Incidental Mutation 'R8178:Rbm39'
ID 634463
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 067603-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8178 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 155989159-156022158 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 155996195 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 397 (I397V)
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
SMART Domains Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620

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: ENSMUST00000109587
AA Change: I397V

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: I397V

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 benign
Transcript: ENSMUST00000142071
SMART Domains Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620

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 probably benign
Transcript: ENSMUST00000146297
SMART Domains Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620

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: ENSMUST00000148794
AA Change: I236V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000117462
Gene: ENSMUSG00000027620
AA Change: I236V

DomainStartEndE-ValueType
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
Meta Mutation Damage Score 0.0607 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 99.0%
Validation Efficiency 99% (68/69)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921513D11Rik A G 17: 79,935,699 (GRCm39) I276V Het
Acsm5 C A 7: 119,141,618 (GRCm39) H538N probably damaging Het
Adamts17 A G 7: 66,499,464 (GRCm39) I4V possibly damaging Het
Adgrg3 T C 8: 95,761,675 (GRCm39) V146A probably damaging Het
Ankrd52 T A 10: 128,225,170 (GRCm39) L877Q probably damaging Het
Aox3 A T 1: 58,189,481 (GRCm39) D394V possibly damaging Het
Arhgap45 G A 10: 79,863,706 (GRCm39) A819T probably damaging Het
Arhgef4 A G 1: 34,761,983 (GRCm39) E413G unknown Het
Arhgef5 T C 6: 43,252,119 (GRCm39) S957P probably benign Het
Arsk G T 13: 76,239,861 (GRCm39) T114K probably damaging Het
Bpifb2 T C 2: 153,733,876 (GRCm39) V406A probably damaging Het
Cbr3 C A 16: 93,480,393 (GRCm39) Q61K probably benign Het
Ccdc73 C T 2: 104,821,557 (GRCm39) S502L probably benign Het
Cdhr3 A T 12: 33,098,931 (GRCm39) probably null Het
Cep170b T A 12: 112,705,719 (GRCm39) M1159K possibly damaging Het
Cep295 A T 9: 15,244,836 (GRCm39) S1159T Het
Cit C T 5: 116,107,131 (GRCm39) R1088W probably damaging Het
Col16a1 A T 4: 129,947,270 (GRCm39) H205L unknown Het
Cpt1c T G 7: 44,609,077 (GRCm39) H748P probably damaging Het
Cstdc4 T G 16: 36,006,772 (GRCm39) Y35* probably null Het
Dcaf8 A T 1: 172,013,886 (GRCm39) D359V probably benign Het
Dcstamp A G 15: 39,618,422 (GRCm39) Y277C probably damaging Het
Dnah10 A G 5: 124,832,790 (GRCm39) K898R probably benign Het
Dnah6 T A 6: 73,037,208 (GRCm39) T3345S probably benign Het
Dpp6 A T 5: 27,803,815 (GRCm39) N254Y probably damaging Het
F2 A T 2: 91,460,618 (GRCm39) probably null Het
Fam216b G C 14: 78,322,504 (GRCm39) H67D possibly damaging Het
Fbxl17 A C 17: 63,794,967 (GRCm39) probably null Het
Gas2 T A 7: 51,547,026 (GRCm39) M59K probably damaging Het
Glud1 G A 14: 34,065,664 (GRCm39) G554D probably damaging Het
Gys2 C T 6: 142,402,138 (GRCm39) G234R probably damaging Het
Ifngr1 A G 10: 19,485,241 (GRCm39) I413M probably benign Het
Inpp5a C T 7: 139,118,153 (GRCm39) R236C probably damaging Het
Kcnip3 A G 2: 127,323,934 (GRCm39) S32P probably benign Het
Lingo3 T A 10: 80,670,464 (GRCm39) T489S possibly damaging Het
Lrpprc A G 17: 85,079,575 (GRCm39) L227P probably damaging Het
Morn1 A G 4: 155,213,160 (GRCm39) Q356R probably benign Het
Naxd A C 8: 11,561,987 (GRCm39) K275Q probably benign Het
Nbeal1 G C 1: 60,276,310 (GRCm39) V684L probably benign Het
Nck1 A T 9: 100,379,790 (GRCm39) W154R probably damaging Het
Or10d5 G A 9: 39,861,708 (GRCm39) R120C probably benign Het
Or1ad8 T A 11: 50,898,437 (GRCm39) C213S probably damaging Het
Or5aq6 C T 2: 86,923,220 (GRCm39) V174M possibly damaging Het
Or7e175 T C 9: 20,048,571 (GRCm39) V53A possibly damaging Het
Pdxk C T 10: 78,289,338 (GRCm39) V38M probably damaging Het
Peg10 GC GCTCC 6: 4,756,452 (GRCm39) probably benign Het
Pes1 T C 11: 3,927,718 (GRCm39) S482P probably benign Het
Pglyrp1 T A 7: 18,618,657 (GRCm39) F3I unknown Het
Pira13 T C 7: 3,824,260 (GRCm39) K631R unknown Het
Plce1 T A 19: 38,761,423 (GRCm39) F2092I possibly damaging Het
Pms1 A G 1: 53,246,505 (GRCm39) S345P probably benign Het
Pom121l12 C A 11: 14,550,011 (GRCm39) P239H probably damaging Het
Prdm2 A G 4: 142,859,018 (GRCm39) I1424T probably benign Het
Prmt6 A G 3: 110,158,140 (GRCm39) Y50H probably damaging Het
Rnf157 A G 11: 116,238,307 (GRCm39) V519A possibly damaging Het
Sec23a T C 12: 59,053,980 (GRCm39) E6G possibly damaging Het
Shank1 T C 7: 43,962,748 (GRCm39) probably null Het
Slfn3 A G 11: 83,105,505 (GRCm39) I378V probably benign Het
Smn1 T A 13: 100,267,303 (GRCm39) probably null Het
Snd1 T C 6: 28,874,975 (GRCm39) F632S possibly damaging Het
Sun5 T C 2: 153,698,131 (GRCm39) probably null Het
Tial1 T C 7: 128,046,614 (GRCm39) R209G probably benign Het
Trhde T C 10: 114,244,598 (GRCm39) I963V possibly damaging Het
Tssc4 G T 7: 142,623,932 (GRCm39) R80L possibly damaging Het
Ttn A T 2: 76,642,852 (GRCm39) N13261K probably damaging Het
Ugdh A T 5: 65,581,005 (GRCm39) probably null Het
Vmn1r218 A T 13: 23,321,472 (GRCm39) E273V probably benign Het
Vmn2r92 T A 17: 18,386,988 (GRCm39) F109Y possibly damaging Het
Zcchc7 A G 4: 44,931,398 (GRCm39) S196G probably benign Het
Zfp788 T A 7: 41,298,335 (GRCm39) C324S probably damaging Het
Zfp976 T C 7: 42,262,959 (GRCm39) T294A probably benign Het
Other mutations in Rbm39
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- GTGTCAAGGACAGCATGTTAAGC -3'
(R):5'- CCCAAAGCCTTGTAAATGAGG -3'

Sequencing Primer
(F):5'- CAAGGACAGCATGTTAAGCTATTTC -3'
(R):5'- CCCAAAGCCTTGTAAATGAGGAATGG -3'
Posted On 2020-07-13