Incidental Mutation 'IGL01473:Rbm39'
ID 88355
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Rbm39
Ensembl Gene ENSMUSG00000027620
Gene Name RNA binding motif protein 39
Synonyms 1500012C14Rik, 2310040E03Rik, caper, Caper alpha, Rnpc2, B330012G18Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL01473
Quality Score
Status
Chromosome 2
Chromosomal Location 155989159-156022158 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 156014899 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Stop codon at position 49 (R49*)
Ref Sequence ENSEMBL: ENSMUSP00000119298 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029149] [ENSMUST00000109584] [ENSMUST00000109587] [ENSMUST00000126992] [ENSMUST00000137566] [ENSMUST00000146297] [ENSMUST00000146288] [ENSMUST00000142071] [ENSMUST00000147098] [ENSMUST00000153514] [ENSMUST00000146549] [ENSMUST00000155837] [ENSMUST00000152919] [ENSMUST00000154677]
AlphaFold Q8VH51
Predicted Effect probably null
Transcript: ENSMUST00000029149
AA Change: R49*
SMART Domains Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620
AA Change: R49*

DomainStartEndE-ValueType
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: ENSMUST00000109584
Predicted Effect probably null
Transcript: ENSMUST00000109587
AA Change: R49*
SMART Domains Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: R49*

DomainStartEndE-ValueType
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 null
Transcript: ENSMUST00000126992
AA Change: R49*
SMART Domains Protein: ENSMUSP00000116950
Gene: ENSMUSG00000027620
AA Change: R49*

DomainStartEndE-ValueType
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 noncoding transcript
Transcript: ENSMUST00000130516
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131625
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132929
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137297
Predicted Effect probably benign
Transcript: ENSMUST00000137566
Predicted Effect probably null
Transcript: ENSMUST00000146297
AA Change: R49*
SMART Domains Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620
AA Change: R49*

DomainStartEndE-ValueType
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 null
Transcript: ENSMUST00000146288
AA Change: R49*
SMART Domains Protein: ENSMUSP00000114824
Gene: ENSMUSG00000027620
AA Change: R49*

DomainStartEndE-ValueType
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 null
Transcript: ENSMUST00000142071
AA Change: R49*
SMART Domains Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620
AA Change: R49*

DomainStartEndE-ValueType
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 noncoding transcript
Transcript: ENSMUST00000140001
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150272
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138381
Predicted Effect probably benign
Transcript: ENSMUST00000147098
Predicted Effect probably benign
Transcript: ENSMUST00000153514
Predicted Effect probably benign
Transcript: ENSMUST00000146549
Predicted Effect probably benign
Transcript: ENSMUST00000155837
Predicted Effect probably benign
Transcript: ENSMUST00000152919
Predicted Effect probably benign
Transcript: ENSMUST00000154677
Coding Region Coverage
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: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atp13a5 T C 16: 29,135,542 (GRCm39) Y350C probably damaging Het
Clca3a1 C T 3: 144,713,539 (GRCm39) M697I probably benign Het
Clcn1 C A 6: 42,268,637 (GRCm39) A181D probably damaging Het
Cylc1 G T X: 110,166,449 (GRCm39) K243N unknown Het
Dsp A G 13: 38,351,547 (GRCm39) Y122C probably damaging Het
Exoc5 A G 14: 49,251,751 (GRCm39) V665A possibly damaging Het
Fcho1 G A 8: 72,164,782 (GRCm39) P500S probably benign Het
Flg2 A G 3: 93,110,327 (GRCm39) E785G unknown Het
Fpr1 A G 17: 18,097,954 (GRCm39) S12P possibly damaging Het
Hydin G T 8: 111,081,585 (GRCm39) G327V probably damaging Het
Hydin A T 8: 111,038,792 (GRCm39) M177L probably benign Het
Itga10 G A 3: 96,554,957 (GRCm39) G97E probably damaging Het
Khdc1c T A 1: 21,439,130 (GRCm39) Y39N possibly damaging Het
Lrp1b T G 2: 40,501,498 (GRCm39) T202P probably damaging Het
Marchf10 T C 11: 105,280,431 (GRCm39) K618R probably damaging Het
Mdc1 C A 17: 36,158,912 (GRCm39) L431I probably benign Het
Mmp17 A G 5: 129,683,472 (GRCm39) D536G probably benign Het
Myh8 G A 11: 67,192,651 (GRCm39) probably null Het
Odad3 C A 9: 21,906,675 (GRCm39) probably null Het
Pop4 A G 7: 37,963,820 (GRCm39) V154A probably benign Het
Ppp1r13l C T 7: 19,109,193 (GRCm39) R608C probably damaging Het
Prss36 T C 7: 127,543,873 (GRCm39) H166R probably damaging Het
Rab11fip3 C T 17: 26,287,709 (GRCm39) R148Q possibly damaging Het
S100a11 T C 3: 93,433,413 (GRCm39) C86R probably damaging Het
Skint7 T C 4: 111,839,402 (GRCm39) I232T probably damaging Het
Smchd1 G A 17: 71,696,745 (GRCm39) T1210I probably benign Het
Speg C T 1: 75,404,929 (GRCm39) T2907I possibly damaging Het
Spz1 A T 13: 92,711,764 (GRCm39) C237* probably null Het
Sun3 G T 11: 8,979,394 (GRCm39) D42E probably benign Het
Tgds C T 14: 118,365,626 (GRCm39) probably benign Het
Tnxb G A 17: 34,904,675 (GRCm39) D1270N probably damaging Het
Vmn2r78 A C 7: 86,569,520 (GRCm39) T138P possibly damaging Het
Wdfy1 T C 1: 79,685,182 (GRCm39) I351V probably benign Het
Other mutations in Rbm39
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00656:Rbm39 APN 2 156,004,791 (GRCm39) missense probably damaging 1.00
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
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
Posted On 2013-11-18