Mutagenetix > Incidental Mutations

Incidental Mutation 'R6970:Rbm39'

542160

Institutional Source

Beutler Lab

Gene Symbol

Rbm39

Ensembl Gene

ENSMUSG00000027620

Gene Name

RNA binding motif protein 39

Synonyms

B330012G18Rik, Caper alpha, 1500012C14Rik, caper, Rnpc2, 2310040E03Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R6970 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

156147239-156180238 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 156167584 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 123 (R123C)

Ref Sequence

ENSEMBL: ENSMUSP00000116950 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029149] [ENSMUST00000109587] [ENSMUST00000126992] [ENSMUST00000142071] [ENSMUST00000146288] [ENSMUST00000146297] [ENSMUST00000153514] [ENSMUST00000155837]

AlphaFold

Q8VH51

Predicted Effect

probably damaging
Transcript: ENSMUST00000029149
AA Change: R124C

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620
AA Change: R124C

Domain	Start	End	E-Value	Type
low complexity region	28	90	N/A	INTRINSIC
low complexity region	117	136	N/A	INTRINSIC
RRM	154	226	2.5e-15	SMART
RRM	251	324	1.39e-31	SMART
low complexity region	332	345	N/A	INTRINSIC
low complexity region	369	380	N/A	INTRINSIC
low complexity region	397	416	N/A	INTRINSIC
RRM	419	498	9.44e-2	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000109587
AA Change: R124C

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: R124C

Domain	Start	End	E-Value	Type
low complexity region	28	90	N/A	INTRINSIC
low complexity region	117	136	N/A	INTRINSIC
RRM	154	226	2.5e-15	SMART
RRM	251	324	1.39e-31	SMART
low complexity region	332	345	N/A	INTRINSIC
low complexity region	369	380	N/A	INTRINSIC
low complexity region	403	422	N/A	INTRINSIC
RRM	425	504	9.44e-2	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000126992
AA Change: R123C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000116950
Gene: ENSMUSG00000027620
AA Change: R123C

Domain	Start	End	E-Value	Type
low complexity region	28	90	N/A	INTRINSIC
low complexity region	117	135	N/A	INTRINSIC
RRM	153	225	2.5e-15	SMART
PDB:2JRS\|A	239	273	9e-18	PDB
Blast:RRM	250	273	4e-9	BLAST
SCOP:d1l3ka1	250	273	9e-5	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000142071
AA Change: R124C

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620
AA Change: R124C

Domain	Start	End	E-Value	Type
low complexity region	28	90	N/A	INTRINSIC
low complexity region	117	136	N/A	INTRINSIC
RRM	154	226	2.5e-15	SMART
RRM	251	324	1.39e-31	SMART
Pfam:RBM39linker	339	404	3.8e-18	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000146288
AA Change: R102C

SMART Domains

Protein: ENSMUSP00000114824
Gene: ENSMUSG00000027620
AA Change: R102C

Domain	Start	End	E-Value	Type
low complexity region	27	114	N/A	INTRINSIC
PDB:2CQ4\|A	115	156	2e-21	PDB
Blast:RRM	132	156	1e-9	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000146297
AA Change: R124C

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620
AA Change: R124C

Domain	Start	End	E-Value	Type
low complexity region	28	90	N/A	INTRINSIC
low complexity region	117	136	N/A	INTRINSIC
RRM	154	226	2.5e-15	SMART
RRM	251	324	1.39e-31	SMART
low complexity region	332	345	N/A	INTRINSIC
low complexity region	369	380	N/A	INTRINSIC
low complexity region	397	416	N/A	INTRINSIC
RRM	419	498	9.44e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000148794

SMART Domains

Protein: ENSMUSP00000117462
Gene: ENSMUSG00000027620

Domain	Start	End	E-Value	Type
RRM	16	88	2.5e-15	SMART
RRM	113	164	2.45e-9	SMART
Pfam:RBM39linker	181	282	6.9e-31	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153514

Predicted Effect

probably benign
Transcript: ENSMUST00000155837

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.2%
20x: 97.2%

Validation Efficiency

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 U2AF65 family of proteins. The encoded protein is found in the nucleus, where it co-localizes with core spliceosomal proteins. It has been shown to play a role in both steroid hormone receptor-mediated transcription and alternative splicing, and it is also a transcriptional coregulator of the viral oncoprotein v-Rel. Multiple transcript variants have been observed for this gene. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Aug 2011]
PHENOTYPE: Homozygous disruption of this locus results in embryonic lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017D01Rik	A	G	19: 11,112,314		probably null	Het
2410089E03Rik	T	C	15: 8,187,548	V750A	probably benign	Het
Acadsb	T	C	7: 131,434,315	Y285H	possibly damaging	Het
Adam17	A	G	12: 21,345,668	S285P	probably benign	Het
Adcy10	A	G	1: 165,556,916	N1082S	probably benign	Het
Ahdc1	T	A	4: 133,062,345	L299Q	possibly damaging	Het
Ambra1	T	A	2: 91,772,600		probably benign	Het
Arfgef1	T	C	1: 10,153,678	Q1465R	probably damaging	Het
Arfgef1	G	T	1: 10,153,679	Q1465K	probably damaging	Het
Atp8a1	A	G	5: 67,738,462	V543A	probably damaging	Het
BC034090	T	A	1: 155,241,439	D311V	probably damaging	Het
Blnk	G	T	19: 40,962,377	P110Q	probably damaging	Het
Cc2d2a	A	G	5: 43,718,585	E968G	probably damaging	Het
Ccdc14	A	T	16: 34,709,533	E394V	probably damaging	Het
Ccdc162	A	T	10: 41,615,958	H1086Q	probably benign	Het
Ccdc85b	T	A	19: 5,457,220	I60F	probably damaging	Het
Ceacam20	T	A	7: 19,989,977	L562Q	probably damaging	Het
Cntrl	T	C	2: 35,118,137	F188L	probably benign	Het
Dclk1	A	T	3: 55,466,601		probably benign	Het
Ddx20	A	T	3: 105,680,358	L434H	probably damaging	Het
Ddx51	G	A	5: 110,656,862	V547M	probably damaging	Het
Dnah11	T	A	12: 118,108,944	Q1472L	probably benign	Het
Dnajb13	T	C	7: 100,507,422	E149G	probably damaging	Het
Fat4	A	G	3: 38,981,775	N3192S	probably damaging	Het
Fat4	A	T	3: 38,995,971	D3994V	probably damaging	Het
Fcgr1	C	A	3: 96,284,620		probably null	Het
Gm11639	A	G	11: 104,776,356	E1422G	probably benign	Het
Gm12185	G	A	11: 48,907,912	R585*	probably null	Het
Gm32687	A	G	10: 81,879,470	H232R	probably benign	Het
Gm5431	G	T	11: 48,888,490	A535D	probably damaging	Het
Gm8300	G	T	12: 87,516,618		probably benign	Het
Gm906	A	T	13: 50,246,971	Y440N	possibly damaging	Het
Jarid2	C	T	13: 44,902,985	P556S	probably damaging	Het
Map3k4	C	A	17: 12,248,916	G1077V	probably damaging	Het
Mast4	C	T	13: 102,804,647	V301I	probably damaging	Het
Mlxip	A	G	5: 123,445,672	T433A	possibly damaging	Het
Mus81	G	T	19: 5,485,526	H199Q	probably benign	Het
Mylk3	G	A	8: 85,359,263	T54M	probably damaging	Het
Nalcn	A	G	14: 123,314,094	F1034L	possibly damaging	Het
Nfatc1	A	C	18: 80,667,013	S513A	probably benign	Het
Ninj2	A	G	6: 120,198,131	I88V	possibly damaging	Het
Nomo1	C	T	7: 46,045,967	P277L	probably damaging	Het
Nup214	C	T	2: 32,051,798	S571L	probably damaging	Het
Olfr1469	T	A	19: 13,411,428	N286K	probably damaging	Het
Olfr461	T	C	6: 40,544,656	S108G	probably benign	Het
Olfr980	T	A	9: 40,006,713	M79L	probably benign	Het
Pcdh15	C	T	10: 74,502,687	P1005S	probably damaging	Het
Pkhd1l1	G	A	15: 44,511,674	A942T	possibly damaging	Het
Plagl1	T	C	10: 13,125,116	C34R	probably damaging	Het
Plekha2	T	C	8: 25,059,264	Q168R	probably benign	Het
Plekha6	G	A	1: 133,263,818	A146T	probably benign	Het
Plekhm3	T	G	1: 64,892,753	K564T	possibly damaging	Het
Plpp2	A	G	10: 79,530,546	V26A	possibly damaging	Het
Prdm10	T	G	9: 31,329,823	Y302*	probably null	Het
Prdm8	A	G	5: 98,184,612	E124G	probably damaging	Het
Prg4	T	G	1: 150,455,906		probably benign	Het
Qser1	A	G	2: 104,788,130	V779A	probably benign	Het
Ric1	C	T	19: 29,587,772	P640S	probably damaging	Het
Rpl14	G	A	9: 120,574,227		probably benign	Het
Rsl1d1	T	A	16: 11,193,694	D382V	probably benign	Het
Rubcn	G	T	16: 32,868,144		probably benign	Het
Sec16a	G	A	2: 26,430,486	R1361C	probably damaging	Het
Slc26a11	T	G	11: 119,356,972	V41G	probably damaging	Het
Slc41a2	A	G	10: 83,316,096	F172L	possibly damaging	Het
Slc4a4	A	C	5: 89,179,831	Y674S	probably damaging	Het
Strc	A	C	2: 121,378,014	M292R	probably benign	Het
Syde2	A	G	3: 145,988,626	T210A	probably benign	Het
Tcf7l2	C	A	19: 55,755,048	A97E	probably benign	Het
Tenm3	C	T	8: 48,236,439	D2038N	probably damaging	Het
Tepsin	G	A	11: 120,095,364	T168M	probably damaging	Het
Tex15	A	T	8: 33,557,428	M178L	probably benign	Het
Tgfbr2	T	C	9: 116,110,051	N236S	probably damaging	Het
Tnrc18	A	G	5: 142,727,989	V2531A	probably damaging	Het
Ttn	T	G	2: 76,895,423		probably benign	Het
Tubgcp3	G	T	8: 12,637,000	D630E	probably damaging	Het
Ubr4	G	A	4: 139,406,528	W745*	probably null	Het
Vmn2r115	G	A	17: 23,346,015	G292D	probably benign	Het
Vmn2r38	T	A	7: 9,075,341	K681*	probably null	Het
Xrcc6	A	G	15: 82,031,174	K98E	probably benign	Het
Zfp423	A	G	8: 87,803,779	V13A	probably benign	Het
Zfp512b	A	G	2: 181,586,348	I5T	possibly damaging	Het
Zmynd8	C	T	2: 165,875,750	E14K	probably damaging	Het

Other mutations in Rbm39

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00656:Rbm39	APN	2	156162871	missense	probably damaging	1.00
IGL01473:Rbm39	APN	2	156172979	nonsense	probably null
R0040:Rbm39	UTSW	2	156148179	missense	possibly damaging	0.90
R1564:Rbm39	UTSW	2	156154257	missense	probably benign	0.01
R2888:Rbm39	UTSW	2	156167583	missense	probably benign	0.01
R4872:Rbm39	UTSW	2	156177346	missense	possibly damaging	0.94
R5124:Rbm39	UTSW	2	156159162	missense	probably damaging	0.99
R5125:Rbm39	UTSW	2	156162865	missense	probably damaging	0.99
R5843:Rbm39	UTSW	2	156162873	missense	possibly damaging	0.84
R6714:Rbm39	UTSW	2	156161618	missense	possibly damaging	0.82
R6820:Rbm39	UTSW	2	156179226	start codon destroyed	probably null	0.66
R8178:Rbm39	UTSW	2	156154275	missense	probably benign	0.00
R8701:Rbm39	UTSW	2	156161587	missense	probably damaging	1.00
R8909:Rbm39	UTSW	2	156177777	intron	probably benign
R8947:Rbm39	UTSW	2	156148356	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGTTGGAAGCTTACTGAGGC -3'
(R):5'- TGAACTTGATCTTAGCAACACACCC -3'

Sequencing Primer
(F):5'- CCAGATGGTCTACAGAGTGAGTTCC -3'
(R):5'- GGATTGCCTCATAGCATCAA -3'

Posted On

2018-11-28