Incidental Mutation 'R4878:Slc25a39'
ID 375075
Institutional Source Beutler Lab
Gene Symbol Slc25a39
Ensembl Gene ENSMUSG00000018677
Gene Name solute carrier family 25, member 39
Synonyms D11Ertd333e, 3010027G13Rik
MMRRC Submission 042487-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.883) question?
Stock # R4878 (G1)
Quality Score 183
Status Validated
Chromosome 11
Chromosomal Location 102293811-102298772 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 102294501 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Cysteine at position 308 (R308C)
Ref Sequence ENSEMBL: ENSMUSP00000018821 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006750] [ENSMUST00000018821] [ENSMUST00000107098] [ENSMUST00000107102] [ENSMUST00000107103] [ENSMUST00000107105] [ENSMUST00000124755] [ENSMUST00000130436] [ENSMUST00000134669] [ENSMUST00000142097] [ENSMUST00000154001] [ENSMUST00000149777] [ENSMUST00000155104]
AlphaFold Q9D8K8
Predicted Effect probably benign
Transcript: ENSMUST00000006750
SMART Domains Protein: ENSMUSP00000006750
Gene: ENSMUSG00000006575

DomainStartEndE-ValueType
RUN 125 187 2.34e-19 SMART
coiled coil region 267 322 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000018821
AA Change: R308C

PolyPhen 2 Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000018821
Gene: ENSMUSG00000018677
AA Change: R308C

DomainStartEndE-ValueType
Pfam:Mito_carr 7 156 6.9e-23 PFAM
Pfam:Mito_carr 158 247 6.1e-19 PFAM
Pfam:Mito_carr 251 352 1.1e-21 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000107098
AA Change: R300C

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000102715
Gene: ENSMUSG00000018677
AA Change: R300C

DomainStartEndE-ValueType
Pfam:Mito_carr 7 148 1.4e-21 PFAM
Pfam:Mito_carr 150 240 3.7e-19 PFAM
Pfam:Mito_carr 243 344 4.6e-21 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000107102
SMART Domains Protein: ENSMUSP00000102719
Gene: ENSMUSG00000006575

DomainStartEndE-ValueType
RUN 125 187 2.34e-19 SMART
coiled coil region 267 322 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000107103
SMART Domains Protein: ENSMUSP00000102720
Gene: ENSMUSG00000006575

DomainStartEndE-ValueType
RUN 120 182 2.34e-19 SMART
coiled coil region 262 317 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000107105
SMART Domains Protein: ENSMUSP00000102722
Gene: ENSMUSG00000006575

DomainStartEndE-ValueType
RUN 125 187 2.34e-19 SMART
coiled coil region 267 320 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146330
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131219
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142157
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128331
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123688
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132876
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141535
Predicted Effect probably benign
Transcript: ENSMUST00000124755
SMART Domains Protein: ENSMUSP00000120021
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 7 71 1.3e-9 PFAM
Pfam:Mito_carr 92 152 9.7e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000128825
SMART Domains Protein: ENSMUSP00000121790
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 35 77 6.5e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000130436
SMART Domains Protein: ENSMUSP00000115087
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 7 70 1.8e-9 PFAM
Pfam:Mito_carr 92 156 5.7e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000134669
SMART Domains Protein: ENSMUSP00000114481
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 7 69 1.9e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000142097
SMART Domains Protein: ENSMUSP00000114365
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 7 63 2e-10 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150982
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183859
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153395
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147860
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147160
Predicted Effect probably benign
Transcript: ENSMUST00000154001
SMART Domains Protein: ENSMUSP00000116336
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 7 70 3.1e-10 PFAM
Pfam:Mito_carr 92 156 9.8e-16 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000149777
SMART Domains Protein: ENSMUSP00000115365
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 7 70 2.7e-9 PFAM
Pfam:Mito_carr 92 156 8.7e-15 PFAM
Pfam:Mito_carr 158 220 6.5e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000155104
SMART Domains Protein: ENSMUSP00000115445
Gene: ENSMUSG00000018677

DomainStartEndE-ValueType
Pfam:Mito_carr 7 69 3.7e-9 PFAM
Pfam:Mito_carr 92 156 1.2e-14 PFAM
Pfam:Mito_carr 158 248 5.4e-21 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.8%
Validation Efficiency 96% (70/73)
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 SLC25 transporter or mitochondrial carrier family of proteins. Members of this family are encoded by the nuclear genome while their protein products are usually embedded in the inner mitochondrial membrane and exhibit wide-ranging substrate specificity. Although the encoded protein is currently considered an orphan transporter, this protein is related to other carriers known to transport amino acids. This protein may play a role in iron homeostasis. [provided by RefSeq, Mar 2016]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl4 C A 4: 144,340,415 (GRCm39) H47N possibly damaging Het
Adgrg3 A T 8: 95,761,714 (GRCm39) N159I possibly damaging Het
Agrn A T 4: 156,255,302 (GRCm39) L1449Q probably damaging Het
Anks6 C T 4: 47,030,795 (GRCm39) G601S probably damaging Het
Atg2a A T 19: 6,300,274 (GRCm39) E694V probably damaging Het
Ccndbp1 T A 2: 120,845,172 (GRCm39) L363* probably null Het
Cdh16 A T 8: 105,344,696 (GRCm39) D478E probably damaging Het
Cep295 A T 9: 15,246,252 (GRCm39) W735R probably benign Het
Cnnm2 C T 19: 46,847,522 (GRCm39) P682S probably benign Het
Daam2 C A 17: 49,767,738 (GRCm39) R951L probably damaging Het
Dmxl1 T A 18: 49,984,543 (GRCm39) F180I probably damaging Het
Dnajc6 T C 4: 101,456,231 (GRCm39) probably benign Het
Efemp2 A T 19: 5,530,789 (GRCm39) probably benign Het
Emilin1 A G 5: 31,074,410 (GRCm39) D217G probably benign Het
Enpep A T 3: 129,070,420 (GRCm39) M829K probably benign Het
Epb41l4a A G 18: 33,931,625 (GRCm39) V623A probably damaging Het
Erlin2 T A 8: 27,517,194 (GRCm39) probably null Het
Fbln2 T C 6: 91,233,977 (GRCm39) probably null Het
Gga3 A T 11: 115,482,147 (GRCm39) I157N probably damaging Het
Gtpbp6 C T 5: 110,255,177 (GRCm39) probably benign Het
Hps4 T C 5: 112,523,234 (GRCm39) V584A probably benign Het
Ighv1-50 T C 12: 115,083,567 (GRCm39) Y51C probably benign Het
Kif13b T C 14: 65,043,603 (GRCm39) L1801P probably benign Het
Kif16b T C 2: 142,689,923 (GRCm39) I330V probably damaging Het
Klb A T 5: 65,505,833 (GRCm39) R27W probably damaging Het
Lrif1 A T 3: 106,642,956 (GRCm39) K169M probably damaging Het
Lrrc37 A G 11: 103,508,717 (GRCm39) probably benign Het
Met A G 6: 17,549,058 (GRCm39) D970G probably damaging Het
Mical3 A T 6: 120,946,348 (GRCm39) M1051K possibly damaging Het
Mios A G 6: 8,215,094 (GRCm39) N97D probably benign Het
Msh5 G A 17: 35,257,432 (GRCm39) R321C probably damaging Het
Mybpc1 T C 10: 88,387,292 (GRCm39) Q473R possibly damaging Het
Ncoa1 C T 12: 4,325,004 (GRCm39) G970D probably damaging Het
Neb T C 2: 52,109,406 (GRCm39) Y232C probably damaging Het
Nefh A G 11: 4,891,333 (GRCm39) S429P probably damaging Het
Notch3 C T 17: 32,366,059 (GRCm39) G1014D probably damaging Het
Nup107 A T 10: 117,587,323 (GRCm39) C859S probably benign Het
Or1d2 T C 11: 74,255,674 (GRCm39) Y60H probably damaging Het
Or2n1d T G 17: 38,646,518 (GRCm39) F157V probably benign Het
Or5m3b A G 2: 85,871,799 (GRCm39) I47V probably benign Het
Otud7b T A 3: 96,043,821 (GRCm39) probably benign Het
Pde1a A T 2: 79,708,483 (GRCm39) S312T probably benign Het
Piwil1 G T 5: 128,818,045 (GRCm39) R94L probably damaging Het
Pnma2 G A 14: 67,154,503 (GRCm39) W309* probably null Het
Ppef2 A C 5: 92,376,599 (GRCm39) probably null Het
Rabac1 T A 7: 24,669,392 (GRCm39) Q212L possibly damaging Het
Rad51 T C 2: 118,950,973 (GRCm39) probably benign Het
Rbm48 A T 5: 3,641,853 (GRCm39) probably benign Het
Rft1 C T 14: 30,399,761 (GRCm39) S315L probably benign Het
Rgs13 C T 1: 144,047,217 (GRCm39) M1I probably null Het
Rhbg A C 3: 88,154,760 (GRCm39) S215A probably benign Het
Rufy2 A T 10: 62,837,990 (GRCm39) N379I probably damaging Het
Slc17a1 T C 13: 24,064,637 (GRCm39) L367P probably damaging Het
Smo A G 6: 29,753,570 (GRCm39) T149A probably benign Het
Sqle A G 15: 59,187,934 (GRCm39) K81E probably benign Het
Tfpi A G 2: 84,282,899 (GRCm39) probably null Het
Tnk2 A G 16: 32,498,448 (GRCm39) D572G probably damaging Het
Ubr5 A T 15: 38,006,808 (GRCm39) M1149K probably benign Het
Utrn T A 10: 12,603,502 (GRCm39) Q626L probably damaging Het
Virma T A 4: 11,544,971 (GRCm39) H1643Q probably damaging Het
Wnt3 G T 11: 103,699,031 (GRCm39) G46C possibly damaging Het
Zkscan7 G T 9: 122,719,865 (GRCm39) G184* probably null Het
Other mutations in Slc25a39
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01451:Slc25a39 APN 11 102,295,726 (GRCm39) missense probably damaging 1.00
IGL01601:Slc25a39 APN 11 102,296,544 (GRCm39) missense probably damaging 1.00
IGL02734:Slc25a39 APN 11 102,295,349 (GRCm39) missense probably benign 0.03
IGL03382:Slc25a39 APN 11 102,297,030 (GRCm39) critical splice donor site probably null
R0218:Slc25a39 UTSW 11 102,297,056 (GRCm39) missense probably benign 0.00
R0359:Slc25a39 UTSW 11 102,297,395 (GRCm39) missense possibly damaging 0.88
R0939:Slc25a39 UTSW 11 102,295,877 (GRCm39) missense probably damaging 1.00
R1702:Slc25a39 UTSW 11 102,297,452 (GRCm39) missense possibly damaging 0.68
R2047:Slc25a39 UTSW 11 102,296,657 (GRCm39) splice site probably benign
R2367:Slc25a39 UTSW 11 102,294,477 (GRCm39) missense possibly damaging 0.52
R4018:Slc25a39 UTSW 11 102,295,850 (GRCm39) missense probably damaging 1.00
R4755:Slc25a39 UTSW 11 102,297,492 (GRCm39) start gained probably benign
R5629:Slc25a39 UTSW 11 102,295,719 (GRCm39) nonsense probably null
R5704:Slc25a39 UTSW 11 102,294,220 (GRCm39) unclassified probably benign
R6092:Slc25a39 UTSW 11 102,295,719 (GRCm39) nonsense probably null
R6502:Slc25a39 UTSW 11 102,295,286 (GRCm39) missense probably damaging 0.99
R6955:Slc25a39 UTSW 11 102,294,344 (GRCm39) missense probably benign 0.00
R6980:Slc25a39 UTSW 11 102,296,601 (GRCm39) missense probably damaging 0.99
R8717:Slc25a39 UTSW 11 102,294,620 (GRCm39) missense probably benign 0.00
R8990:Slc25a39 UTSW 11 102,295,895 (GRCm39) missense possibly damaging 0.92
R9574:Slc25a39 UTSW 11 102,295,390 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- AGCCTCTGGAAGAAGCTTTTG -3'
(R):5'- ACCCTTCGATGTGGTGAAG -3'

Sequencing Primer
(F):5'- TGCCAAACTCGTAAGTGCTG -3'
(R):5'- AGACACAGCGACAGATGTC -3'
Posted On 2016-03-17