Incidental Mutation 'R5841:Ptbp1'
ID 450445
Institutional Source Beutler Lab
Gene Symbol Ptbp1
Ensembl Gene ENSMUSG00000006498
Gene Name polypyrimidine tract binding protein 1
Synonyms Ptb, hnRNP I
MMRRC Submission 044061-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5841 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 79690502-79700269 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 79695766 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 289 (D289G)
Ref Sequence ENSEMBL: ENSMUSP00000059481 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057343] [ENSMUST00000092325] [ENSMUST00000095457] [ENSMUST00000165724] [ENSMUST00000165704] [ENSMUST00000169483] [ENSMUST00000168683] [ENSMUST00000167250] [ENSMUST00000172282] [ENSMUST00000171599]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000057343
AA Change: D289G

PolyPhen 2 Score 0.311 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000059481
Gene: ENSMUSG00000006498
AA Change: D289G

DomainStartEndE-ValueType
low complexity region 32 38 N/A INTRINSIC
RRM 59 128 9.8e-9 SMART
low complexity region 161 178 N/A INTRINSIC
RRM 184 253 4.75e-7 SMART
low complexity region 305 330 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000092325
SMART Domains Protein: ENSMUSP00000089979
Gene: ENSMUSG00000035835

DomainStartEndE-ValueType
transmembrane domain 17 39 N/A INTRINSIC
transmembrane domain 69 91 N/A INTRINSIC
acidPPc 132 276 1.38e-16 SMART
coiled coil region 430 460 N/A INTRINSIC
low complexity region 562 581 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000095457
AA Change: D249G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000093109
Gene: ENSMUSG00000006498
AA Change: D249G

DomainStartEndE-ValueType
Pfam:RRM_6 36 86 1.9e-5 PFAM
Pfam:RRM_5 38 90 3.6e-12 PFAM
low complexity region 121 138 N/A INTRINSIC
RRM 144 213 4.75e-7 SMART
low complexity region 265 290 N/A INTRINSIC
RRM 296 365 1.84e-13 SMART
RRM 413 483 2.6e-13 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000099958
Predicted Effect noncoding transcript
Transcript: ENSMUST00000113452
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164385
Predicted Effect probably benign
Transcript: ENSMUST00000165724
AA Change: D72G

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000130749
Gene: ENSMUSG00000006498
AA Change: D72G

DomainStartEndE-ValueType
Pfam:RRM_5 2 40 5.3e-7 PFAM
low complexity region 114 139 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000165704
AA Change: D289G

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000127783
Gene: ENSMUSG00000006498
AA Change: D289G

DomainStartEndE-ValueType
low complexity region 32 38 N/A INTRINSIC
RRM 59 128 9.8e-9 SMART
low complexity region 161 178 N/A INTRINSIC
RRM 184 253 4.75e-7 SMART
low complexity region 305 330 N/A INTRINSIC
RRM 336 405 1.84e-13 SMART
RRM 453 523 2.6e-13 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000165153
Predicted Effect noncoding transcript
Transcript: ENSMUST00000168216
Predicted Effect noncoding transcript
Transcript: ENSMUST00000168988
Predicted Effect noncoding transcript
Transcript: ENSMUST00000166593
Predicted Effect noncoding transcript
Transcript: ENSMUST00000168521
Predicted Effect noncoding transcript
Transcript: ENSMUST00000166057
Predicted Effect probably benign
Transcript: ENSMUST00000169483
SMART Domains Protein: ENSMUSP00000127507
Gene: ENSMUSG00000006498

DomainStartEndE-ValueType
low complexity region 32 38 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000168683
SMART Domains Protein: ENSMUSP00000132383
Gene: ENSMUSG00000006498

DomainStartEndE-ValueType
low complexity region 2 8 N/A INTRINSIC
SCOP:d2u1a__ 17 55 3e-3 SMART
PDB:2AD9|A 18 55 9e-19 PDB
Blast:RRM 29 55 2e-11 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000169091
SMART Domains Protein: ENSMUSP00000128449
Gene: ENSMUSG00000006498

DomainStartEndE-ValueType
low complexity region 13 19 N/A INTRINSIC
Pfam:RRM_5 29 81 3.5e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000167250
SMART Domains Protein: ENSMUSP00000130695
Gene: ENSMUSG00000035835

DomainStartEndE-ValueType
transmembrane domain 17 39 N/A INTRINSIC
transmembrane domain 69 91 N/A INTRINSIC
acidPPc 132 276 1.38e-16 SMART
low complexity region 437 454 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000171216
Predicted Effect probably benign
Transcript: ENSMUST00000172282
AA Change: D289G

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000126192
Gene: ENSMUSG00000006498
AA Change: D289G

DomainStartEndE-ValueType
low complexity region 32 38 N/A INTRINSIC
RRM 59 128 9.8e-9 SMART
low complexity region 161 178 N/A INTRINSIC
RRM 184 253 4.75e-7 SMART
low complexity region 331 356 N/A INTRINSIC
RRM 362 431 1.84e-13 SMART
RRM 479 549 2.6e-13 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184090
Predicted Effect noncoding transcript
Transcript: ENSMUST00000169580
Predicted Effect noncoding transcript
Transcript: ENSMUST00000217802
Predicted Effect probably benign
Transcript: ENSMUST00000171599
SMART Domains Protein: ENSMUSP00000131296
Gene: ENSMUSG00000006498

DomainStartEndE-ValueType
low complexity region 87 93 N/A INTRINSIC
Meta Mutation Damage Score 0.0604 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.6%
  • 20x: 96.2%
Validation Efficiency 100% (67/67)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has four repeats of quasi-RNA recognition motif (RRM) domains that bind RNAs. This protein binds to the intronic polypyrimidine tracts that requires pre-mRNA splicing and acts via the protein degradation ubiquitin-proteasome pathway. It may also promote the binding of U2 snRNP to pre-mRNAs. This protein is localized in the nucleoplasm and it is also detected in the perinucleolar structure. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele die before E6.5. Mice homozygous for a conditional allele activated in neuronal stem cells (NSCs) exhibit premature death, and non-obstructive hydrocephaly with loss of ependymal cells due to precocious NSC differentiation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb6 A T 1: 75,150,994 (GRCm39) F565L possibly damaging Het
Abhd6 T A 14: 8,049,596 (GRCm38) V188D probably benign Het
Bbs12 T G 3: 37,373,670 (GRCm39) N39K probably benign Het
Bend5 A G 4: 111,290,667 (GRCm39) Y221C probably damaging Het
Brd8 A G 18: 34,738,576 (GRCm39) S683P probably damaging Het
Caskin1 A G 17: 24,715,183 (GRCm39) D79G probably damaging Het
Cdyl T C 13: 36,056,544 (GRCm39) L509P probably damaging Het
Cenpf G T 1: 189,389,641 (GRCm39) T1397N possibly damaging Het
Ckap5 T A 2: 91,431,027 (GRCm39) M1479K probably benign Het
Cpsf2 T C 12: 101,951,497 (GRCm39) S145P probably damaging Het
Cyp4a12a A T 4: 115,183,899 (GRCm39) H235L probably benign Het
Cyp7b1 A T 3: 18,151,670 (GRCm39) F181Y probably damaging Het
Dennd5b T C 6: 148,946,253 (GRCm39) T453A probably benign Het
Dlgap3 A G 4: 127,089,193 (GRCm39) D263G probably damaging Het
Dnah3 TTCCTC TTC 7: 119,550,244 (GRCm39) probably benign Het
Dync2li1 G A 17: 84,940,990 (GRCm39) G69R probably damaging Het
Edc3 T C 9: 57,651,885 (GRCm39) V331A probably benign Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Ganc C T 2: 120,242,020 (GRCm39) T66I possibly damaging Het
Gm11595 C A 11: 99,663,143 (GRCm39) C179F unknown Het
Gnptg A G 17: 25,454,391 (GRCm39) S159P probably damaging Het
Gsdmc2 C T 15: 63,698,059 (GRCm39) V349I probably benign Het
Hydin T C 8: 111,259,846 (GRCm39) I2606T possibly damaging Het
Ino80d A G 1: 63,097,999 (GRCm39) S632P probably damaging Het
Kcnn2 G A 18: 45,692,463 (GRCm39) R13H probably benign Het
Klb A T 5: 65,536,667 (GRCm39) K666* probably null Het
Kmt2d G A 15: 98,749,990 (GRCm39) probably benign Het
Kpna7 T C 5: 144,930,766 (GRCm39) I360V possibly damaging Het
Lmbrd2 A G 15: 9,182,657 (GRCm39) K576E possibly damaging Het
Lrp2 T A 2: 69,310,497 (GRCm39) Y2692F probably benign Het
Meis2 T A 2: 115,889,145 (GRCm39) E202D probably benign Het
Mgat4c A T 10: 102,224,826 (GRCm39) T347S probably damaging Het
Mmp12 G A 9: 7,347,501 (GRCm39) C26Y possibly damaging Het
Mrpl24 G A 3: 87,830,292 (GRCm39) R145Q probably damaging Het
Mtpn C T 6: 35,489,225 (GRCm39) D100N probably benign Het
Mycbpap T A 11: 94,396,436 (GRCm39) R135W probably damaging Het
Myo1g T A 11: 6,457,000 (GRCm39) Y942F probably benign Het
Myrf T C 19: 10,200,911 (GRCm39) K52R probably null Het
Ncf2 A T 1: 152,697,269 (GRCm39) silent Het
Nherf2 A T 17: 24,863,851 (GRCm39) M8K probably benign Het
Or51f1e T C 7: 102,747,161 (GRCm39) F71S probably damaging Het
Otx1 T C 11: 21,948,594 (GRCm39) probably benign Het
Pcnx1 T A 12: 81,965,429 (GRCm39) V532D possibly damaging Het
Pik3r5 T C 11: 68,383,096 (GRCm39) L305P probably damaging Het
Pira13 T A 7: 3,825,898 (GRCm39) R324* probably null Het
Polr3a A T 14: 24,500,766 (GRCm39) C1341S probably benign Het
Ppp1r3a T C 6: 14,718,983 (GRCm39) T644A probably benign Het
Pramel22 A G 4: 143,382,109 (GRCm39) S196P possibly damaging Het
Pwp2 A G 10: 78,007,952 (GRCm39) F868L probably benign Het
Rgs8 A G 1: 153,568,574 (GRCm39) E153G probably damaging Het
Rhbdf2 G A 11: 116,493,180 (GRCm39) probably benign Het
Sbf1 T C 15: 89,192,271 (GRCm39) H78R probably damaging Het
Sdr16c6 C T 4: 4,062,728 (GRCm39) A197T possibly damaging Het
Slc36a3 A T 11: 55,016,547 (GRCm39) Y349* probably null Het
Slc38a9 T C 13: 112,831,856 (GRCm39) L202P possibly damaging Het
Slc40a1 A T 1: 45,951,509 (GRCm39) M216K probably damaging Het
Srebf1 T A 11: 60,094,410 (GRCm39) Q568H possibly damaging Het
Srp54b A G 12: 55,299,614 (GRCm39) N315S probably benign Het
Strc A G 2: 121,196,358 (GRCm39) F1557L probably benign Het
Susd3 C A 13: 49,392,202 (GRCm39) probably benign Het
Usp54 G A 14: 20,600,351 (GRCm39) T1462I probably benign Het
Vmn1r11 T A 6: 57,114,787 (GRCm39) N150K probably damaging Het
Vwa8 C T 14: 79,231,958 (GRCm39) H606Y probably benign Het
Zmym6 A G 4: 126,994,463 (GRCm39) I206V possibly damaging Het
Other mutations in Ptbp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01115:Ptbp1 APN 10 79,695,796 (GRCm39) splice site probably benign
IGL01335:Ptbp1 APN 10 79,698,708 (GRCm39) splice site probably null
IGL03119:Ptbp1 APN 10 79,695,458 (GRCm39) missense probably damaging 1.00
carillon UTSW 10 79,694,897 (GRCm39) missense probably damaging 0.98
Citi UTSW 10 79,695,766 (GRCm39) missense probably benign 0.31
R1433:Ptbp1 UTSW 10 79,699,107 (GRCm39) missense probably damaging 1.00
R2418:Ptbp1 UTSW 10 79,695,511 (GRCm39) missense probably damaging 0.98
R4222:Ptbp1 UTSW 10 79,695,047 (GRCm39) missense probably benign 0.07
R4223:Ptbp1 UTSW 10 79,695,047 (GRCm39) missense probably benign 0.07
R4224:Ptbp1 UTSW 10 79,695,047 (GRCm39) missense probably benign 0.07
R4688:Ptbp1 UTSW 10 79,692,342 (GRCm39) missense possibly damaging 0.87
R6961:Ptbp1 UTSW 10 79,695,111 (GRCm39) splice site probably null
R7242:Ptbp1 UTSW 10 79,692,222 (GRCm39) missense unknown
R7579:Ptbp1 UTSW 10 79,694,954 (GRCm39) missense probably benign 0.02
R8341:Ptbp1 UTSW 10 79,699,045 (GRCm39) missense probably benign
R8832:Ptbp1 UTSW 10 79,699,023 (GRCm39) missense probably damaging 1.00
R9141:Ptbp1 UTSW 10 79,694,897 (GRCm39) missense probably damaging 0.98
R9426:Ptbp1 UTSW 10 79,694,897 (GRCm39) missense probably damaging 0.98
R9465:Ptbp1 UTSW 10 79,695,615 (GRCm39) missense possibly damaging 0.93
Predicted Primers PCR Primer
(F):5'- AATCCTATGACTGGCCCACG -3'
(R):5'- CGGAGAGGCTGACATTATGC -3'

Sequencing Primer
(F):5'- TATGACTGGCCCACGCACTC -3'
(R):5'- TGACATTATGCCGGGCG -3'
Posted On 2016-12-20