Incidental Mutation 'R5125:Rbm39'
ID 393484
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 042713-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5125 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 155989159-156022158 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 156004785 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 184 (M184K)
Ref Sequence ENSEMBL: ENSMUSP00000116820 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029149] [ENSMUST00000109587] [ENSMUST00000126992] [ENSMUST00000142071] [ENSMUST00000146297] [ENSMUST00000146288] [ENSMUST00000155837] [ENSMUST00000153514]
AlphaFold Q8VH51
Predicted Effect possibly damaging
Transcript: ENSMUST00000029149
AA Change: M184K

PolyPhen 2 Score 0.660 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620
AA Change: M184K

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 possibly damaging
Transcript: ENSMUST00000109587
AA Change: M184K

PolyPhen 2 Score 0.660 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: M184K

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 damaging
Transcript: ENSMUST00000126992
AA Change: M183K

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000116950
Gene: ENSMUSG00000027620
AA Change: M183K

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: ENSMUST00000135274
Predicted Effect probably damaging
Transcript: ENSMUST00000142071
AA Change: M184K

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620
AA Change: M184K

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 possibly damaging
Transcript: ENSMUST00000146297
AA Change: M184K

PolyPhen 2 Score 0.660 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620
AA Change: M184K

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 unknown
Transcript: ENSMUST00000148794
AA Change: M45K
SMART Domains Protein: ENSMUSP00000117462
Gene: ENSMUSG00000027620
AA Change: M45K

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 noncoding transcript
Transcript: ENSMUST00000138381
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150272
Predicted Effect probably benign
Transcript: ENSMUST00000146288
SMART Domains Protein: ENSMUSP00000114824
Gene: ENSMUSG00000027620

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 benign
Transcript: ENSMUST00000155837
Predicted Effect probably benign
Transcript: ENSMUST00000153514
Meta Mutation Damage Score 0.8661 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 91.9%
Validation Efficiency 96% (49/51)
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abt1 G T 13: 23,606,819 (GRCm39) A94E possibly damaging Het
Carmil2 G T 8: 106,423,521 (GRCm39) G1207V probably damaging Het
Cyp2c66 A G 19: 39,159,473 (GRCm39) Y308C probably damaging Het
Dcc A G 18: 71,589,948 (GRCm39) F683L probably benign Het
Denr A T 5: 124,065,144 (GRCm39) I166F probably damaging Het
Dhx29 T G 13: 113,069,134 (GRCm39) S155A possibly damaging Het
Dsg1b G A 18: 20,530,560 (GRCm39) G405E probably damaging Het
Ei24 T A 9: 36,693,742 (GRCm39) probably benign Het
Exo5 A T 4: 120,778,734 (GRCm39) probably null Het
Gm7356 T C 17: 14,221,576 (GRCm39) D151G probably damaging Het
Grin1 T C 2: 25,186,839 (GRCm39) probably benign Het
Grin2b C T 6: 135,900,297 (GRCm39) V195M possibly damaging Het
Hephl1 T A 9: 14,997,468 (GRCm39) K399N probably damaging Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Kmt2c A G 5: 25,489,379 (GRCm39) V4520A probably damaging Het
Lair1 G A 7: 4,013,488 (GRCm39) T82I possibly damaging Het
Lmx1a C T 1: 167,658,256 (GRCm39) S213L possibly damaging Het
Ly6g6d A G 17: 35,293,418 (GRCm39) I8T possibly damaging Het
Mcm4 T A 16: 15,453,167 (GRCm39) D174V probably benign Het
Mcph1 T A 8: 18,657,342 (GRCm39) D60E probably damaging Het
Med12l G A 3: 59,174,635 (GRCm39) G1851D possibly damaging Het
Or13c7b T A 4: 43,820,480 (GRCm39) I294F probably benign Het
Or7e174 T A 9: 20,012,488 (GRCm39) C144* probably null Het
P2rx2 G A 5: 110,490,517 (GRCm39) T66I possibly damaging Het
Pcdh15 A G 10: 74,419,912 (GRCm39) E1197G probably damaging Het
Pira1 T A 7: 3,742,396 (GRCm39) K44* probably null Het
Ppwd1 A T 13: 104,356,943 (GRCm39) S191T probably benign Het
Reln A G 5: 22,118,239 (GRCm39) V2935A possibly damaging Het
Robo4 T C 9: 37,319,256 (GRCm39) W535R probably damaging Het
Rsf1 A G 7: 97,311,079 (GRCm39) D603G possibly damaging Het
Sh3rf3 C G 10: 58,967,012 (GRCm39) P785A probably benign Het
Slc22a26 T C 19: 7,767,540 (GRCm39) T289A possibly damaging Het
Slc24a3 T C 2: 145,360,767 (GRCm39) V120A possibly damaging Het
Sost C T 11: 101,854,767 (GRCm39) G181R probably damaging Het
Sp2 A G 11: 96,846,664 (GRCm39) F554L probably benign Het
Stim2 T C 5: 54,267,939 (GRCm39) S87P probably damaging Het
Tecta T C 9: 42,286,481 (GRCm39) D725G probably damaging Het
Trgc4 A G 13: 19,528,932 (GRCm39) probably benign Het
Ube4b T C 4: 149,427,449 (GRCm39) M900V probably damaging Het
Ugt2b38 A G 5: 87,559,671 (GRCm39) M407T probably damaging Het
Vmn1r87 G T 7: 12,865,792 (GRCm39) A165E possibly damaging Het
Zc3h6 A G 2: 128,856,399 (GRCm39) H493R possibly damaging Het
Zfhx2 A T 14: 55,312,232 (GRCm39) F154Y probably benign Het
Zfp729a A G 13: 67,785,764 (GRCm39) probably null Het
Zfp976 A G 7: 42,261,925 (GRCm39) probably null Het
Zhx1 C G 15: 57,917,470 (GRCm39) G259R probably damaging Het
Znfx1 A T 2: 166,888,859 (GRCm39) V783E possibly damaging 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
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'- GACTCACTGATTTGCCATTTGG -3'
(R):5'- GCCTCCTTCAGTGCTTTATTAAAAC -3'

Sequencing Primer
(F):5'- GTGTTAAGTGGTACAACATCCAGCTC -3'
(R):5'- CATTCTTGCAACTTTGGAGGCAGAG -3'
Posted On 2016-06-15