Incidental Mutation 'R0097:Slc3a1'
ID 41179
Institutional Source Beutler Lab
Gene Symbol Slc3a1
Ensembl Gene ENSMUSG00000024131
Gene Name solute carrier family 3, member 1
Synonyms NTAA, D2H
MMRRC Submission 038383-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0097 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 85335804-85371664 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 85340288 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 237 (I237F)
Ref Sequence ENSEMBL: ENSMUSP00000024944 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000024944]
AlphaFold Q91WV7
Predicted Effect probably damaging
Transcript: ENSMUST00000024944
AA Change: I237F

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000024944
Gene: ENSMUSG00000024131
AA Change: I237F

DomainStartEndE-ValueType
transmembrane domain 87 109 N/A INTRINSIC
Aamy 124 504 6.7e-110 SMART
Meta Mutation Damage Score 0.8385 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.2%
Validation Efficiency 100% (57/57)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associated with cystinuria. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mutation of this locus results in renal absorption defects and cystine urolithiasis. Homozygous mutant mice serve as a mouse model for human cystinuria type I. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700006A11Rik A T 3: 124,206,129 (GRCm39) I353K probably benign Het
Albfm1 T A 5: 90,732,795 (GRCm39) S535R probably benign Het
Arfgap2 T A 2: 91,105,160 (GRCm39) V422E probably benign Het
Baz1b T C 5: 135,227,113 (GRCm39) S105P probably benign Het
Bbs10 T C 10: 111,134,705 (GRCm39) V41A probably damaging Het
Cacna1s T A 1: 136,028,360 (GRCm39) M899K possibly damaging Het
Ccnd2 G A 6: 127,123,015 (GRCm39) A180V probably benign Het
Ciao3 T C 17: 25,995,976 (GRCm39) S67P possibly damaging Het
Cldnd1 A G 16: 58,550,078 (GRCm39) N87S possibly damaging Het
Cyp2c54 T A 19: 40,036,102 (GRCm39) probably benign Het
Cyp2c54 G T 19: 40,036,103 (GRCm39) probably benign Het
Dab2ip G A 2: 35,608,928 (GRCm39) V629M possibly damaging Het
Ddx41 A T 13: 55,683,691 (GRCm39) probably benign Het
Dmrta1 A T 4: 89,577,109 (GRCm39) R188S probably benign Het
Eml3 T A 19: 8,914,015 (GRCm39) F465L probably benign Het
Gm9938 T A 19: 23,701,828 (GRCm39) probably benign Het
Gpr87 G A 3: 59,086,506 (GRCm39) T333I probably damaging Het
Krt81 C A 15: 101,361,508 (GRCm39) R24L possibly damaging Het
Llgl2 T A 11: 115,735,323 (GRCm39) Y59* probably null Het
Lzic A G 4: 149,572,533 (GRCm39) E41G probably damaging Het
Mprip T A 11: 59,649,317 (GRCm39) L1007Q possibly damaging Het
Mtfr2 T A 10: 20,224,122 (GRCm39) S19T probably damaging Het
Mycbp2 A T 14: 103,393,198 (GRCm39) M3121K probably damaging Het
Myocd T A 11: 65,069,840 (GRCm39) M667L possibly damaging Het
Ncam2 A G 16: 81,314,425 (GRCm39) D467G probably damaging Het
Neb T C 2: 52,094,906 (GRCm39) N4882S probably damaging Het
Neu2 A G 1: 87,525,188 (GRCm39) D391G probably benign Het
Nol4 C A 18: 22,852,198 (GRCm39) A456S probably benign Het
Or5m13 T C 2: 85,749,184 (GRCm39) V305A probably benign Het
Padi6 C T 4: 140,458,268 (GRCm39) V513M probably benign Het
Pign G A 1: 105,515,701 (GRCm39) probably benign Het
Plpp2 T C 10: 79,366,371 (GRCm39) E91G possibly damaging Het
Pnp T A 14: 51,188,873 (GRCm39) V222D probably damaging Het
Pnp2 C T 14: 51,200,958 (GRCm39) R148C probably benign Het
Pramel30 T C 4: 144,057,857 (GRCm39) S155P probably benign Het
Prss38 A G 11: 59,266,434 (GRCm39) L8S possibly damaging Het
Rab5b A T 10: 128,518,809 (GRCm39) F108I probably damaging Het
Rbbp5 T A 1: 132,418,227 (GRCm39) H15Q possibly damaging Het
Rhox4f A C X: 36,789,122 (GRCm39) V15G probably benign Het
Rsl1 A C 13: 67,329,966 (GRCm39) Q138P probably damaging Het
Ryr3 T C 2: 112,630,400 (GRCm39) D2157G probably damaging Het
Secisbp2l T C 2: 125,613,376 (GRCm39) D206G probably damaging Het
Sh3pxd2b T A 11: 32,353,978 (GRCm39) I182N probably damaging Het
Svs3b T C 2: 164,098,159 (GRCm39) E54G probably damaging Het
T A T 17: 8,658,733 (GRCm39) probably benign Het
Tenm4 A T 7: 96,542,133 (GRCm39) D1882V probably damaging Het
Tgfbr1 T A 4: 47,403,451 (GRCm39) L283* probably null Het
Tppp3 C T 8: 106,194,554 (GRCm39) A149T probably benign Het
Ubp1 T C 9: 113,802,575 (GRCm39) probably benign Het
Ushbp1 C T 8: 71,843,357 (GRCm39) C314Y probably damaging Het
Vav2 A T 2: 27,189,374 (GRCm39) probably benign Het
Vmn1r228 T C 17: 20,996,625 (GRCm39) M298V probably benign Het
Zmpste24 A T 4: 120,952,740 (GRCm39) probably benign Het
Other mutations in Slc3a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00321:Slc3a1 APN 17 85,368,261 (GRCm39) missense probably damaging 1.00
IGL00647:Slc3a1 APN 17 85,371,233 (GRCm39) missense probably damaging 0.99
IGL02755:Slc3a1 APN 17 85,344,605 (GRCm39) missense probably damaging 1.00
IGL03079:Slc3a1 APN 17 85,367,251 (GRCm39) nonsense probably null
IGL03390:Slc3a1 APN 17 85,340,205 (GRCm39) missense probably damaging 1.00
R0031:Slc3a1 UTSW 17 85,340,274 (GRCm39) missense probably damaging 1.00
R0097:Slc3a1 UTSW 17 85,340,288 (GRCm39) missense probably damaging 0.99
R0363:Slc3a1 UTSW 17 85,340,273 (GRCm39) missense probably damaging 1.00
R0531:Slc3a1 UTSW 17 85,336,077 (GRCm39) missense possibly damaging 0.66
R0636:Slc3a1 UTSW 17 85,340,222 (GRCm39) missense possibly damaging 0.78
R0662:Slc3a1 UTSW 17 85,344,635 (GRCm39) missense possibly damaging 0.89
R0725:Slc3a1 UTSW 17 85,368,263 (GRCm39) nonsense probably null
R0930:Slc3a1 UTSW 17 85,367,171 (GRCm39) missense probably benign 0.01
R1141:Slc3a1 UTSW 17 85,336,077 (GRCm39) missense possibly damaging 0.66
R2025:Slc3a1 UTSW 17 85,340,273 (GRCm39) missense probably damaging 1.00
R2271:Slc3a1 UTSW 17 85,371,220 (GRCm39) missense probably benign 0.00
R4196:Slc3a1 UTSW 17 85,368,306 (GRCm39) missense probably damaging 1.00
R4740:Slc3a1 UTSW 17 85,354,181 (GRCm39) missense probably benign 0.00
R5049:Slc3a1 UTSW 17 85,340,273 (GRCm39) missense probably damaging 1.00
R5255:Slc3a1 UTSW 17 85,335,881 (GRCm39) splice site probably null
R5261:Slc3a1 UTSW 17 85,359,403 (GRCm39) missense probably damaging 1.00
R5601:Slc3a1 UTSW 17 85,340,319 (GRCm39) missense probably benign 0.00
R5853:Slc3a1 UTSW 17 85,340,008 (GRCm39) missense probably damaging 1.00
R6063:Slc3a1 UTSW 17 85,335,951 (GRCm39) missense probably benign
R6332:Slc3a1 UTSW 17 85,335,860 (GRCm39) start codon destroyed probably damaging 0.99
R7162:Slc3a1 UTSW 17 85,371,442 (GRCm39) nonsense probably null
R7269:Slc3a1 UTSW 17 85,339,873 (GRCm39) missense probably damaging 1.00
R7516:Slc3a1 UTSW 17 85,371,190 (GRCm39) missense probably damaging 1.00
R7807:Slc3a1 UTSW 17 85,371,371 (GRCm39) missense probably benign 0.09
R8269:Slc3a1 UTSW 17 85,339,982 (GRCm39) missense probably benign 0.00
R8351:Slc3a1 UTSW 17 85,335,924 (GRCm39) missense possibly damaging 0.68
R8361:Slc3a1 UTSW 17 85,344,640 (GRCm39) nonsense probably null
R8451:Slc3a1 UTSW 17 85,335,924 (GRCm39) missense possibly damaging 0.68
R8543:Slc3a1 UTSW 17 85,335,925 (GRCm39) missense probably benign 0.42
R9764:Slc3a1 UTSW 17 85,371,419 (GRCm39) missense probably damaging 1.00
X0020:Slc3a1 UTSW 17 85,336,236 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAATTTGGTTGCTGCCATCCATGAC -3'
(R):5'- TACCTTTGCCCAGGAGACCTATGC -3'

Sequencing Primer
(F):5'- GCTGCCATCCATGACAAAGG -3'
(R):5'- TACAGCCGTTCAACAATGATG -3'
Posted On 2013-05-23