ttll7	A	G	3: 146,600,224 (GRCm39)	N44S	probably damaging	Het
Uba7	T	C	9: 107,857,038 (GRCm39)		probably null	Het
Ube2j2	G	A	4: 156,030,841 (GRCm39)	M1I	probably null	Het
Ubr5	C	A	15: 38,009,912 (GRCm39)	A1022S	probably benign	Het
Usf1	T	G	1: 171,243,331 (GRCm39)	I36S	probably damaging	Het
Vmn1r181	A	T	7: 23,683,790 (GRCm39)	D85V	probably damaging	Het
Vmn1r3	A	T	4: 3,185,009 (GRCm39)	Y99*	probably null	Het
Vmn1r72	T	C	7: 11,404,300 (GRCm39)	I49M	possibly damaging	Het
Vmn2r99	A	G	17: 19,582,397 (GRCm39)	M1V	probably null	Het
Vsig10	T	A	5: 117,482,040 (GRCm39)	V410E	probably damaging	Het
Zc3h7b	A	G	15: 81,663,334 (GRCm39)	Y442C	probably damaging	Het
Zfyve26	G	T	12: 79,327,159 (GRCm39)	Y730*	probably null	Het

Other mutations in Rufy3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00705:Rufy3	APN	5	88,769,209 (GRCm39)	missense	probably damaging	0.96
IGL01964:Rufy3	APN	5	88,762,929 (GRCm39)	missense	probably damaging	1.00
IGL02537:Rufy3	APN	5	88,788,521 (GRCm39)	utr 3 prime	probably benign
R0111:Rufy3	UTSW	5	88,778,443 (GRCm39)	missense	probably damaging	1.00
R0552:Rufy3	UTSW	5	88,732,129 (GRCm39)	missense	possibly damaging	0.79
R1441:Rufy3	UTSW	5	88,780,374 (GRCm39)	missense	probably damaging	0.97
R1565:Rufy3	UTSW	5	88,788,491 (GRCm39)	missense	probably damaging	1.00
R2507:Rufy3	UTSW	5	88,797,757 (GRCm39)	missense	probably damaging	1.00
R2508:Rufy3	UTSW	5	88,797,757 (GRCm39)	missense	probably damaging	1.00
R3707:Rufy3	UTSW	5	88,790,891 (GRCm39)	missense	probably benign	0.28
R4907:Rufy3	UTSW	5	88,732,051 (GRCm39)	missense	possibly damaging	0.95
R5134:Rufy3	UTSW	5	88,793,426 (GRCm39)	missense	probably benign	0.01
R5420:Rufy3	UTSW	5	88,788,518 (GRCm39)	makesense	probably null
R5482:Rufy3	UTSW	5	88,785,191 (GRCm39)	frame shift	probably null
R6029:Rufy3	UTSW	5	88,775,114 (GRCm39)	missense	probably damaging	1.00
R6254:Rufy3	UTSW	5	88,732,168 (GRCm39)	missense	probably benign	0.01
R6444:Rufy3	UTSW	5	88,785,166 (GRCm39)	missense	probably damaging	1.00
R7219:Rufy3	UTSW	5	88,797,715 (GRCm39)	missense	probably benign	0.22
R7256:Rufy3	UTSW	5	88,762,806 (GRCm39)	missense	possibly damaging	0.91
R7327:Rufy3	UTSW	5	88,790,811 (GRCm39)	missense	probably damaging	0.99
R7352:Rufy3	UTSW	5	88,785,053 (GRCm39)	missense	possibly damaging	0.92
R7484:Rufy3	UTSW	5	88,746,331 (GRCm39)	missense	probably benign	0.01
R7645:Rufy3	UTSW	5	88,788,476 (GRCm39)	missense	probably benign	0.01
R7953:Rufy3	UTSW	5	88,790,851 (GRCm39)	missense	probably benign	0.01
R8043:Rufy3	UTSW	5	88,790,851 (GRCm39)	missense	probably benign	0.01
R8478:Rufy3	UTSW	5	88,762,895 (GRCm39)	missense	probably damaging	1.00
R8549:Rufy3	UTSW	5	88,795,073 (GRCm39)	splice site	probably null
R9112:Rufy3	UTSW	5	88,780,336 (GRCm39)	missense
R9399:Rufy3	UTSW	5	88,797,725 (GRCm39)	missense	possibly damaging	0.92
R9438:Rufy3	UTSW	5	88,796,124 (GRCm39)	missense	probably benign	0.00
X0066:Rufy3	UTSW	5	88,765,277 (GRCm39)	missense	probably benign	0.10

Predicted Primers

PCR Primer
(F):5'- GCCAGATGCCTCTACTCTATCAG -3'
(R):5'- AGTCTACAGAAGAGGCGTGC -3'

Sequencing Primer
(F):5'- GATGCCTCTACTCTATCAGAAACAC -3'
(R):5'- TATGGGCAGCACCAGGAGTTC -3'

Posted On

2016-06-06