Mutagenetix > Incidental Mutation

Incidental Mutation 'R1564:Rbm39'

175085

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

039603-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1564 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

155989159-156022158 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 155996177 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Isoleucine at position 403 (L403I)

Ref Sequence

ENSEMBL: ENSMUSP00000105216 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029149] [ENSMUST00000109587] [ENSMUST00000142071] [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 benign
Transcript: ENSMUST00000029149
AA Change: L397I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620
AA Change: L397I

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: ENSMUST00000109587
AA Change: L403I

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: L403I

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: ENSMUST00000142071
AA Change: L397I

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620
AA Change: L397I

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: ENSMUST00000146297
AA Change: L397I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620
AA Change: L397I

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

unknown
Transcript: ENSMUST00000148794
AA Change: L242I

SMART Domains

Protein: ENSMUSP00000117462
Gene: ENSMUSG00000027620
AA Change: L242I

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: 99.0%
3x: 98.1%
10x: 95.7%
20x: 91.0%

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
Abca13	C	T	11: 9,384,316 (GRCm39)	Q3923*	probably null	Het
Abcc12	T	A	8: 87,244,115 (GRCm39)	T1013S	probably benign	Het
Acad9	T	C	3: 36,143,578 (GRCm39)	I558T	possibly damaging	Het
Agbl4	C	A	4: 110,812,761 (GRCm39)		probably null	Het
Akr1b1	C	T	6: 34,283,470 (GRCm39)		probably null	Het
Aktip	A	G	8: 91,857,709 (GRCm39)	M1T	probably null	Het
Apc	G	T	18: 34,448,202 (GRCm39)	Q1665H	probably benign	Het
Arfgef3	T	C	10: 18,467,452 (GRCm39)	D1916G	probably damaging	Het
Arhgef11	T	C	3: 87,609,817 (GRCm39)	V365A	probably benign	Het
Bank1	C	A	3: 135,919,602 (GRCm39)	E265*	probably null	Het
Bbs7	A	T	3: 36,629,944 (GRCm39)	D578E	probably damaging	Het
Bin3	T	C	14: 70,372,218 (GRCm39)	F172L	probably damaging	Het
Bves	A	G	10: 45,245,377 (GRCm39)	D350G	probably benign	Het
Cacna1h	A	T	17: 25,596,835 (GRCm39)	C80*	probably null	Het
Cacna2d4	T	C	6: 119,218,156 (GRCm39)	F164L	possibly damaging	Het
Cenpj	T	C	14: 56,789,523 (GRCm39)	D842G	probably benign	Het
Col12a1	C	A	9: 79,521,122 (GRCm39)	R2781L	probably damaging	Het
Cyp2c68	A	T	19: 39,724,024 (GRCm39)	C213*	probably null	Het
Defb33	T	A	8: 21,387,597 (GRCm39)	C45S	possibly damaging	Het
Dolk	A	T	2: 30,175,633 (GRCm39)	N137K	probably damaging	Het
Fam171b	G	A	2: 83,710,628 (GRCm39)	E767K	probably damaging	Het
Fbxl20	A	T	11: 97,989,312 (GRCm39)	D189E	probably damaging	Het
Gm10643	A	T	8: 84,791,111 (GRCm39)	M1K	probably null	Het
Gm572	T	G	4: 148,735,643 (GRCm39)	I24S	possibly damaging	Het
Gnpda1	A	G	18: 38,471,142 (GRCm39)		probably null	Het
Gpr141b	T	C	13: 19,913,470 (GRCm39)		noncoding transcript	Het
Helz2	G	T	2: 180,875,021 (GRCm39)	N1824K	probably benign	Het
Insl3	G	T	8: 72,142,935 (GRCm39)	A99S	possibly damaging	Het
Lpin2	G	A	17: 71,532,055 (GRCm39)	V137I	probably benign	Het
Lrrc9	A	G	12: 72,533,827 (GRCm39)	E1032G	probably damaging	Het
Macf1	T	C	4: 123,353,150 (GRCm39)	T1510A	probably benign	Het
Mnd1	T	C	3: 84,023,738 (GRCm39)	E116G	probably benign	Het
Mycbp2	A	G	14: 103,407,287 (GRCm39)		probably null	Het
Myoz3	G	A	18: 60,713,914 (GRCm39)	S23L	probably benign	Het
Napsa	G	T	7: 44,236,073 (GRCm39)	V371F	probably damaging	Het
Nefh	T	C	11: 4,889,878 (GRCm39)	T914A	unknown	Het
Neurod2	A	T	11: 98,218,250 (GRCm39)	C305S	probably damaging	Het
Nmnat3	T	C	9: 98,236,219 (GRCm39)		probably null	Het
Nuf2	A	G	1: 169,326,362 (GRCm39)	V463A	unknown	Het
Olfml1	A	T	7: 107,170,346 (GRCm39)	T78S	possibly damaging	Het
Opcml	G	A	9: 28,814,612 (GRCm39)	C288Y	probably damaging	Het
Oprl1	T	C	2: 181,360,733 (GRCm39)	I222T	possibly damaging	Het
Or13a28	G	A	7: 140,217,967 (GRCm39)	V118I	probably benign	Het
Or4c104	A	T	2: 88,587,000 (GRCm39)	N6K	possibly damaging	Het
Or4c122	G	T	2: 89,080,016 (GRCm39)	N7K	probably benign	Het
Or6c210	T	C	10: 129,495,884 (GRCm39)	F70L	probably benign	Het
Pcsk5	A	G	19: 17,632,120 (GRCm39)	Y349H	probably damaging	Het
Pla2g4d	C	A	2: 120,099,384 (GRCm39)	R706L	possibly damaging	Het
Pmm1	A	G	15: 81,840,401 (GRCm39)	Y55H	probably damaging	Het
Polb	A	G	8: 23,120,357 (GRCm39)		probably null	Het
Pom121l2	T	C	13: 22,167,523 (GRCm39)	I598T	possibly damaging	Het
Pxmp2	C	T	5: 110,429,062 (GRCm39)		probably null	Het
Rec8	T	C	14: 55,859,732 (GRCm39)		probably null	Het
Reck	T	C	4: 43,912,061 (GRCm39)	I190T	probably benign	Het
Rer1	A	T	4: 155,160,050 (GRCm39)	I166N	probably damaging	Het
Rgs17	T	A	10: 5,792,567 (GRCm39)	K60*	probably null	Het
Ripor2	C	T	13: 24,859,768 (GRCm39)	T152M	probably damaging	Het
Scgb1b2	A	T	7: 30,991,200 (GRCm39)		probably benign	Het
Scn3a	C	A	2: 65,344,979 (GRCm39)	R503M	probably damaging	Het
Scn4a	C	A	11: 106,236,367 (GRCm39)	D298Y	probably benign	Het
Scn9a	A	G	2: 66,314,648 (GRCm39)	F1679S	probably damaging	Het
Scyl3	G	T	1: 163,767,553 (GRCm39)		probably null	Het
Sec23ip	A	G	7: 128,368,005 (GRCm39)		probably null	Het
She	C	T	3: 89,756,921 (GRCm39)	A325V	possibly damaging	Het
Skint2	T	G	4: 112,483,195 (GRCm39)	M200R	probably damaging	Het
Slc17a5	A	T	9: 78,485,981 (GRCm39)	C35S	probably damaging	Het
Slc25a24	T	A	3: 109,070,819 (GRCm39)	S393T	probably damaging	Het
Slc6a19	C	T	13: 73,834,243 (GRCm39)	V320M	probably damaging	Het
Snap91	T	C	9: 86,674,249 (GRCm39)	D579G	possibly damaging	Het
Spats2l	C	T	1: 57,985,383 (GRCm39)	R479C	probably damaging	Het
Syngr3	G	C	17: 24,905,642 (GRCm39)		probably null	Het
Tas2r107	A	C	6: 131,636,785 (GRCm39)	I88R	probably damaging	Het
Them7	A	T	2: 105,128,259 (GRCm39)	N80I	probably damaging	Het
Tmprss7	C	T	16: 45,482,516 (GRCm39)		probably null	Het
Tnrc6b	A	G	15: 80,764,369 (GRCm39)	N624D	possibly damaging	Het
Trpm2	T	G	10: 77,778,833 (GRCm39)	I378L	probably benign	Het
Ttn	C	A	2: 76,554,876 (GRCm39)	W30676L	probably damaging	Het
Ttn	A	G	2: 76,774,384 (GRCm39)	V2220A	unknown	Het
Uba6	T	C	5: 86,302,266 (GRCm39)	T134A	probably benign	Het
Vmn2r55	A	G	7: 12,418,678 (GRCm39)	S81P	probably damaging	Het
Zfp616	T	A	11: 73,975,548 (GRCm39)	S606T	probably damaging	Het
Zfp653	C	A	9: 21,967,155 (GRCm39)	A577S	probably damaging	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
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
R8701:Rbm39	UTSW	2	156,003,507 (GRCm39)	missense	probably damaging	1.00
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'- GCCCACACTGTGATGTTTTAAGTCTGG -3'
(R):5'- ACGAAAGGTCCCAAAGCCTTGTAAATG -3'

Sequencing Primer
(F):5'- CTTTTTGAAGTGTCAAGGACAGC -3'
(R):5'- CCCAAAGCCTTGTAAATGAGGAATG -3'

Posted On

2014-04-24