Incidental Mutation 'R9198:Nt5c3'
ID 698039
Institutional Source Beutler Lab
Gene Symbol Nt5c3
Ensembl Gene ENSMUSG00000029780
Gene Name 5'-nucleotidase, cytosolic III
Synonyms lupin, cN-III, Umph-1, p36, 1600024P05Rik, PN-1, 2610206B05Rik, Umph1, PN-I, PSN1
MMRRC Submission
Accession Numbers
Essential gene? Probably non essential (E-score: 0.194) question?
Stock # R9198 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 56859385-56900917 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 56859955 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Arginine at position 328 (Q328R)
Ref Sequence ENSEMBL: ENSMUSP00000031793 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031793] [ENSMUST00000031795] [ENSMUST00000101367] [ENSMUST00000135558] [ENSMUST00000152447]
AlphaFold Q9D020
PDB Structure X-Ray Structure of a Cytosolic 5'-Nucleotidase III from Mus Musculus MM.158936 [X-RAY DIFFRACTION]
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, with bound magnesium(II) [X-RAY DIFFRACTION]
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate analog with Beryllium fluoride [X-RAY DIFFRACTION]
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product-transition complex analog with Aluminum fluoride [X-RAY DIFFRACTION]
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product complex [X-RAY DIFFRACTION]
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site [X-RAY DIFFRACTION]
Ensemble refinement of the protein crystal structure of a cytosolic 5'-nucleotidase III from Mus musculus Mm.158936 [X-RAY DIFFRACTION]
Structure of murine cytosolic 5'-nucleotidase III complexed with uridinine monophosphate [X-RAY DIFFRACTION]
Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate [X-RAY DIFFRACTION]
Cytosolic 5'-nucleotidase III complexed with cytidine 5'-monophosphate [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000031793
AA Change: Q328R

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000031793
Gene: ENSMUSG00000029780
AA Change: Q328R

DomainStartEndE-ValueType
transmembrane domain 9 31 N/A INTRINSIC
Pfam:UMPH-1 86 331 5.6e-119 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000031795
SMART Domains Protein: ENSMUSP00000031795
Gene: ENSMUSG00000029781

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Pfam:FKBP_C 47 139 8.2e-31 PFAM
Pfam:FKBP_C 159 251 5.8e-28 PFAM
Pfam:FKBP_C 271 362 1.3e-27 PFAM
Pfam:FKBP_C 382 474 2.8e-27 PFAM
EFh 492 520 2.35e0 SMART
EFh 537 565 1.98e0 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000101367
AA Change: Q294R

PolyPhen 2 Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000098918
Gene: ENSMUSG00000029780
AA Change: Q294R

DomainStartEndE-ValueType
Pfam:UMPH-1 52 297 2.1e-118 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000135558
SMART Domains Protein: ENSMUSP00000145230
Gene: ENSMUSG00000029780

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000152447
Predicted Effect probably benign
Transcript: ENSMUST00000205087
Meta Mutation Damage Score 0.0654 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.9%
  • 20x: 99.5%
Validation Efficiency 97% (61/63)
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 5'-nucleotidase family of enzymes that catalyze the dephosphorylation of nucleoside 5'-monophosphates. The encoded protein is the type 1 isozyme of pyrimidine 5' nucleotidase and catalyzes the dephosphorylation of pyrimidine 5' monophosphates. Mutations in this gene are a cause of hemolytic anemia due to uridine 5-prime monophosphate hydrolase deficiency. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and pseudogenes of this gene are located on the long arm of chromosomes 3 and 4. [provided by RefSeq, Mar 2012]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam22 A G 5: 8,167,583 (GRCm39) probably null Het
Adamts9 A T 6: 92,837,170 (GRCm39) S1164T probably benign Het
Bcat1 A T 6: 144,985,222 (GRCm39) I140N probably damaging Het
Bod1l T C 5: 41,957,129 (GRCm39) T2832A probably benign Het
Brca2 A T 5: 150,459,977 (GRCm39) E417D possibly damaging Het
Ccdc88b T C 19: 6,831,268 (GRCm39) D558G possibly damaging Het
Ccdc88b T C 19: 6,833,213 (GRCm39) E278G probably damaging Het
Celsr1 G T 15: 85,917,286 (GRCm39) S229* probably null Het
Cenpf G T 1: 189,388,987 (GRCm39) T1615K probably damaging Het
Cep250 T C 2: 155,830,354 (GRCm39) probably null Het
Clec4d T C 6: 123,251,757 (GRCm39) F213S probably damaging Het
Clip4 G A 17: 72,117,884 (GRCm39) G310R probably damaging Het
Csmd1 G A 8: 15,962,430 (GRCm39) R3255W probably damaging Het
Ctsm T C 13: 61,687,612 (GRCm39) D82G probably damaging Het
Cyp26a1 A G 19: 37,686,790 (GRCm39) T81A probably damaging Het
Dld A G 12: 31,390,885 (GRCm39) V187A probably benign Het
Dmrt2 T A 19: 25,655,477 (GRCm39) Y359N probably benign Het
Dnah9 T C 11: 65,846,570 (GRCm39) N2914S probably benign Het
Dpyd A T 3: 118,553,303 (GRCm39) probably null Het
Fgl2 A C 5: 21,577,920 (GRCm39) Q69P probably damaging Het
Gadd45gip1 A T 8: 85,560,780 (GRCm39) I132F probably damaging Het
Gm15446 T C 5: 110,090,743 (GRCm39) C332R probably damaging Het
Gm15737 A T 6: 92,856,640 (GRCm39) E23V unknown Het
Gm5111 A G 6: 48,567,037 (GRCm39) H84R unknown Het
Golga3 G A 5: 110,355,619 (GRCm39) S991N probably benign Het
H2-M10.3 A G 17: 36,678,919 (GRCm39) Y50H probably damaging Het
Hivep2 C T 10: 14,005,621 (GRCm39) H740Y probably benign Het
Il18rap C T 1: 40,582,177 (GRCm39) T366M probably benign Het
Ints7 T A 1: 191,351,872 (GRCm39) S860R probably benign Het
Lipi T A 16: 75,362,461 (GRCm39) T217S possibly damaging Het
Lrrc2 G T 9: 110,791,722 (GRCm39) C158F probably benign Het
Lrrc30 T C 17: 67,938,854 (GRCm39) D242G probably benign Het
Map1a A T 2: 121,133,854 (GRCm39) M1557L probably benign Het
Matn2 A G 15: 34,423,924 (GRCm39) E594G probably damaging Het
Mfsd12 T C 10: 81,198,544 (GRCm39) L345P probably damaging Het
Mmp24 A G 2: 155,640,041 (GRCm39) R124G probably benign Het
Ngef T A 1: 87,406,797 (GRCm39) H240L unknown Het
Nmur1 T G 1: 86,315,256 (GRCm39) D203A probably benign Het
Ogfr T C 2: 180,232,850 (GRCm39) probably null Het
Or4k1 A T 14: 50,377,990 (GRCm39) Y35* probably null Het
Or52ac1 T A 7: 104,245,635 (GRCm39) Y251F probably damaging Het
Or5h19 A G 16: 58,856,263 (GRCm39) V279A probably benign Het
Osbpl10 G A 9: 115,061,211 (GRCm39) W588* probably null Het
Pask A T 1: 93,265,205 (GRCm39) S17T possibly damaging Het
Pfkfb3 C T 2: 11,491,084 (GRCm39) R170K probably damaging Het
Plec A G 15: 76,069,937 (GRCm39) C960R unknown Het
Pramel11 T A 4: 143,623,646 (GRCm39) N176I probably benign Het
R3hdm2 T G 10: 127,293,521 (GRCm39) S142A probably damaging Het
Rfx7 T C 9: 72,524,163 (GRCm39) L451P probably damaging Het
Rimbp2 T A 5: 128,883,552 (GRCm39) E76V probably damaging Het
Rock2 A G 12: 17,015,557 (GRCm39) N818S probably benign Het
Ryk A T 9: 102,758,854 (GRCm39) I248F possibly damaging Het
Setd2 A G 9: 110,378,168 (GRCm39) Q661R possibly damaging Het
Siae T C 9: 37,539,105 (GRCm39) V172A probably benign Het
Slc35f4 A G 14: 49,556,377 (GRCm39) S9P unknown Het
Smg1 T C 7: 117,795,179 (GRCm39) E456G unknown Het
Srgap3 C T 6: 112,743,865 (GRCm39) A458T probably damaging Het
Tgfbrap1 T A 1: 43,093,799 (GRCm39) R564S probably damaging Het
Usp15 A G 10: 123,004,143 (GRCm39) Y204H probably damaging Het
Usp35 A G 7: 96,962,276 (GRCm39) Y527H probably damaging Het
Usp8 T A 2: 126,600,524 (GRCm39) *1092K probably null Het
Vmn2r73 A T 7: 85,518,987 (GRCm39) M545K probably benign Het
Ylpm1 A T 12: 85,080,689 (GRCm39) probably null Het
Zscan22 G T 7: 12,641,130 (GRCm39) R458L probably damaging Het
Other mutations in Nt5c3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02142:Nt5c3 APN 6 56,863,670 (GRCm39) missense probably damaging 1.00
IGL02819:Nt5c3 APN 6 56,860,718 (GRCm39) missense probably damaging 1.00
R0426:Nt5c3 UTSW 6 56,860,797 (GRCm39) missense probably benign
R0523:Nt5c3 UTSW 6 56,860,666 (GRCm39) missense probably damaging 1.00
R0791:Nt5c3 UTSW 6 56,863,734 (GRCm39) missense probably benign 0.02
R0792:Nt5c3 UTSW 6 56,863,734 (GRCm39) missense probably benign 0.02
R1340:Nt5c3 UTSW 6 56,860,018 (GRCm39) missense probably benign 0.02
R3703:Nt5c3 UTSW 6 56,860,652 (GRCm39) unclassified probably benign
R5942:Nt5c3 UTSW 6 56,874,839 (GRCm39) splice site probably null
R6047:Nt5c3 UTSW 6 56,859,964 (GRCm39) missense probably damaging 0.99
R6894:Nt5c3 UTSW 6 56,859,958 (GRCm39) nonsense probably null
R7923:Nt5c3 UTSW 6 56,860,027 (GRCm39) missense probably benign 0.12
R8708:Nt5c3 UTSW 6 56,874,758 (GRCm39) critical splice donor site probably null
R8753:Nt5c3 UTSW 6 56,860,677 (GRCm39) missense probably damaging 1.00
R8937:Nt5c3 UTSW 6 56,861,701 (GRCm39) missense probably damaging 1.00
R9206:Nt5c3 UTSW 6 56,874,793 (GRCm39) start codon destroyed probably null 0.72
Predicted Primers PCR Primer
(F):5'- TCACAGGTTCCACACGTCTG -3'
(R):5'- CCTGTCCATGATAAGTCTGAGAG -3'

Sequencing Primer
(F):5'- ACACGTCTGAAGATCGTCTG -3'
(R):5'- CCAGCGATCATGATGCTGAG -3'
Posted On 2022-02-07