Incidental Mutation 'R0791:Nt5c3'
ID 82389
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 038971-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.194) question?
Stock # R0791 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 56859385-56900917 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 56863734 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 149 (T149A)
Ref Sequence ENSEMBL: ENSMUSP00000031793 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031793] [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: T149A

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000031793
Gene: ENSMUSG00000029780
AA Change: T149A

DomainStartEndE-ValueType
transmembrane domain 9 31 N/A INTRINSIC
Pfam:UMPH-1 86 331 5.6e-119 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000101367
AA Change: T115A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000098918
Gene: ENSMUSG00000029780
AA Change: T115A

DomainStartEndE-ValueType
Pfam:UMPH-1 52 297 2.1e-118 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126137
Predicted Effect probably benign
Transcript: ENSMUST00000135558
SMART Domains Protein: ENSMUSP00000145230
Gene: ENSMUSG00000029780

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138647
Predicted Effect probably benign
Transcript: ENSMUST00000152447
Predicted Effect unknown
Transcript: ENSMUST00000205087
AA Change: T87A
Meta Mutation Damage Score 0.0870 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.3%
  • 20x: 94.8%
Validation Efficiency 98% (59/60)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ahnak G A 19: 8,994,098 (GRCm39) M5127I probably benign Het
Akr1c13 T C 13: 4,244,111 (GRCm39) Y55H probably damaging Het
Armh3 A T 19: 45,922,307 (GRCm39) probably null Het
Atp2b2 C T 6: 113,750,349 (GRCm39) R625H probably damaging Het
Bpifb2 T C 2: 153,720,439 (GRCm39) V66A probably benign Het
Ccdc33 T C 9: 57,936,046 (GRCm39) T950A possibly damaging Het
Ceacam19 A T 7: 19,616,557 (GRCm39) probably null Het
Cenpn T A 8: 117,667,559 (GRCm39) probably benign Het
Ces1f A T 8: 93,998,517 (GRCm39) Y160N possibly damaging Het
Clca3a1 A C 3: 144,710,615 (GRCm39) S863A probably benign Het
Cntrl T A 2: 35,045,291 (GRCm39) I781K possibly damaging Het
Dock4 C T 12: 40,754,480 (GRCm39) R490W probably damaging Het
Evpl T A 11: 116,118,549 (GRCm39) Q686L probably damaging Het
Fbxw10 A G 11: 62,738,282 (GRCm39) S59G probably benign Het
Glb1l2 A G 9: 26,681,047 (GRCm39) V218A possibly damaging Het
Gpatch1 A T 7: 34,980,801 (GRCm39) probably benign Het
Grin2c G A 11: 115,141,472 (GRCm39) P882L probably damaging Het
H2-Ob C A 17: 34,461,588 (GRCm39) T109N probably damaging Het
Ipo8 A G 6: 148,723,225 (GRCm39) V64A possibly damaging Het
Jpt2 C A 17: 25,167,647 (GRCm39) A101S probably benign Het
Lamc1 C A 1: 153,110,326 (GRCm39) Q1116H possibly damaging Het
Lamc1 T C 1: 153,110,358 (GRCm39) S1106G probably benign Het
Lamc1 T G 1: 153,110,341 (GRCm39) Q1111H probably damaging Het
Large1 A G 8: 73,775,107 (GRCm39) probably benign Het
Lig4 A T 8: 10,023,012 (GRCm39) V256E possibly damaging Het
Mpz C A 1: 170,986,343 (GRCm39) Q86K possibly damaging Het
Mrps24 A G 11: 5,654,684 (GRCm39) V90A possibly damaging Het
Mtdh A G 15: 34,116,528 (GRCm39) probably benign Het
Mtor T C 4: 148,547,367 (GRCm39) V450A probably benign Het
Mycbpap A G 11: 94,402,449 (GRCm39) probably null Het
Myo6 T A 9: 80,169,656 (GRCm39) probably benign Het
Myom1 A T 17: 71,428,131 (GRCm39) I1450F probably damaging Het
Nbas T A 12: 13,532,634 (GRCm39) S1781T probably benign Het
Nedd1 T C 10: 92,555,476 (GRCm39) E3G probably damaging Het
Or5p56 A G 7: 107,589,740 (GRCm39) H56R probably benign Het
Osbp2 G A 11: 3,661,882 (GRCm39) probably benign Het
Paip1 T C 13: 119,566,854 (GRCm39) S54P possibly damaging Het
Pole2 G A 12: 69,254,703 (GRCm39) L381F probably benign Het
Prdm14 G T 1: 13,195,968 (GRCm39) A31E probably benign Het
Ptpn14 C T 1: 189,568,637 (GRCm39) probably benign Het
Rims2 A G 15: 39,543,021 (GRCm39) probably benign Het
Rnf20 A G 4: 49,638,197 (GRCm39) N103S possibly damaging Het
Sema3g T A 14: 30,942,861 (GRCm39) probably benign Het
Slc30a6 T C 17: 74,722,640 (GRCm39) S236P possibly damaging Het
Slc5a1 T C 5: 33,315,421 (GRCm39) probably benign Het
Snx25 A T 8: 46,577,119 (GRCm39) M1K probably null Het
Synpo2 A G 3: 122,906,835 (GRCm39) V827A probably benign Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Trak2 A T 1: 58,942,820 (GRCm39) M862K probably benign Het
Trim42 A T 9: 97,247,732 (GRCm39) H321Q probably damaging Het
Twnk T C 19: 44,998,693 (GRCm39) probably benign Het
Tymp T C 15: 89,259,021 (GRCm39) K221R probably damaging Het
Uaca C A 9: 60,779,341 (GRCm39) Q1243K possibly damaging Het
Vwa8 T C 14: 79,232,016 (GRCm39) probably benign Het
Wnt4 C T 4: 137,016,594 (GRCm39) R83W probably damaging Het
Zfp820 T C 17: 22,038,509 (GRCm39) D273G probably benign Het
Zfp974 A T 7: 27,609,510 (GRCm39) Y738* probably null Het
Zkscan4 A C 13: 21,668,081 (GRCm39) E177D probably benign 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
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
R9198:Nt5c3 UTSW 6 56,859,955 (GRCm39) missense probably benign 0.03
R9206:Nt5c3 UTSW 6 56,874,793 (GRCm39) start codon destroyed probably null 0.72
Predicted Primers PCR Primer
(F):5'- TTCCAATGCACTTACCACCTGTAGC -3'
(R):5'- ACCATCACGAATTTAAGCGCCTCAG -3'

Sequencing Primer
(F):5'- tgccacctttccagccc -3'
(R):5'- TTAAGCGCCTCAGTGTCAAAG -3'
Posted On 2013-11-08