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

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

MMRRC Submission

068555-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8701 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

155989159-156022158 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 156003507 bp (GRCm39)

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
Abcc4	T	C	14: 118,836,785 (GRCm39)	I659V	probably benign	Het
Adamtsl4	T	A	3: 95,592,276 (GRCm39)	D24V	possibly damaging	Het
Agtr1b	A	T	3: 20,370,256 (GRCm39)	F117I	probably damaging	Het
Aldh3b2	A	G	19: 4,028,448 (GRCm39)	E116G	probably damaging	Het
Alox5	T	A	6: 116,390,787 (GRCm39)	I455F	possibly damaging	Het
Arnt	C	T	3: 95,401,076 (GRCm39)	S675F	possibly damaging	Het
Camkv	A	G	9: 107,825,240 (GRCm39)	T414A	possibly damaging	Het
Ccn5	G	T	2: 163,670,786 (GRCm39)	G98W	probably damaging	Het
Cd209c	C	T	8: 3,995,892 (GRCm39)	R6H	probably benign	Het
Cip2a	T	A	16: 48,827,504 (GRCm39)	Y456*	probably null	Het
Cnr1	A	G	4: 33,944,739 (GRCm39)	I376V	probably benign	Het
Cyp2j12	T	A	4: 96,009,810 (GRCm39)	K183M	possibly damaging	Het
Dact3	G	T	7: 16,619,201 (GRCm39)	R232L	probably damaging	Het
Dlg5	G	A	14: 24,226,768 (GRCm39)	T378M	probably benign	Het
Dnah10	T	A	5: 124,803,911 (GRCm39)	D79E	probably benign	Het
Dsc1	A	T	18: 20,240,739 (GRCm39)	Y195*	probably null	Het
Elovl1	A	T	4: 118,287,707 (GRCm39)	M1L	probably benign	Het
Fam107a	A	G	14: 8,298,755 (GRCm38)	F124L	probably damaging	Het
Fam219a	A	G	4: 41,520,283 (GRCm39)	M155T	probably damaging	Het
Gm28308	C	G	6: 52,140,430 (GRCm39)		probably benign	Het
Gpr153	C	T	4: 152,363,558 (GRCm39)		probably benign	Het
Gtf2ird2	T	A	5: 134,245,077 (GRCm39)	I445N	probably damaging	Het
Gzmb	A	T	14: 56,497,817 (GRCm39)	V141E	probably benign	Het
Hmcn1	A	T	1: 150,631,008 (GRCm39)	M930K	probably benign	Het
Hunk	T	A	16: 90,183,498 (GRCm39)	F52Y	probably damaging	Het
Il18rap	A	G	1: 40,578,501 (GRCm39)	E304G	probably benign	Het
Klk14	A	G	7: 43,343,566 (GRCm39)	S133G	possibly damaging	Het
Man2b1	T	C	8: 85,821,782 (GRCm39)	S695P	probably damaging	Het
Mccc1	A	T	3: 36,049,933 (GRCm39)	D86E	probably benign	Het
Mcu	T	A	10: 59,303,475 (GRCm39)	I121F	probably damaging	Het
Mlxipl	T	C	5: 135,136,045 (GRCm39)	F90S	possibly damaging	Het
Muc2	A	G	7: 141,281,850 (GRCm39)	D536G	probably damaging	Het
Naa11	T	C	5: 97,539,817 (GRCm39)	S114G	possibly damaging	Het
Ncaph	T	C	2: 126,948,058 (GRCm39)	K676E	probably benign	Het
Neurl2	C	T	2: 164,675,054 (GRCm39)	D103N	probably benign	Het
Nup210l	T	C	3: 90,030,121 (GRCm39)	M278T	probably benign	Het
Or10g6	A	G	9: 39,933,815 (GRCm39)	N42S	probably damaging	Het
Or4p4	A	G	2: 88,482,831 (GRCm39)	I112V	possibly damaging	Het
Or51r1	A	T	7: 102,227,899 (GRCm39)	M66L	possibly damaging	Het
Or8c19-ps1	A	T	9: 38,220,734 (GRCm39)	L214F	unknown	Het
Or8g4	A	T	9: 39,662,210 (GRCm39)	H176L	probably damaging	Het
Pcdh20	A	T	14: 88,705,849 (GRCm39)	Y484N	possibly damaging	Het
Pkhd1l1	A	G	15: 44,438,079 (GRCm39)	Y3598C	probably damaging	Het
Plcg2	T	A	8: 118,308,416 (GRCm39)	L336Q	probably damaging	Het
Ppp1r8	T	C	4: 132,557,953 (GRCm39)	D207G	possibly damaging	Het
Prdm13	C	T	4: 21,678,615 (GRCm39)	C625Y	probably damaging	Het
Ptcd3	T	C	6: 71,862,495 (GRCm39)	D480G	possibly damaging	Het
Repin1	G	T	6: 48,574,279 (GRCm39)	E403*	probably null	Het
Rnf220	T	C	4: 117,347,190 (GRCm39)	H74R	probably damaging	Het
Sp6	A	T	11: 96,913,090 (GRCm39)	T268S	probably damaging	Het
Spata31e2	A	T	1: 26,724,526 (GRCm39)	V218D	probably benign	Het
Sphk2	A	T	7: 45,360,249 (GRCm39)	V585E	probably damaging	Het
Syne1	G	A	10: 5,155,026 (GRCm39)	Q5638*	probably null	Het
Tas1r3	C	T	4: 155,945,503 (GRCm39)	V573I	probably benign	Het
Tdrd1	T	C	19: 56,839,916 (GRCm39)	S659P	possibly damaging	Het
Tead4	T	A	6: 128,219,529 (GRCm39)	K237N	probably damaging	Het
Tex24	T	A	8: 27,835,152 (GRCm39)	C227S	probably benign	Het
Tom1	A	T	8: 75,778,796 (GRCm39)	T174S	probably benign	Het
Tpm3	C	T	3: 89,994,987 (GRCm39)	R168C	possibly damaging	Het
Trpv3	A	G	11: 73,169,762 (GRCm39)	E111G	possibly damaging	Het
Unc80	A	G	1: 66,677,191 (GRCm39)	D2040G	possibly damaging	Het
Usp47	A	G	7: 111,692,402 (GRCm39)	T955A	probably damaging	Het
Vmn2r11	G	A	5: 109,195,556 (GRCm39)	A590V	probably damaging	Het
Zfp112	A	G	7: 23,825,165 (GRCm39)	R382G	probably damaging	Het
Zfp606	T	A	7: 12,215,025 (GRCm39)	D84E	unknown	Het

Other mutations in Rbm39

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00656:Rbm39	APN	2	156,004,791 (GRCm39)	missense	probably damaging	1.00
IGL01473:Rbm39	APN	2	156,014,899 (GRCm39)	nonsense	probably null
R0040:Rbm39	UTSW	2	155,990,099 (GRCm39)	missense	possibly damaging	0.90
R1564:Rbm39	UTSW	2	155,996,177 (GRCm39)	missense	probably benign	0.01
R2888:Rbm39	UTSW	2	156,009,503 (GRCm39)	missense	probably benign	0.01
R4872:Rbm39	UTSW	2	156,019,266 (GRCm39)	missense	possibly damaging	0.94
R5124:Rbm39	UTSW	2	156,001,082 (GRCm39)	missense	probably damaging	0.99
R5125:Rbm39	UTSW	2	156,004,785 (GRCm39)	missense	probably damaging	0.99
R5843:Rbm39	UTSW	2	156,004,793 (GRCm39)	missense	possibly damaging	0.84
R6714:Rbm39	UTSW	2	156,003,538 (GRCm39)	missense	possibly damaging	0.82
R6820:Rbm39	UTSW	2	156,021,146 (GRCm39)	start codon destroyed	probably null	0.66
R6970:Rbm39	UTSW	2	156,009,504 (GRCm39)	missense	probably damaging	1.00
R8178:Rbm39	UTSW	2	155,996,195 (GRCm39)	missense	probably benign	0.00
R8909:Rbm39	UTSW	2	156,019,697 (GRCm39)	intron	probably benign
R8947:Rbm39	UTSW	2	155,990,276 (GRCm39)	missense	probably damaging	1.00
R9619:Rbm39	UTSW	2	156,001,117 (GRCm39)	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