Incidental Mutation 'R1517:Tnfsf13'
ID 167113
Institutional Source Beutler Lab
Gene Symbol Tnfsf13
Ensembl Gene ENSMUSG00000089669
Gene Name tumor necrosis factor (ligand) superfamily, member 13
Synonyms 2310026N09Rik, TRDL1, TALL2, APRIL
MMRRC Submission 039563-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1517 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 69573672-69576610 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 69575564 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 246 (S246G)
Ref Sequence ENSEMBL: ENSMUSP00000133951 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005336] [ENSMUST00000018896] [ENSMUST00000066760] [ENSMUST00000108648] [ENSMUST00000108649] [ENSMUST00000180587] [ENSMUST00000174159] [ENSMUST00000181261] [ENSMUST00000181810]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000005336
SMART Domains Protein: ENSMUSP00000005336
Gene: ENSMUSG00000005204

DomainStartEndE-ValueType
low complexity region 25 40 N/A INTRINSIC
low complexity region 42 53 N/A INTRINSIC
low complexity region 74 86 N/A INTRINSIC
low complexity region 118 131 N/A INTRINSIC
low complexity region 183 195 N/A INTRINSIC
Pfam:Peptidase_C48 394 566 4.9e-49 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000018896
AA Change: S78G

PolyPhen 2 Score 0.190 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000018896
Gene: ENSMUSG00000089669
AA Change: S78G

DomainStartEndE-ValueType
Blast:TNF 39 87 1e-22 BLAST
low complexity region 101 106 N/A INTRINSIC
TNF 107 240 7.41e-3 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000066760
SMART Domains Protein: ENSMUSP00000066581
Gene: ENSMUSG00000005204

DomainStartEndE-ValueType
low complexity region 25 40 N/A INTRINSIC
low complexity region 42 53 N/A INTRINSIC
low complexity region 74 86 N/A INTRINSIC
low complexity region 118 131 N/A INTRINSIC
low complexity region 183 195 N/A INTRINSIC
Pfam:Peptidase_C48 394 566 4.9e-49 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108648
AA Change: S78G

PolyPhen 2 Score 0.190 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000104288
Gene: ENSMUSG00000089669
AA Change: S78G

DomainStartEndE-ValueType
Blast:TNF 39 87 1e-22 BLAST
TNF 97 224 6.21e-2 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000108649
AA Change: S167G

PolyPhen 2 Score 0.120 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000104289
Gene: ENSMUSG00000018752
AA Change: S167G

DomainStartEndE-ValueType
low complexity region 4 14 N/A INTRINSIC
transmembrane domain 20 42 N/A INTRINSIC
low complexity region 90 109 N/A INTRINSIC
PDB:4HT1|T 110 166 1e-31 PDB
Blast:TNF 117 166 4e-27 BLAST
low complexity region 190 195 N/A INTRINSIC
TNF 196 329 7.41e-3 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140371
Predicted Effect possibly damaging
Transcript: ENSMUST00000180587
AA Change: S247G

PolyPhen 2 Score 0.639 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000137973
Gene: ENSMUSG00000018752
AA Change: S247G

DomainStartEndE-ValueType
low complexity region 4 14 N/A INTRINSIC
transmembrane domain 20 42 N/A INTRINSIC
low complexity region 91 110 N/A INTRINSIC
TNF 118 256 6.18e-10 SMART
low complexity region 270 275 N/A INTRINSIC
TNF 276 410 1.91e-2 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000174159
AA Change: S246G

PolyPhen 2 Score 0.911 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000133951
Gene: ENSMUSG00000018752
AA Change: S246G

DomainStartEndE-ValueType
low complexity region 4 14 N/A INTRINSIC
transmembrane domain 20 42 N/A INTRINSIC
low complexity region 90 109 N/A INTRINSIC
TNF 117 255 6.18e-10 SMART
low complexity region 269 274 N/A INTRINSIC
TNF 275 408 7.41e-3 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145435
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144033
Predicted Effect probably benign
Transcript: ENSMUST00000181261
SMART Domains Protein: ENSMUSP00000137916
Gene: ENSMUSG00000097328

DomainStartEndE-ValueType
low complexity region 52 71 N/A INTRINSIC
Blast:TNF 72 98 8e-8 BLAST
PDB:4HT1|T 72 98 1e-12 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000181810
SMART Domains Protein: ENSMUSP00000137972
Gene: ENSMUSG00000097328

DomainStartEndE-ValueType
low complexity region 4 14 N/A INTRINSIC
transmembrane domain 20 42 N/A INTRINSIC
low complexity region 90 109 N/A INTRINSIC
TNF 117 248 3.67e-35 SMART
Meta Mutation Damage Score 0.0661 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.9%
  • 20x: 91.9%
Validation Efficiency 100% (67/67)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the tumor necrosis factor (TNF) ligand family. This protein is a ligand for TNFRSF17/BCMA, a member of the TNF receptor family. This protein and its receptor are both found to be important for B cell development. In vitro experiments suggested that this protein may be able to induce apoptosis through its interaction with other TNF receptor family proteins such as TNFRSF6/FAS and TNFRSF14/HVEM. Alternative splicing results in multiple transcript variants. Some transcripts that skip the last exon of the upstream gene (TNFSF12) and continue into the second exon of this gene have been identified; such read-through transcripts are contained in GeneID 407977, TNFSF12-TNFSF13. [provided by RefSeq, Oct 2010]
PHENOTYPE: Homozygous null mice are viable and fertile. No apparent defects of the immune system have been reported. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8b T C 11: 109,862,640 (GRCm39) K375R possibly damaging Het
Adrb2 T C 18: 62,311,871 (GRCm39) N318S probably damaging Het
Akap5 A C 12: 76,376,036 (GRCm39) E489D possibly damaging Het
Aldh7a1 T A 18: 56,665,133 (GRCm39) I385F probably damaging Het
Astn1 T A 1: 158,407,146 (GRCm39) probably benign Het
Atp7b T A 8: 22,487,374 (GRCm39) T1314S probably damaging Het
Bhmt2 C A 13: 93,798,847 (GRCm39) G325C probably damaging Het
Brpf1 T A 6: 113,296,050 (GRCm39) V781E probably benign Het
Cacna1c T A 6: 118,575,720 (GRCm39) Y1860F probably benign Het
Ccdc7a T C 8: 129,788,162 (GRCm39) T56A probably damaging Het
Cep78 A G 19: 15,937,027 (GRCm39) S560P probably damaging Het
Cnot1 G A 8: 96,469,841 (GRCm39) T1343I probably benign Het
Coq10b T C 1: 55,103,416 (GRCm39) S65P probably damaging Het
Creld1 T A 6: 113,466,745 (GRCm39) C243S probably damaging Het
Cst12 A T 2: 148,635,172 (GRCm39) I121F possibly damaging Het
Cyp26a1 A C 19: 37,687,308 (GRCm39) E165A probably benign Het
Cyp2d12 T G 15: 82,442,337 (GRCm39) M273R probably damaging Het
Dnajb7 T A 15: 81,291,657 (GRCm39) S227C probably damaging Het
Evc T A 5: 37,476,379 (GRCm39) Q390L probably damaging Het
F830016B08Rik T A 18: 60,433,970 (GRCm39) L351* probably null Het
Fga T C 3: 82,939,145 (GRCm39) S507P probably benign Het
Gba1 A T 3: 89,113,455 (GRCm39) Y239F probably damaging Het
Golga2 C A 2: 32,195,996 (GRCm39) Y843* probably null Het
Gria4 C A 9: 4,793,865 (GRCm39) L64F probably damaging Het
Hectd3 A G 4: 116,860,191 (GRCm39) Y803C probably damaging Het
Hmcn1 T C 1: 150,545,172 (GRCm39) K2812E probably damaging Het
Il17b T G 18: 61,823,316 (GRCm39) V50G probably damaging Het
Itga2b A T 11: 102,357,151 (GRCm39) L243* probably null Het
Kank4 C A 4: 98,667,266 (GRCm39) V394L possibly damaging Het
Kat14 T A 2: 144,215,711 (GRCm39) D65E probably benign Het
Kcnh3 T C 15: 99,136,090 (GRCm39) Y696H probably damaging Het
Kctd19 C A 8: 106,122,008 (GRCm39) D180Y probably damaging Het
Klra8 A C 6: 130,092,603 (GRCm39) S233A probably benign Het
Masp2 A T 4: 148,696,563 (GRCm39) T387S possibly damaging Het
Midn C A 10: 79,989,957 (GRCm39) T275N probably damaging Het
Mis18bp1 A G 12: 65,180,587 (GRCm39) F965L probably benign Het
Myo3a G T 2: 22,287,445 (GRCm39) V186L probably damaging Het
Ncoa2 T A 1: 13,235,281 (GRCm39) N884I probably benign Het
Or10d4 T C 9: 39,581,016 (GRCm39) I221T probably damaging Het
Or13c25 A T 4: 52,911,502 (GRCm39) C97* probably null Het
Or8k35 T A 2: 86,424,948 (GRCm39) T75S probably damaging Het
Osr2 T C 15: 35,300,813 (GRCm39) V123A probably benign Het
P4ha2 A G 11: 54,008,471 (GRCm39) H226R probably benign Het
Pcdhb16 T A 18: 37,611,151 (GRCm39) V37E probably benign Het
Pcdhb18 T A 18: 37,622,673 (GRCm39) M1K probably null Het
Pcsk1 T A 13: 75,246,166 (GRCm39) Y181* probably null Het
Pros1 G T 16: 62,705,875 (GRCm39) C63F probably damaging Het
Ranbp3l T A 15: 9,065,081 (GRCm39) C353* probably null Het
Rev3l T C 10: 39,714,439 (GRCm39) Y2388H probably benign Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Rpl12-ps1 G T 1: 36,997,458 (GRCm39) noncoding transcript Het
Rttn T C 18: 89,131,474 (GRCm39) V1951A probably benign Het
Scn9a G A 2: 66,335,371 (GRCm39) probably benign Het
Sdk1 T C 5: 142,113,591 (GRCm39) F1546S probably damaging Het
Sh3glb2 C T 2: 30,244,987 (GRCm39) R71Q probably damaging Het
Slc30a6 T C 17: 74,715,842 (GRCm39) F101L probably benign Het
Snrpd1 T C 18: 10,626,913 (GRCm39) I60T probably damaging Het
Sox10 T A 15: 79,043,378 (GRCm39) E218D probably benign Het
Tekt3 C A 11: 62,961,316 (GRCm39) H162N probably damaging Het
Trim10 T A 17: 37,183,346 (GRCm39) I214N probably damaging Het
Trp63 C A 16: 25,708,003 (GRCm39) D566E probably damaging Het
Uck2 T C 1: 167,062,293 (GRCm39) D156G probably damaging Het
Zfp386 T A 12: 116,023,225 (GRCm39) S314R possibly damaging Het
Zfp467 C T 6: 48,415,170 (GRCm39) R494H probably damaging Het
Zfp735 A T 11: 73,601,470 (GRCm39) D138V probably benign Het
Zfyve26 T C 12: 79,298,925 (GRCm39) E445G probably damaging Het
Other mutations in Tnfsf13
AlleleSourceChrCoordTypePredicted EffectPPH Score
R1745:Tnfsf13 UTSW 11 69,575,973 (GRCm39) missense probably benign 0.02
R4825:Tnfsf13 UTSW 11 69,576,075 (GRCm39) nonsense probably null
R5613:Tnfsf13 UTSW 11 69,574,821 (GRCm39) splice site probably null
R6254:Tnfsf13 UTSW 11 69,575,309 (GRCm39) critical splice donor site probably null
R7027:Tnfsf13 UTSW 11 69,575,958 (GRCm39) critical splice acceptor site probably null
R7778:Tnfsf13 UTSW 11 69,575,989 (GRCm39) missense probably damaging 0.96
R8094:Tnfsf13 UTSW 11 69,575,983 (GRCm39) missense probably damaging 0.99
R8095:Tnfsf13 UTSW 11 69,575,983 (GRCm39) missense probably damaging 0.99
R8096:Tnfsf13 UTSW 11 69,575,983 (GRCm39) missense probably damaging 0.99
R8392:Tnfsf13 UTSW 11 69,574,688 (GRCm39) missense probably damaging 1.00
R9453:Tnfsf13 UTSW 11 69,576,010 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AAACAGCAGTGTTGACCTGCCC -3'
(R):5'- TGATCCAACAGACAGAGCTGCAAAG -3'

Sequencing Primer
(F):5'- TGTTGACCTGCCCTGGAG -3'
(R):5'- GGGTCTCAGAGCCTCTCAATC -3'
Posted On 2014-04-13