Incidental Mutation 'YA93:Ptbp3'
ID79
Institutional Source Beutler Lab
Gene Symbol Ptbp3
Ensembl Gene ENSMUSG00000028382
Gene Namepolypyrimidine tract binding protein 3
SynonymsRod1, 5830471K22Rik
Accession Numbers

Genbank: NM_144904; MGI: 1923334; Ensembl: ENSMUST00000030076

Is this an essential gene? Possibly non essential (E-score: 0.356) question?
Stock #YA93 of strain inept
Quality Score
Status Validated
Chromosome4
Chromosomal Location59471868-59549364 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 59524413 bp
ZygosityHeterozygous
Amino Acid Change Threonine to Alanine at position 38 (T38A)
Ref Sequence ENSEMBL: ENSMUSP00000133612 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030076] [ENSMUST00000102883] [ENSMUST00000134879] [ENSMUST00000140925] [ENSMUST00000148331] [ENSMUST00000172768] [ENSMUST00000173699] [ENSMUST00000173884] [ENSMUST00000174586] [ENSMUST00000174748]
Predicted Effect probably benign
Transcript: ENSMUST00000030076
AA Change: T5A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000030076
Gene: ENSMUSG00000028382
AA Change: T5A

DomainStartEndE-ValueType
RRM 31 100 2.24e-3 SMART
low complexity region 115 130 N/A INTRINSIC
RRM 154 223 2.51e-6 SMART
low complexity region 277 293 N/A INTRINSIC
RRM 330 399 2.13e-9 SMART
RRM 447 517 1.29e-8 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000102883
AA Change: T36A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000099947
Gene: ENSMUSG00000028382
AA Change: T36A

DomainStartEndE-ValueType
RRM 59 128 2.24e-3 SMART
low complexity region 143 158 N/A INTRINSIC
RRM 182 251 2.51e-6 SMART
low complexity region 305 321 N/A INTRINSIC
RRM 358 427 2.13e-9 SMART
RRM 475 545 1.29e-8 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000134879
Predicted Effect possibly damaging
Transcript: ENSMUST00000140925
AA Change: T38A

PolyPhen 2 Score 0.710 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000122138
Gene: ENSMUSG00000028382
AA Change: T38A

DomainStartEndE-ValueType
SCOP:d1qm9a2 53 99 2e-4 SMART
PDB:2CQ1|A 54 101 8e-19 PDB
Blast:RRM 64 100 4e-19 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000148331
AA Change: T5A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000122840
Gene: ENSMUSG00000028382
AA Change: T5A

DomainStartEndE-ValueType
RRM 28 97 2.24e-3 SMART
low complexity region 112 127 N/A INTRINSIC
RRM 151 220 2.51e-6 SMART
low complexity region 274 290 N/A INTRINSIC
RRM 327 396 2.13e-9 SMART
RRM 444 514 1.29e-8 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000172768
AA Change: T5A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000134102
Gene: ENSMUSG00000028382
AA Change: T5A

DomainStartEndE-ValueType
RRM 28 97 2.24e-3 SMART
low complexity region 112 127 N/A INTRINSIC
RRM 151 220 2.51e-6 SMART
low complexity region 274 290 N/A INTRINSIC
RRM 327 396 2.13e-9 SMART
RRM 444 514 1.29e-8 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000173699
SMART Domains Protein: ENSMUSP00000134290
Gene: ENSMUSG00000028382

DomainStartEndE-ValueType
PDB:2CQ1|A 2 44 7e-18 PDB
low complexity region 49 64 N/A INTRINSIC
RRM 88 157 2.51e-6 SMART
low complexity region 211 227 N/A INTRINSIC
RRM 264 333 2.13e-9 SMART
RRM 381 451 1.29e-8 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000173884
SMART Domains Protein: ENSMUSP00000133996
Gene: ENSMUSG00000028382

DomainStartEndE-ValueType
low complexity region 16 28 N/A INTRINSIC
RRM 52 121 2.51e-6 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000174586
AA Change: T36A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000133612
Gene: ENSMUSG00000028382
AA Change: T36A

DomainStartEndE-ValueType
RRM 62 131 2.24e-3 SMART
low complexity region 146 161 N/A INTRINSIC
RRM 185 254 2.51e-6 SMART
low complexity region 308 324 N/A INTRINSIC
RRM 361 430 2.13e-9 SMART
RRM 478 548 1.29e-8 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000174748
AA Change: T36A

PolyPhen 2 Score 0.659 (Sensitivity: 0.86; Specificity: 0.91)
Meta Mutation Damage Score 0.108 question?
Coding Region Coverage
  • 1x: 90.4%
  • 3x: 81.3%
Validation Efficiency 88% (101/115)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene binds RNA and is a regulator of cell differentiation. The encoded protein preferentially binds to poly(G) and poly(U) sequences in vitro. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Allele List at MGI

All alleles(6) : Gene trapped(6)

Other mutations in this stock
Total: 15 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arhgef4 C T 1: 34,732,217 R1202W probably benign Het
B4galnt4 T A 7: 141,067,411 I358K possibly damaging Homo
Chodl A G 16: 78,941,282 H46R probably benign Homo
Cubn C A 2: 13,383,992 R1468L probably benign Het
Dlg5 G A 14: 24,155,133 noncoding transcript Het
Dntt A C 19: 41,053,187 M437L probably benign Het
Gm8251 A G 1: 44,065,085 probably null Het
Grsf1 G A 5: 88,673,735 P157S probably damaging Het
Lct C T 1: 128,301,320 G812D probably damaging Het
Osbpl5 T A 7: 143,693,870 I744F probably benign Homo
Pbld2 T A 10: 63,054,445 Y211N possibly damaging Het
Peg3 T A 7: 6,711,647 E192V probably null Het
Rpap3 T A 15: 97,693,233 E241V possibly damaging Het
Scara3 C A 14: 65,930,949 M406I probably damaging Het
Serpinf2 C A 11: 75,432,684 V399L probably benign Het
Other mutations in Ptbp3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00932:Ptbp3 APN 4 59477228 missense probably benign 0.29
IGL03035:Ptbp3 APN 4 59477218 missense probably benign 0.00
IGL03118:Ptbp3 APN 4 59501470 missense probably benign 0.03
IGL03257:Ptbp3 APN 4 59493370 unclassified probably benign
IGL03279:Ptbp3 APN 4 59476937 missense possibly damaging 0.68
R0557:Ptbp3 UTSW 4 59517684 nonsense probably null
R1741:Ptbp3 UTSW 4 59482624 missense probably damaging 0.98
R1914:Ptbp3 UTSW 4 59517635 missense probably damaging 1.00
R1915:Ptbp3 UTSW 4 59517635 missense probably damaging 1.00
R2679:Ptbp3 UTSW 4 59494615 splice site probably benign
R3798:Ptbp3 UTSW 4 59546166 missense probably benign 0.05
R4793:Ptbp3 UTSW 4 59514297 missense possibly damaging 0.71
R4869:Ptbp3 UTSW 4 59524443 missense possibly damaging 0.79
R5573:Ptbp3 UTSW 4 59485626 missense probably damaging 1.00
R5986:Ptbp3 UTSW 4 59493311 missense probably benign 0.37
R6350:Ptbp3 UTSW 4 59482624 missense probably damaging 0.98
Nature of Mutation
DNA sequencing using the SOLiD technique identified an A to G transition at position 315 of the Rod1 transcript in exon 2 of 14 total exons using Ensembl record ENSMUST00000030076. Four transcripts of the Rod1 gene are displayed on Ensembl and Vega. The mutated nucleotide causes a threonine to alanine substitution at amino acid 5 of the encoded protein. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).
Protein Function & Prediction
The Rod1 gene encodes a 523 amino acid protein that contains four RNA recognition motifs (RRM) domains at amino acids 30-114, 153-229, 329-403, and 446-521 (Uniprot Q8BHD7). Rod1 is able to bind to RNA in vitro, preferentially to poly(G) and poly(U).
 
The T5A change is predicted to be probably benign by the PolyPhen program.
Posted OnMar 01, 2010