Mutagenetix > Incidental Mutation

Incidental Mutation 'R0040:Rbm39'

64653

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

038334-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0040 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

155989159-156022158 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 155990099 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 496 (T496I)

Ref Sequence

ENSEMBL: ENSMUSP00000119298 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029147] [ENSMUST00000029149] [ENSMUST00000088610] [ENSMUST00000109587] [ENSMUST00000109597] [ENSMUST00000109598] [ENSMUST00000109600] [ENSMUST00000146297] [ENSMUST00000155837] [ENSMUST00000142071] [ENSMUST00000119950] [ENSMUST00000153514]

AlphaFold

Q8VH51

Predicted Effect

probably benign
Transcript: ENSMUST00000029147

SMART Domains

Protein: ENSMUSP00000029147
Gene: ENSMUSG00000027618

Domain	Start	End	E-Value	Type
low complexity region	10	31	N/A	INTRINSIC
Pfam:Aminotran_5	61	424	6.2e-94	PFAM
Pfam:Beta_elim_lyase	94	344	7.8e-12	PFAM
Pfam:DegT_DnrJ_EryC1	100	250	1.8e-6	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029149
AA Change: T496I

PolyPhen 2 Score 0.898 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620
AA Change: T496I

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: ENSMUST00000088610

SMART Domains

Protein: ENSMUSP00000085981
Gene: ENSMUSG00000067847

Domain	Start	End	E-Value	Type
Pfam:Romo1	13	79	2e-30	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000109587
AA Change: T502I

PolyPhen 2 Score 0.785 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: T502I

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: ENSMUST00000109597

SMART Domains

Protein: ENSMUSP00000105226
Gene: ENSMUSG00000067847

Domain	Start	End	E-Value	Type
Pfam:Romo1	13	79	2e-30	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000109598

SMART Domains

Protein: ENSMUSP00000105227
Gene: ENSMUSG00000067847

Domain	Start	End	E-Value	Type
Romo1	13	79	1.34e-31	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000109600

SMART Domains

Protein: ENSMUSP00000105229
Gene: ENSMUSG00000027618

Domain	Start	End	E-Value	Type
low complexity region	10	31	N/A	INTRINSIC
Pfam:Aminotran_5	61	118	3.5e-12	PFAM
low complexity region	138	147	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000146297
AA Change: T496I

PolyPhen 2 Score 0.898 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620
AA Change: T496I

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

noncoding transcript
Transcript: ENSMUST00000125449

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: ENSMUST00000155837

Predicted Effect

probably benign
Transcript: ENSMUST00000142071

SMART Domains

Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620

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: ENSMUST00000119950

SMART Domains

Protein: ENSMUSP00000113943
Gene: ENSMUSG00000067847

Domain	Start	End	E-Value	Type
Pfam:Romo1	13	79	2e-30	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153514

Meta Mutation Damage Score

0.2278

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.0%
20x: 93.6%

Validation Efficiency

100% (88/88)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ahrr	G	A	13: 74,431,143 (GRCm39)		probably benign	Het
Antxr2	G	A	5: 98,086,284 (GRCm39)	T441I	possibly damaging	Het
Apcs	A	G	1: 172,722,023 (GRCm39)	Y108H	probably benign	Het
Atad5	A	G	11: 79,988,840 (GRCm39)	T666A	probably benign	Het
Atcay	C	T	10: 81,046,353 (GRCm39)		probably null	Het
Bahcc1	A	G	11: 120,159,196 (GRCm39)	D141G	probably damaging	Het
Ceacam10	A	G	7: 24,477,689 (GRCm39)	Y68C	probably damaging	Het
Cfap54	T	A	10: 92,812,901 (GRCm39)	Q1344L	probably benign	Het
Cyb5r4	A	G	9: 86,948,795 (GRCm39)		probably null	Het
Cyp2b9	G	T	7: 25,872,899 (GRCm39)	S14I	possibly damaging	Het
Dusp12	A	G	1: 170,708,226 (GRCm39)	Y164H	probably damaging	Het
Eml2	T	C	7: 18,930,539 (GRCm39)	V373A	possibly damaging	Het
Fat1	A	G	8: 45,479,441 (GRCm39)	D2829G	probably damaging	Het
Fbxl13	T	C	5: 21,691,371 (GRCm39)	T671A	probably damaging	Het
Fbxo28	G	T	1: 182,153,805 (GRCm39)		probably benign	Het
Fbxo44	A	G	4: 148,243,152 (GRCm39)	L89P	probably damaging	Het
Fndc3b	T	A	3: 27,610,266 (GRCm39)		probably null	Het
Gm9955	G	T	18: 24,842,209 (GRCm39)		probably benign	Het
Gprc6a	T	A	10: 51,491,080 (GRCm39)	K819*	probably null	Het
Gxylt1	A	T	15: 93,152,436 (GRCm39)		probably benign	Het
Hspa12a	T	C	19: 58,788,056 (GRCm39)	T589A	probably benign	Het
Idh2	A	G	7: 79,747,570 (GRCm39)	S317P	probably damaging	Het
Ifi30	T	C	8: 71,216,421 (GRCm39)		probably null	Het
Ifna16	G	A	4: 88,594,867 (GRCm39)	A76V	probably benign	Het
Itpr2	C	T	6: 146,246,638 (GRCm39)	E1127K	probably damaging	Het
Kank4	A	G	4: 98,667,457 (GRCm39)	V330A	probably benign	Het
Kpna1	T	A	16: 35,843,611 (GRCm39)	D328E	probably damaging	Het
Krt71	T	A	15: 101,646,868 (GRCm39)	H280L	possibly damaging	Het
Lrrc37	G	A	11: 103,433,816 (GRCm39)	P942S	probably damaging	Het
Mapt	A	G	11: 104,196,224 (GRCm39)	M446V	probably damaging	Het
Med1	C	T	11: 98,057,081 (GRCm39)		probably null	Het
Mif	T	A	10: 75,695,614 (GRCm39)	H63L	probably damaging	Het
Mycbp2	A	G	14: 103,461,708 (GRCm39)	V1447A	probably benign	Het
Myo1b	A	T	1: 51,821,148 (GRCm39)	I451N	probably damaging	Het
Nme2	A	T	11: 93,842,756 (GRCm39)		probably null	Het
Nubp1	A	G	16: 10,238,981 (GRCm39)	T199A	probably damaging	Het
Nup210l	T	A	3: 90,089,212 (GRCm39)	V1165D	probably damaging	Het
Nup98	T	A	7: 101,841,241 (GRCm39)	T122S	probably damaging	Het
Or14a258	A	T	7: 86,035,715 (GRCm39)	L51Q	probably benign	Het
Or1n2	T	C	2: 36,797,470 (GRCm39)	F171L	probably damaging	Het
Or5j1	C	T	2: 86,879,548 (GRCm39)	E11K	probably damaging	Het
Or6c202	T	A	10: 128,996,608 (GRCm39)	I82L	probably benign	Het
Pard3b	A	T	1: 62,676,979 (GRCm39)	Y1170F	probably damaging	Het
Pear1	T	C	3: 87,661,665 (GRCm39)	D536G	probably damaging	Het
Phrf1	G	T	7: 140,823,770 (GRCm39)	R196L	probably damaging	Het
Plxna2	G	T	1: 194,326,204 (GRCm39)	R46L	probably benign	Het
Rpl14	C	G	9: 120,401,167 (GRCm39)	F3L	possibly damaging	Het
Rtf2	G	A	2: 172,286,616 (GRCm39)	S40N	probably damaging	Het
Runx2	G	A	17: 44,919,141 (GRCm39)	S481L	possibly damaging	Het
Sh3rf1	T	A	8: 61,782,286 (GRCm39)	Y143N	possibly damaging	Het
Siglec15	G	A	18: 78,092,092 (GRCm39)		probably benign	Het
Slc4a8	T	A	15: 100,687,727 (GRCm39)	I288N	probably damaging	Het
Ttc38	C	A	15: 85,725,690 (GRCm39)	F184L	probably damaging	Het
Vmn1r28	T	C	6: 58,242,879 (GRCm39)	Y241H	probably damaging	Het
Vmn2r110	A	T	17: 20,816,346 (GRCm39)	V59D	probably benign	Het
Wdpcp	A	G	11: 21,661,638 (GRCm39)	I303M	probably damaging	Het
Zc3h12d	G	A	10: 7,743,678 (GRCm39)	A483T	probably benign	Het
Zfp106	C	A	2: 120,362,094 (GRCm39)	K1008N	probably damaging	Het
Zfp334	A	G	2: 165,223,492 (GRCm39)	Y184H	probably benign	Het
Zfp68	G	A	5: 138,606,041 (GRCm39)	T94I	probably benign	Het
Zkscan3	A	T	13: 21,579,090 (GRCm39)		probably null	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
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
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'- GGAAACCTTTGCTGAACCATGAGCC -3'
(R):5'- TGAAGTGCCCATCTATTGCTGCG -3'

Sequencing Primer
(F):5'- GATAATGAGCACACTGCATTCCTG -3'
(R):5'- GGCTATTGCTGCTGTCAATGC -3'

Posted On

2013-08-06