Mutagenetix > Incidental Mutation

Incidental Mutation 'R1819:Rubcn'

204744

Institutional Source

Beutler Lab

Gene Symbol

Rubcn

Ensembl Gene

ENSMUSG00000035629

Gene Name

RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein

Synonyms

1700021K19Rik

MMRRC Submission

039847-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.888) question?

Stock #

R1819 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

32642072-32698121 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 32647284 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 703 (K703R)

Ref Sequence

ENSEMBL: ENSMUSP00000155943 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040986] [ENSMUST00000089684] [ENSMUST00000115105] [ENSMUST00000119810] [ENSMUST00000231478] [ENSMUST00000232269]

AlphaFold

Q80U62

Predicted Effect

possibly damaging
Transcript: ENSMUST00000040986
AA Change: K703R

PolyPhen 2 Score 0.928 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000048811
Gene: ENSMUSG00000035629
AA Change: K703R

Domain	Start	End	E-Value	Type
low complexity region	4	20	N/A	INTRINSIC
RUN	123	183	1.67e-15	SMART
low complexity region	230	254	N/A	INTRINSIC
low complexity region	339	371	N/A	INTRINSIC
Blast:DUF4206	469	687	1e-66	BLAST
DUF4206	706	908	1.66e-113	SMART
low complexity region	915	941	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000089684
AA Change: K718R

PolyPhen 2 Score 0.882 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000087114
Gene: ENSMUSG00000035629
AA Change: K718R

Domain	Start	End	E-Value	Type
low complexity region	4	20	N/A	INTRINSIC
RUN	123	183	1.67e-15	SMART
low complexity region	230	254	N/A	INTRINSIC
low complexity region	339	371	N/A	INTRINSIC
Blast:DUF4206	484	702	1e-66	BLAST
DUF4206	721	923	1.66e-113	SMART
low complexity region	930	956	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115105
AA Change: K689R

PolyPhen 2 Score 0.723 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000110757
Gene: ENSMUSG00000035629
AA Change: K689R

Domain	Start	End	E-Value	Type
low complexity region	4	20	N/A	INTRINSIC
RUN	123	183	1.67e-15	SMART
low complexity region	230	254	N/A	INTRINSIC
low complexity region	340	357	N/A	INTRINSIC
Blast:DUF4206	455	673	1e-66	BLAST
DUF4206	692	894	1.66e-113	SMART
low complexity region	901	927	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000119810
AA Change: K642R

PolyPhen 2 Score 0.882 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000113087
Gene: ENSMUSG00000035629
AA Change: K642R

Domain	Start	End	E-Value	Type
RUN	62	122	1.67e-15	SMART
low complexity region	169	193	N/A	INTRINSIC
low complexity region	278	310	N/A	INTRINSIC
Blast:DUF4206	408	626	6e-67	BLAST
DUF4206	645	847	1.66e-113	SMART
low complexity region	854	880	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135480

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140229

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152920

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231478
AA Change: K718R

PolyPhen 2 Score 0.882 (Sensitivity: 0.82; Specificity: 0.94)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000232269
AA Change: K703R

PolyPhen 2 Score 0.928 (Sensitivity: 0.81; Specificity: 0.94)

Meta Mutation Damage Score

0.1403

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.1%
20x: 91.9%

Validation Efficiency

100% (91/91)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a negative regulator of autophagy and endocytic trafficking and controls endosome maturation. This protein contains two conserved domains, an N-terminal RUN domain and a C-terminal DUF4206 domain. The RUN domain is involved in Ras-like GTPase signaling, and the DUF4206 domain contains a diacylglycerol (DAG) binding-like motif. Mutation in this gene results in deletion of the DAG binding-like motif and causes a recessive ataxia. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Apr 2014]

Allele List at MGI

Other mutations in this stock

Total: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	T	C	11: 109,871,882 (GRCm39)		probably null	Het
Abhd17a	T	C	10: 80,422,470 (GRCm39)	T71A	probably benign	Het
Acad11	G	A	9: 103,991,738 (GRCm39)		probably null	Het
Adgrf1	C	A	17: 43,620,924 (GRCm39)	T387K	probably benign	Het
Afdn	A	G	17: 14,071,110 (GRCm39)	T783A	probably damaging	Het
Akap13	T	A	7: 75,258,453 (GRCm39)	M359K	probably benign	Het
Asxl3	A	T	18: 22,655,433 (GRCm39)	N1148Y	probably damaging	Het
Atl1	T	C	12: 70,010,074 (GRCm39)	S547P	probably benign	Het
Bace1	A	T	9: 45,768,460 (GRCm39)	T252S	possibly damaging	Het
BC034090	A	G	1: 155,101,575 (GRCm39)	S230P	possibly damaging	Het
Bnc2	A	G	4: 84,210,111 (GRCm39)	F778L	possibly damaging	Het
Capn2	T	A	1: 182,300,162 (GRCm39)	K609N	probably benign	Het
Capn8	T	A	1: 182,426,391 (GRCm39)	I242N	probably damaging	Het
Car9	G	T	4: 43,512,439 (GRCm39)		probably null	Het
Ccdc180	A	G	4: 45,926,195 (GRCm39)	E1135G	possibly damaging	Het
Ccdc181	C	T	1: 164,110,047 (GRCm39)	Q385*	probably null	Het
Cdh10	G	T	15: 18,992,051 (GRCm39)	G437*	probably null	Het
Ceacam1	T	A	7: 25,163,285 (GRCm39)	Q316L	possibly damaging	Het
Cecr2	A	G	6: 120,708,228 (GRCm39)	T77A	probably damaging	Het
Cers4	T	A	8: 4,571,232 (GRCm39)	M267K	probably benign	Het
Csmd3	T	C	15: 47,617,131 (GRCm39)	D1930G	possibly damaging	Het
Cyp2j11	A	T	4: 96,185,976 (GRCm39)	V403D	probably damaging	Het
Cyp4v3	G	A	8: 45,768,673 (GRCm39)	R296C	possibly damaging	Het
Ddx59	A	G	1: 136,360,245 (GRCm39)	I420V	probably damaging	Het
Dnah5	T	A	15: 28,246,546 (GRCm39)	L628*	probably null	Het
Dnah7a	A	C	1: 53,598,307 (GRCm39)	D1409E	probably benign	Het
Dus2	T	A	8: 106,778,480 (GRCm39)	W377R	probably damaging	Het
E330034G19Rik	A	G	14: 24,348,081 (GRCm39)	D111G	probably damaging	Het
Erich4	C	T	7: 25,314,715 (GRCm39)	R66Q	possibly damaging	Het
Fcgbp	G	T	7: 27,784,708 (GRCm39)	R256L	probably benign	Het
Fdxr	A	T	11: 115,166,930 (GRCm39)	F53Y	probably damaging	Het
Fkbp10	G	T	11: 100,306,715 (GRCm39)	A36S	probably benign	Het
Foxo3	A	T	10: 42,073,607 (GRCm39)	D84E	probably benign	Het
Gin1	A	G	1: 97,712,951 (GRCm39)		probably null	Het
Gli3	C	T	13: 15,900,377 (GRCm39)	Q1255*	probably null	Het
Gm4847	T	A	1: 166,465,788 (GRCm39)	H267L	probably damaging	Het
Gpr171	T	C	3: 59,005,341 (GRCm39)	I145V	probably benign	Het
Gpr68	T	A	12: 100,844,662 (GRCm39)	H294L	possibly damaging	Het
Gys2	T	C	6: 142,406,912 (GRCm39)	E148G	probably damaging	Het
Heatr5b	T	C	17: 79,098,940 (GRCm39)	D1320G	probably damaging	Het
Ifnlr1	G	T	4: 135,413,834 (GRCm39)		probably benign	Het
Ift88	G	A	14: 57,692,976 (GRCm39)	E392K	probably damaging	Het
Igsf9b	T	A	9: 27,222,889 (GRCm39)	S97T	probably damaging	Het
Il18rap	A	G	1: 40,570,687 (GRCm39)	I210V	probably benign	Het
Kcnj11	C	T	7: 45,748,580 (GRCm39)	G248S	probably benign	Het
Kif28	T	C	1: 179,533,319 (GRCm39)	K541E	possibly damaging	Het
Lilrb4a	A	G	10: 51,372,124 (GRCm39)	Y205C	probably damaging	Het
Lima1	T	A	15: 99,717,817 (GRCm39)	H63L	probably benign	Het
Lonrf3	A	G	X: 35,622,361 (GRCm39)	I687V	probably damaging	Het
Lrba	A	G	3: 86,449,941 (GRCm39)	T2099A	possibly damaging	Het
Morn5	C	T	2: 35,942,987 (GRCm39)	T29M	probably damaging	Het
Neurl1b	G	A	17: 26,657,674 (GRCm39)	R22H	probably benign	Het
Nr2e3	T	C	9: 59,850,720 (GRCm39)	I380V	probably damaging	Het
Oas1c	G	A	5: 120,946,800 (GRCm39)	A10V	possibly damaging	Het
Or1e35	T	C	11: 73,797,505 (GRCm39)	E271G	probably benign	Het
Or52e8	C	T	7: 104,624,605 (GRCm39)	V196I	probably benign	Het
P3h3	T	C	6: 124,831,895 (GRCm39)	T297A	probably benign	Het
Pdpk1	T	C	17: 24,329,878 (GRCm39)	K53E	probably damaging	Het
Plec	C	T	15: 76,064,106 (GRCm39)	R2056Q	probably damaging	Het
Plxna2	T	A	1: 194,472,494 (GRCm39)	N1079K	probably benign	Het
Prr12	G	C	7: 44,698,121 (GRCm39)		probably benign	Het
Psip1	A	G	4: 83,376,400 (GRCm39)	S480P	probably benign	Het
Ptpre	A	G	7: 135,270,722 (GRCm39)		probably benign	Het
Pvalb	A	C	15: 78,086,784 (GRCm39)	V44G	probably damaging	Het
Rab3c	T	G	13: 110,220,669 (GRCm39)	Q164P	possibly damaging	Het
Setd7	T	G	3: 51,450,060 (GRCm39)	H122P	probably benign	Het
Slc26a8	A	T	17: 28,903,808 (GRCm39)	F19I	probably benign	Het
Slc6a14	A	G	X: 21,607,286 (GRCm39)	D625G	probably benign	Het
Snx6	C	T	12: 54,830,259 (GRCm39)	V67I	possibly damaging	Het
Syngr3	A	G	17: 24,906,696 (GRCm39)	F40L	possibly damaging	Het
Syt8	G	A	7: 141,991,971 (GRCm39)	G21R	possibly damaging	Het
Tagln	A	G	9: 45,842,138 (GRCm39)	F152L	probably benign	Het
Tcf12	G	A	9: 72,016,999 (GRCm39)	T36M	probably damaging	Het
Tdrd6	C	T	17: 43,937,442 (GRCm39)	S1202N	probably benign	Het
Tekt2	T	C	4: 126,217,529 (GRCm39)	K179E	probably damaging	Het
Tekt4	G	T	17: 25,692,785 (GRCm39)		probably null	Het
Tmprss5	G	T	9: 49,018,464 (GRCm39)	R98L	probably benign	Het
Tns1	G	T	1: 73,955,635 (GRCm39)		probably benign	Het
Tpcn1	A	C	5: 120,674,292 (GRCm39)		probably null	Het
Ttc6	T	C	12: 57,741,286 (GRCm39)		probably null	Het
Ttf1	A	G	2: 28,964,796 (GRCm39)	N706S	possibly damaging	Het
Washc4	C	T	10: 83,386,748 (GRCm39)	T124I	probably benign	Het
Wdr17	A	T	8: 55,143,159 (GRCm39)	S140T	probably benign	Het
Wdr19	A	T	5: 65,370,234 (GRCm39)	I123F	possibly damaging	Het
Zer1	C	T	2: 30,000,230 (GRCm39)	A317T	probably benign	Het
Zfp474	A	G	18: 52,771,872 (GRCm39)	D175G	probably damaging	Het
Zfp598	T	C	17: 24,900,104 (GRCm39)		probably benign	Het
Zfp646	G	A	7: 127,482,292 (GRCm39)	G1490S	probably benign	Het
Zranb3	A	T	1: 127,945,293 (GRCm39)		probably null	Het

Other mutations in Rubcn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00654:Rubcn	APN	16	32,644,747 (GRCm39)	critical splice donor site	probably null
IGL00777:Rubcn	APN	16	32,656,933 (GRCm39)	missense	probably damaging	0.98
IGL01402:Rubcn	APN	16	32,647,666 (GRCm39)	missense	probably damaging	1.00
IGL01404:Rubcn	APN	16	32,647,666 (GRCm39)	missense	probably damaging	1.00
IGL02255:Rubcn	APN	16	32,647,715 (GRCm39)	missense	probably benign	0.04
IGL03019:Rubcn	APN	16	32,647,077 (GRCm39)	missense	probably damaging	0.98
IGL03388:Rubcn	APN	16	32,661,938 (GRCm39)	missense	probably benign	0.02
R0254:Rubcn	UTSW	16	32,668,316 (GRCm39)	missense	probably benign	0.00
R0373:Rubcn	UTSW	16	32,656,350 (GRCm39)	missense	probably damaging	1.00
R0636:Rubcn	UTSW	16	32,649,056 (GRCm39)	missense	probably damaging	1.00
R0839:Rubcn	UTSW	16	32,647,713 (GRCm39)	missense	probably damaging	0.98
R0967:Rubcn	UTSW	16	32,646,087 (GRCm39)	missense	probably benign	0.00
R1711:Rubcn	UTSW	16	32,663,471 (GRCm39)	missense	probably damaging	1.00
R1840:Rubcn	UTSW	16	32,646,542 (GRCm39)	missense	possibly damaging	0.83
R2511:Rubcn	UTSW	16	32,667,624 (GRCm39)	missense	probably damaging	1.00
R3932:Rubcn	UTSW	16	32,649,629 (GRCm39)	splice site	probably null
R3933:Rubcn	UTSW	16	32,649,629 (GRCm39)	splice site	probably null
R4384:Rubcn	UTSW	16	32,677,272 (GRCm39)	missense	probably damaging	0.96
R4788:Rubcn	UTSW	16	32,656,778 (GRCm39)	critical splice donor site	probably null
R4852:Rubcn	UTSW	16	32,663,678 (GRCm39)	missense	probably damaging	1.00
R4921:Rubcn	UTSW	16	32,667,664 (GRCm39)	missense	probably damaging	1.00
R4950:Rubcn	UTSW	16	32,663,563 (GRCm39)	missense	probably damaging	1.00
R5234:Rubcn	UTSW	16	32,656,828 (GRCm39)	missense	probably damaging	1.00
R5527:Rubcn	UTSW	16	32,647,081 (GRCm39)	missense	probably damaging	1.00
R5616:Rubcn	UTSW	16	32,647,293 (GRCm39)	missense	possibly damaging	0.76
R5823:Rubcn	UTSW	16	32,670,091 (GRCm39)	missense	probably damaging	0.98
R6970:Rubcn	UTSW	16	32,688,514 (GRCm39)	intron	probably benign
R7120:Rubcn	UTSW	16	32,656,839 (GRCm39)	missense	probably damaging	1.00
R7121:Rubcn	UTSW	16	32,656,839 (GRCm39)	missense	probably damaging	1.00
R7221:Rubcn	UTSW	16	32,687,293 (GRCm39)	splice site	probably null
R7833:Rubcn	UTSW	16	32,688,644 (GRCm39)	start gained	probably benign
R8108:Rubcn	UTSW	16	32,677,320 (GRCm39)	missense	probably damaging	1.00
R8211:Rubcn	UTSW	16	32,656,913 (GRCm39)	missense	possibly damaging	0.87
R8923:Rubcn	UTSW	16	32,646,049 (GRCm39)	missense	probably damaging	1.00
R9046:Rubcn	UTSW	16	32,661,940 (GRCm39)	missense	probably benign	0.00
R9587:Rubcn	UTSW	16	32,663,679 (GRCm39)	missense	probably damaging	1.00
R9694:Rubcn	UTSW	16	32,663,481 (GRCm39)	missense	probably benign	0.22
X0065:Rubcn	UTSW	16	32,668,355 (GRCm39)	missense	possibly damaging	0.85
Z1176:Rubcn	UTSW	16	32,663,533 (GRCm39)	missense	probably benign	0.00
Z1177:Rubcn	UTSW	16	32,645,959 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGCGCTATTGATGTCCTGC -3'
(R):5'- TCACTGCAGCTAGGCTCTTAG -3'

Sequencing Primer
(F):5'- CTGCACATTGAAGAGAGGATCATTCC -3'
(R):5'- ACTGGATTTGGATTCTTCAGTAGCC -3'

Posted On

2014-06-23