Mutagenetix > Incidental Mutation

Incidental Mutation 'R8701:Rbm39'

669037

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

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8701 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

156147239-156180238 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 156161587 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Methionine at position 291 (K291M)

Ref Sequence

ENSEMBL: ENSMUSP00000105216 (fasta)

Gene Model

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

AlphaFold

Q8VH51

PDB Structure

NMR structure of the RNA binding motif 39 (RBM39) from Mus musculus [SOLUTION NMR]
Crystal structure of a RNA binding motif protein 39 (RBM39) from Mus musculuS at 0.95 A resolution [X-RAY DIFFRACTION]
Room temperature crystal structure of a RNA binding motif protein 39 (Rbm39) from Mus musculus at 1.11 A resolution [X-RAY DIFFRACTION]
Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000029149
AA Change: K291M

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

SMART Domains

Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620
AA Change: K291M

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: K291M

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

SMART Domains

Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: K291M

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 benign
Transcript: ENSMUST00000126992

SMART Domains

Protein: ENSMUSP00000116950
Gene: ENSMUSG00000027620

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: K291M

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

SMART Domains

Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620
AA Change: K291M

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

probably benign
Transcript: ENSMUST00000146288

SMART Domains

Protein: ENSMUSP00000114824
Gene: ENSMUSG00000027620

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: K291M

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

SMART Domains

Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620
AA Change: K291M

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: 99.7%
20x: 98.8%

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931408C20Rik	A	T	1: 26,685,445	V218D	probably benign	Het
Abcc4	T	C	14: 118,599,373	I659V	probably benign	Het
Adamtsl4	T	A	3: 95,684,966	D24V	possibly damaging	Het
Agtr1b	A	T	3: 20,316,092	F117I	probably damaging	Het
Aldh3b2	A	G	19: 3,978,448	E116G	probably damaging	Het
Alox5	T	A	6: 116,413,826	I455F	possibly damaging	Het
Arnt	C	T	3: 95,493,765	S675F	possibly damaging	Het
C330027C09Rik	T	A	16: 49,007,141	Y456*	probably null	Het
Camkv	A	G	9: 107,948,041	T414A	possibly damaging	Het
Cd209c	C	T	8: 3,945,892	R6H	probably benign	Het
Cnr1	A	G	4: 33,944,739	I376V	probably benign	Het
Cyp2j12	T	A	4: 96,121,573	K183M	possibly damaging	Het
Dact3	G	T	7: 16,885,276	R232L	probably damaging	Het
Dlg5	G	A	14: 24,176,700	T378M	probably benign	Het
Dnah10	T	A	5: 124,726,847	D79E	probably benign	Het
Dsc1	A	T	18: 20,107,682	Y195*	probably null	Het
Elovl1	A	T	4: 118,430,510	M1L	probably benign	Het
Fam107a	A	G	14: 8,298,755	F124L	probably damaging	Het
Fam219a	A	G	4: 41,520,283	M155T	probably damaging	Het
Gm28308	C	G	6: 52,163,450		probably benign	Het
Gpr153	C	T	4: 152,279,101		probably benign	Het
Gtf2ird2	T	A	5: 134,216,235	I445N	probably damaging	Het
Gzmb	A	T	14: 56,260,360	V141E	probably benign	Het
Hmcn1	A	T	1: 150,755,257	M930K	probably benign	Het
Hunk	T	A	16: 90,386,610	F52Y	probably damaging	Het
Il18rap	A	G	1: 40,539,341	E304G	probably benign	Het
Klk14	A	G	7: 43,694,142	S133G	possibly damaging	Het
Man2b1	T	C	8: 85,095,153	S695P	probably damaging	Het
Mccc1	A	T	3: 35,995,784	D86E	probably benign	Het
Mcu	T	A	10: 59,467,653	I121F	probably damaging	Het
Mlxipl	T	C	5: 135,107,191	F90S	possibly damaging	Het
Muc2	A	G	7: 141,695,607	D536G	probably damaging	Het
Naa11	T	C	5: 97,391,958	S114G	possibly damaging	Het
Ncaph	T	C	2: 127,106,138	K676E	probably benign	Het
Neurl2	C	T	2: 164,833,134	D103N	probably benign	Het
Nup210l	T	C	3: 90,122,814	M278T	probably benign	Het
Olfr1192-ps1	A	G	2: 88,652,487	I112V	possibly damaging	Het
Olfr550	A	T	7: 102,578,692	M66L	possibly damaging	Het
Olfr897-ps1	A	T	9: 38,309,438	L214F	unknown	Het
Olfr967	A	T	9: 39,750,914	H176L	probably damaging	Het
Olfr981	A	G	9: 40,022,519	N42S	probably damaging	Het
Pcdh20	A	T	14: 88,468,413	Y484N	possibly damaging	Het
Pkhd1l1	A	G	15: 44,574,683	Y3598C	probably damaging	Het
Plcg2	T	A	8: 117,581,677	L336Q	probably damaging	Het
Ppp1r8	T	C	4: 132,830,642	D207G	possibly damaging	Het
Prdm13	C	T	4: 21,678,615	C625Y	probably damaging	Het
Ptcd3	T	C	6: 71,885,511	D480G	possibly damaging	Het
Repin1	G	T	6: 48,597,345	E403*	probably null	Het
Rnf220	T	C	4: 117,489,993	H74R	probably damaging	Het
Sp6	A	T	11: 97,022,264	T268S	probably damaging	Het
Sphk2	A	T	7: 45,710,825	V585E	probably damaging	Het
Syne1	G	A	10: 5,205,026	Q5638*	probably null	Het
Tas1r3	C	T	4: 155,861,046	V573I	probably benign	Het
Tdrd1	T	C	19: 56,851,484	S659P	possibly damaging	Het
Tead4	T	A	6: 128,242,566	K237N	probably damaging	Het
Tex24	T	A	8: 27,345,124	C227S	probably benign	Het
Tom1	A	T	8: 75,052,168	T174S	probably benign	Het
Tpm3	C	T	3: 90,087,680	R168C	possibly damaging	Het
Trpv3	A	G	11: 73,278,936	E111G	possibly damaging	Het
Unc80	A	G	1: 66,638,032	D2040G	possibly damaging	Het
Usp47	A	G	7: 112,093,195	T955A	probably damaging	Het
Vmn2r11	G	A	5: 109,047,690	A590V	probably damaging	Het
Wisp2	G	T	2: 163,828,866	G98W	probably damaging	Het
Zfp112	A	G	7: 24,125,740	R382G	probably damaging	Het
Zfp606	T	A	7: 12,481,098	D84E	unknown	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
R6970:Rbm39	UTSW	2	156167584	missense	probably damaging	1.00
R8178:Rbm39	UTSW	2	156154275	missense	probably benign	0.00
R8909:Rbm39	UTSW	2	156177777	intron	probably benign
R8947:Rbm39	UTSW	2	156148356	missense	probably damaging	1.00
R9619:Rbm39	UTSW	2	156159197	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCCAGGCAGATGTGACAAAGTTAG -3'
(R):5'- TCCAATCAGGGGAATTGGGG -3'

Sequencing Primer
(F):5'- GTTAGACTATATGAATACCAGCA -3'
(R):5'- GGAATTGGGGGTTTATATGTAAAGC -3'

Posted On

2021-04-30