Incidental Mutation 'R2888:Rbm39'
| ID |
259983 |
| 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 |
040476-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2888 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
155989159-156022158 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 156009503 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Histidine
at position 123
(R123H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000116950
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029149]
[ENSMUST00000109587]
[ENSMUST00000126992]
[ENSMUST00000142071]
[ENSMUST00000146288]
[ENSMUST00000146297]
[ENSMUST00000155837]
[ENSMUST00000153514]
|
| AlphaFold |
Q8VH51 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029149
AA Change: R124H
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000029149
Gene: ENSMUSG00000027620
AA Change: R124H
| 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: R124H
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000105216
Gene: ENSMUSG00000027620
AA Change: R124H
| 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: ENSMUST00000126992
AA Change: R123H
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000116950
Gene: ENSMUSG00000027620
AA Change: R123H
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
noncoding transcript
Transcript: ENSMUST00000138381
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150272
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000142071
AA Change: R124H
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000116820
Gene: ENSMUSG00000027620
AA Change: R124H
| 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 |
unknown
Transcript: ENSMUST00000146288
AA Change: R102H
|
| SMART Domains |
Protein: ENSMUSP00000114824
Gene: ENSMUSG00000027620
AA Change: R102H
| Domain | Start | End | E-Value | Type |
|---|
|
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: ENSMUST00000146297
AA Change: R124H
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000119298
Gene: ENSMUSG00000027620
AA Change: R124H
| 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: ENSMUST00000140001
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000155837
|
| 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: ENSMUST00000153514
|
| Meta Mutation Damage Score |
0.1311 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
100% (39/39) |
| 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: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930480E11Rik |
A |
T |
X: 77,414,288 (GRCm39) |
I338F |
probably damaging |
Het |
| Acd |
A |
G |
8: 106,425,470 (GRCm39) |
S288P |
probably benign |
Het |
| Aimp2 |
T |
C |
5: 143,846,553 (GRCm39) |
|
probably benign |
Het |
| Atp8b2 |
T |
C |
3: 89,865,600 (GRCm39) |
D100G |
probably damaging |
Het |
| Cacna1i |
A |
T |
15: 80,258,968 (GRCm39) |
I1226F |
probably damaging |
Het |
| Dsp |
C |
A |
13: 38,376,224 (GRCm39) |
N1336K |
possibly damaging |
Het |
| Extl2 |
T |
C |
3: 115,820,906 (GRCm39) |
F251S |
probably damaging |
Het |
| Gusb |
T |
C |
5: 130,029,343 (GRCm39) |
H146R |
probably damaging |
Het |
| Itpr2 |
C |
T |
6: 146,072,791 (GRCm39) |
G2380S |
probably damaging |
Het |
| Kansl1l |
T |
C |
1: 66,763,764 (GRCm39) |
K762E |
probably benign |
Het |
| Krtap4-9 |
C |
A |
11: 99,676,245 (GRCm39) |
C55* |
probably null |
Het |
| Lamp1 |
T |
A |
8: 13,223,891 (GRCm39) |
L341H |
probably damaging |
Het |
| Llcfc1 |
A |
T |
6: 41,661,537 (GRCm39) |
K29M |
probably damaging |
Het |
| Malrd1 |
A |
T |
2: 16,079,568 (GRCm39) |
I1762F |
unknown |
Het |
| Muc5b |
G |
A |
7: 141,415,291 (GRCm39) |
V2746M |
probably damaging |
Het |
| Mug1 |
T |
A |
6: 121,858,802 (GRCm39) |
D1173E |
probably benign |
Het |
| Myo5b |
G |
C |
18: 74,895,689 (GRCm39) |
E1782Q |
probably damaging |
Het |
| Or2t46 |
T |
C |
11: 58,471,988 (GRCm39) |
F106S |
possibly damaging |
Het |
| Pcdha5 |
A |
G |
18: 37,094,940 (GRCm39) |
D483G |
probably damaging |
Het |
| Phex |
T |
C |
X: 156,093,954 (GRCm39) |
I439V |
probably benign |
Het |
| Pkd1l1 |
T |
A |
11: 8,897,251 (GRCm39) |
S103C |
probably damaging |
Het |
| Plekha4 |
C |
T |
7: 45,187,668 (GRCm39) |
R176C |
probably damaging |
Het |
| Ppp1r3a |
T |
G |
6: 14,718,248 (GRCm39) |
S889R |
possibly damaging |
Het |
| Pramel23 |
G |
T |
4: 143,423,460 (GRCm39) |
T443K |
probably benign |
Het |
| Prol1 |
C |
A |
5: 88,476,168 (GRCm39) |
A186E |
unknown |
Het |
| Rtn4 |
T |
C |
11: 29,643,687 (GRCm39) |
S167P |
probably damaging |
Het |
| Slc35a5 |
A |
G |
16: 44,971,923 (GRCm39) |
C114R |
probably damaging |
Het |
| Smoc2 |
T |
C |
17: 14,617,887 (GRCm39) |
|
probably null |
Het |
| Sptbn2 |
A |
G |
19: 4,798,664 (GRCm39) |
T1998A |
possibly damaging |
Het |
| Tbc1d5 |
T |
A |
17: 51,242,577 (GRCm39) |
E173D |
probably damaging |
Het |
| Tsc2 |
A |
G |
17: 24,850,969 (GRCm39) |
|
probably null |
Het |
| Umps |
A |
T |
16: 33,784,240 (GRCm39) |
V71E |
probably damaging |
Het |
| Vmn2r13 |
T |
C |
5: 109,339,840 (GRCm39) |
D45G |
possibly damaging |
Het |
| Wdfy4 |
C |
A |
14: 32,831,476 (GRCm39) |
E917* |
probably null |
Het |
| Zfhx2 |
T |
C |
14: 55,302,260 (GRCm39) |
K1908R |
possibly damaging |
Het |
| Zfp511 |
A |
C |
7: 139,619,295 (GRCm39) |
D204A |
probably benign |
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 |
|
R1564:Rbm39
|
UTSW |
2 |
155,996,177 (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'- GGAAGCTTACTGAGGCATAAAC -3'
(R):5'- GCTCCGGACCAAAATTTAACAG -3'
Sequencing Primer
(F):5'- CCAGATGGTCTACAGAGTGAGTTCC -3'
(R):5'- TTTAACAGTGCCATCCGAGG -3'
|
| Posted On |
2015-01-23 |
Incidental Mutation