Incidental Mutation 'R5538:Slc19a3'
ID 434900
Institutional Source Beutler Lab
Gene Symbol Slc19a3
Ensembl Gene ENSMUSG00000038496
Gene Name solute carrier family 19, member 3
Synonyms ThTr2, A230084E24Rik
MMRRC Submission 043096-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.129) question?
Stock # R5538 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 82990244-83016169 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 83000282 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 245 (N245I)
Ref Sequence ENSEMBL: ENSMUSP00000126646 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000045560] [ENSMUST00000164473]
AlphaFold Q99PL8
Predicted Effect possibly damaging
Transcript: ENSMUST00000045560
AA Change: N245I

PolyPhen 2 Score 0.510 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000041683
Gene: ENSMUSG00000038496
AA Change: N245I

DomainStartEndE-ValueType
Pfam:Folate_carrier 11 435 1.4e-178 PFAM
Pfam:MFS_1 16 416 1.6e-17 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142805
Predicted Effect possibly damaging
Transcript: ENSMUST00000164473
AA Change: N245I

PolyPhen 2 Score 0.510 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000126646
Gene: ENSMUSG00000038496
AA Change: N245I

DomainStartEndE-ValueType
Pfam:Folate_carrier 11 435 1.3e-178 PFAM
Pfam:MFS_1 16 416 1.9e-17 PFAM
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.3%
  • 20x: 95.1%
Validation Efficiency 94% (73/78)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a ubiquitously expressed transmembrane thiamine transporter that lacks folate transport activity. Mutations in this gene cause biotin-responsive basal ganglia disease (BBGD); a recessive disorder manifested in childhood that progresses to chronic encephalopathy, dystonia, quadriparesis, and death if untreated. Patients with BBGD have bilateral necrosis in the head of the caudate nucleus and in the putamen. Administration of high doses of biotin in the early progression of the disorder eliminates pathological symptoms while delayed treatment results in residual paraparesis, mild mental retardation, or dystonia. Administration of thiamine is ineffective in the treatment of this disorder. Experiments have failed to show that this protein can transport biotin. Mutations in this gene also cause a Wernicke's-like encephalopathy.[provided by RefSeq, Jan 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit premature death within a year of age, impaired thiamin uptake, lethargy, cachexia, injured liver parenchyma, hepatic necrosis, liver and kidney inflammmation, and nephrosclerosis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrv1 C A 13: 81,581,808 (GRCm39) R4745S probably benign Het
Ank3 A G 10: 69,823,257 (GRCm39) E642G probably damaging Het
Arhgap11a G T 2: 113,667,875 (GRCm39) D375E probably benign Het
Arl8b C A 6: 108,760,297 (GRCm39) L28M probably damaging Het
Bbs2 G A 8: 94,816,391 (GRCm39) T157M probably damaging Het
C2cd3 T A 7: 100,104,700 (GRCm39) probably null Het
C6 T A 15: 4,844,311 (GRCm39) I911N possibly damaging Het
Cc2d2a T C 5: 43,852,518 (GRCm39) I365T possibly damaging Het
Cd46 T G 1: 194,750,478 (GRCm39) probably null Het
Ceacam3 A T 7: 16,892,346 (GRCm39) D363V probably damaging Het
Cep63 A T 9: 102,465,992 (GRCm39) L678* probably null Het
Clasrp A C 7: 19,318,707 (GRCm39) probably benign Het
Clk2 T A 3: 89,082,962 (GRCm39) Y412N probably damaging Het
Col24a1 C T 3: 144,998,882 (GRCm39) A5V probably damaging Het
Cox16 T C 12: 81,531,703 (GRCm39) N13D possibly damaging Het
Cybb C G X: 9,316,989 (GRCm39) D246H probably benign Het
Dhx32 A T 7: 133,324,946 (GRCm39) M437K probably benign Het
Dnm2 T C 9: 21,416,923 (GRCm39) F819L probably benign Het
Dpysl4 A G 7: 138,671,906 (GRCm39) T85A probably benign Het
Dspp A T 5: 104,323,096 (GRCm39) K80* probably null Het
Dync2h1 T C 9: 7,168,630 (GRCm39) probably benign Het
Ern1 A G 11: 106,312,727 (GRCm39) V218A possibly damaging Het
Fbn2 G A 18: 58,204,973 (GRCm39) R1157C probably benign Het
Fez1 T A 9: 36,780,172 (GRCm39) I323N probably damaging Het
Fmo9 T A 1: 166,501,198 (GRCm39) T199S probably benign Het
Fry T A 5: 150,419,313 (GRCm39) L915Q probably damaging Het
Gatd1 A G 7: 140,986,758 (GRCm39) probably benign Het
Gm10719 T C 9: 3,018,962 (GRCm39) L69S probably benign Het
Gnpda2 A T 5: 69,735,394 (GRCm39) H230Q probably damaging Het
Gramd1c T A 16: 43,802,455 (GRCm39) N652I probably damaging Het
H2-T13 T A 17: 36,392,178 (GRCm39) H178L probably benign Het
Hells T A 19: 38,942,096 (GRCm39) F462Y probably benign Het
Htr7 A G 19: 35,947,235 (GRCm39) F260L probably benign Het
Itsn1 C A 16: 91,580,990 (GRCm39) A23D probably damaging Het
Jak3 A G 8: 72,131,417 (GRCm39) D94G probably benign Het
Kctd16 T A 18: 40,390,319 (GRCm39) Y97* probably null Het
Kif20b A T 19: 34,930,364 (GRCm39) K25* probably null Het
Klf2 T C 8: 73,073,316 (GRCm39) L40P probably damaging Het
Kmt2a A G 9: 44,731,639 (GRCm39) probably benign Het
Kmt2d G A 15: 98,749,990 (GRCm39) probably benign Het
Lonrf1 T A 8: 36,690,178 (GRCm39) probably null Het
Lrp1b A T 2: 40,587,486 (GRCm39) I154K unknown Het
Mybpc1 T A 10: 88,381,891 (GRCm39) I600L possibly damaging Het
Npnt T C 3: 132,610,724 (GRCm39) N285S probably damaging Het
Or4c12b T A 2: 89,646,964 (GRCm39) F92Y probably damaging Het
Or51h5 A G 7: 102,577,728 (GRCm39) T298A probably damaging Het
Or6c69 T A 10: 129,747,871 (GRCm39) Y92F probably benign Het
Or6n1 T C 1: 173,917,544 (GRCm39) *313R probably null Het
Pcnx1 T C 12: 81,907,183 (GRCm39) V13A probably damaging Het
Phkb G A 8: 86,648,756 (GRCm39) V191I possibly damaging Het
Pnpla6 A G 8: 3,581,508 (GRCm39) M594V probably benign Het
Potefam3e A C 8: 19,799,430 (GRCm39) probably null Het
Prkdc A G 16: 15,469,333 (GRCm39) E146G probably damaging Het
Ror1 T C 4: 100,298,208 (GRCm39) M527T probably benign Het
Scnm1 A G 3: 95,037,066 (GRCm39) probably benign Het
Skint11 A T 4: 114,088,959 (GRCm39) N251I probably damaging Het
Slc1a3 A T 15: 8,675,188 (GRCm39) D272E probably damaging Het
Smok2b T A 17: 13,454,440 (GRCm39) V200D possibly damaging Het
Sspo T C 6: 48,429,112 (GRCm39) Y417H probably damaging Het
Stk11ip C A 1: 75,504,979 (GRCm39) S388R probably damaging Het
Svep1 T C 4: 58,049,282 (GRCm39) probably null Het
Sytl2 A G 7: 90,038,114 (GRCm39) I525V probably benign Het
Tie1 T C 4: 118,343,390 (GRCm39) N158D probably benign Het
Tle2 T C 10: 81,416,418 (GRCm39) L180P probably damaging Het
Txlnb T C 10: 17,714,657 (GRCm39) L363P probably damaging Het
Upk3b C G 5: 136,072,890 (GRCm39) A258G probably benign Het
Usp32 A T 11: 84,908,612 (GRCm39) D1031E possibly damaging Het
Vmn2r116 C T 17: 23,620,041 (GRCm39) L592F probably benign Het
Zfp607b A G 7: 27,402,294 (GRCm39) H250R probably damaging Het
Other mutations in Slc19a3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03066:Slc19a3 APN 1 82,992,557 (GRCm39) missense probably damaging 0.99
tag UTSW 1 83,003,981 (GRCm39) missense probably damaging 1.00
R0437:Slc19a3 UTSW 1 83,000,286 (GRCm39) missense probably benign 0.00
R0526:Slc19a3 UTSW 1 83,000,454 (GRCm39) missense probably damaging 1.00
R1160:Slc19a3 UTSW 1 83,000,413 (GRCm39) missense possibly damaging 0.85
R1306:Slc19a3 UTSW 1 83,000,483 (GRCm39) missense probably damaging 1.00
R1832:Slc19a3 UTSW 1 83,000,468 (GRCm39) missense probably damaging 0.99
R1938:Slc19a3 UTSW 1 82,997,089 (GRCm39) missense possibly damaging 0.76
R1961:Slc19a3 UTSW 1 83,000,519 (GRCm39) missense probably benign 0.00
R2058:Slc19a3 UTSW 1 82,992,512 (GRCm39) missense probably damaging 0.98
R2200:Slc19a3 UTSW 1 83,000,664 (GRCm39) missense probably damaging 0.96
R2245:Slc19a3 UTSW 1 82,991,691 (GRCm39) missense possibly damaging 0.84
R2261:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R2404:Slc19a3 UTSW 1 83,000,756 (GRCm39) missense probably benign 0.16
R3891:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R3892:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R3907:Slc19a3 UTSW 1 82,992,534 (GRCm39) missense possibly damaging 0.76
R3912:Slc19a3 UTSW 1 83,000,424 (GRCm39) missense probably benign 0.09
R3922:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R3923:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R3961:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R4083:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R4106:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R4107:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R4109:Slc19a3 UTSW 1 83,000,678 (GRCm39) missense probably damaging 1.00
R4667:Slc19a3 UTSW 1 83,000,520 (GRCm39) missense probably benign
R4768:Slc19a3 UTSW 1 83,000,834 (GRCm39) missense probably damaging 1.00
R4769:Slc19a3 UTSW 1 82,997,062 (GRCm39) missense probably damaging 1.00
R5001:Slc19a3 UTSW 1 83,000,341 (GRCm39) missense probably benign 0.33
R5588:Slc19a3 UTSW 1 83,000,776 (GRCm39) nonsense probably null
R6143:Slc19a3 UTSW 1 83,004,060 (GRCm39) missense probably benign 0.00
R6546:Slc19a3 UTSW 1 83,004,081 (GRCm39) missense probably benign 0.02
R6547:Slc19a3 UTSW 1 83,000,621 (GRCm39) missense probably damaging 1.00
R7059:Slc19a3 UTSW 1 83,000,090 (GRCm39) missense probably damaging 1.00
R7497:Slc19a3 UTSW 1 82,991,649 (GRCm39) missense probably damaging 1.00
R7509:Slc19a3 UTSW 1 83,003,981 (GRCm39) missense probably damaging 1.00
R7584:Slc19a3 UTSW 1 83,000,469 (GRCm39) missense possibly damaging 0.79
R7810:Slc19a3 UTSW 1 82,997,162 (GRCm39) missense probably benign 0.02
R8150:Slc19a3 UTSW 1 83,000,216 (GRCm39) missense probably damaging 1.00
R8412:Slc19a3 UTSW 1 82,992,533 (GRCm39) missense probably damaging 0.97
R8970:Slc19a3 UTSW 1 83,000,822 (GRCm39) missense probably damaging 1.00
R9314:Slc19a3 UTSW 1 83,000,094 (GRCm39) missense possibly damaging 0.62
R9671:Slc19a3 UTSW 1 83,000,297 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TGCCTTGTGTTCCCATAGGAC -3'
(R):5'- GACGAACCTGCCATACTCTAG -3'

Sequencing Primer
(F):5'- TGTGTTCCCATAGGACTTGAAC -3'
(R):5'- ATATATCCTTGGCCTGTGTCTCTGTG -3'
Posted On 2016-10-24