Incidental Mutation 'R5310:Cd40'
ID 404762
Institutional Source Beutler Lab
Gene Symbol Cd40
Ensembl Gene ENSMUSG00000017652
Gene Name CD40 antigen
Synonyms Tnfrsf5, p50, Bp50, Cd40
MMRRC Submission 042893-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5310 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 164897535-164913574 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to C at 164905483 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000080059 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000017799] [ENSMUST00000073707] [ENSMUST00000081310] [ENSMUST00000140951] [ENSMUST00000154443] [ENSMUST00000184221]
AlphaFold P27512
Predicted Effect probably null
Transcript: ENSMUST00000017799
SMART Domains Protein: ENSMUSP00000017799
Gene: ENSMUSG00000017652

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
TNFR 26 59 9.45e-6 SMART
TNFR 62 103 2.38e-11 SMART
TNFR 105 143 4.55e-8 SMART
TNFR 146 186 2.42e-3 SMART
transmembrane domain 193 215 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000073707
SMART Domains Protein: ENSMUSP00000073386
Gene: ENSMUSG00000017652

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
TNFR 26 59 9.45e-6 SMART
TNFR 62 103 2.38e-11 SMART
TNFR 105 143 4.55e-8 SMART
TNFR 146 186 2.42e-3 SMART
Predicted Effect probably null
Transcript: ENSMUST00000081310
SMART Domains Protein: ENSMUSP00000080059
Gene: ENSMUSG00000017652

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
TNFR 26 59 9.45e-6 SMART
TNFR 62 103 2.38e-11 SMART
TNFR 105 143 4.55e-8 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140951
SMART Domains Protein: ENSMUSP00000122981
Gene: ENSMUSG00000017652

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
TNFR 64 97 9.45e-6 SMART
Blast:TNFR 100 121 1e-8 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153105
Predicted Effect probably benign
Transcript: ENSMUST00000154443
Predicted Effect probably benign
Transcript: ENSMUST00000184221
SMART Domains Protein: ENSMUSP00000139193
Gene: ENSMUSG00000017652

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
TNFR 26 59 9.45e-6 SMART
TNFR 62 103 2.38e-11 SMART
TNFR 105 143 4.55e-8 SMART
TNFR 146 186 2.42e-3 SMART
Meta Mutation Damage Score 0.9499 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.9%
  • 10x: 97.9%
  • 20x: 96.7%
Validation Efficiency 100% (74/74)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the TNF-receptor superfamily. The encoded protein is a receptor on antigen-presenting cells of the immune system and is essential for mediating a broad variety of immune and inflammatory responses including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. AT-hook transcription factor AKNA is reported to coordinately regulate the expression of this receptor and its ligand, which may be important for homotypic cell interactions. Adaptor protein TNFR2 interacts with this receptor and serves as a mediator of the signal transduction. The interaction of this receptor and its ligand is found to be necessary for amyloid-beta-induced microglial activation, and thus is thought to be an early event in Alzheimer disease pathogenesis. Mutations affecting this gene are the cause of autosomal recessive hyper-IgM immunodeficiency type 3 (HIGM3). Multiple alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Nov 2014]
PHENOTYPE: Homozygous inactivation of this gene may cause impaired immunoglobulin class switching and germinal center formation, reduced susceptibility to type II hypersensitivity reaction, impaired priming of T cells and control of M. tuberculosis infection, and altered response to transplant. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca15 A T 7: 119,931,839 (GRCm39) I31L possibly damaging Het
Abca17 T C 17: 24,500,204 (GRCm39) K1329R probably benign Het
Acap2 A G 16: 30,952,427 (GRCm39) Y197H probably benign Het
Adgrv1 A G 13: 81,624,809 (GRCm39) V3720A possibly damaging Het
Alms1 T A 6: 85,592,350 (GRCm39) S870T possibly damaging Het
Anapc4 A G 5: 53,016,501 (GRCm39) E493G probably benign Het
Ap2a1 A G 7: 44,555,489 (GRCm39) probably null Het
Arhgef38 A G 3: 132,822,227 (GRCm39) L179P probably damaging Het
Bicral T C 17: 47,124,909 (GRCm39) D630G possibly damaging Het
Ccdc97 A T 7: 25,415,201 (GRCm39) L154Q probably damaging Het
Celsr1 T A 15: 85,810,423 (GRCm39) N2155I possibly damaging Het
Cemip A T 7: 83,641,241 (GRCm39) L261H probably damaging Het
Cep57 G A 9: 13,730,164 (GRCm39) H98Y probably damaging Het
Chrna7 A T 7: 62,755,805 (GRCm39) L247Q probably damaging Het
Cyp2c40 T A 19: 39,766,474 (GRCm39) M374L probably damaging Het
Cyp4f13 T C 17: 33,144,795 (GRCm39) D372G probably damaging Het
Dazl C A 17: 50,588,311 (GRCm39) S288I probably damaging Het
Dnah5 T C 15: 28,311,474 (GRCm39) F1818L probably damaging Het
Echdc1 T C 10: 29,210,204 (GRCm39) V143A possibly damaging Het
Eif4enif1 T A 11: 3,192,687 (GRCm39) H838Q probably damaging Het
Erich3 A T 3: 154,469,217 (GRCm39) D1223V probably damaging Het
Fbxl2 A G 9: 113,815,576 (GRCm39) I229T possibly damaging Het
Gfm2 G A 13: 97,299,659 (GRCm39) A406T probably damaging Het
Ggnbp2 A G 11: 84,760,794 (GRCm39) M1T probably null Het
Glb1l2 C T 9: 26,708,162 (GRCm39) probably benign Het
Gnl2 A G 4: 124,946,633 (GRCm39) K618R probably benign Het
Greb1 A T 12: 16,766,760 (GRCm39) I346K probably benign Het
Greb1l G A 18: 10,542,427 (GRCm39) E1341K probably damaging Het
Gtse1 A G 15: 85,757,993 (GRCm39) Q533R probably benign Het
Hemgn A G 4: 46,403,927 (GRCm39) S23P possibly damaging Het
Htr6 G T 4: 138,788,977 (GRCm39) H359Q probably damaging Het
Ifit1 T C 19: 34,626,204 (GRCm39) F447L probably benign Het
Kansl1 T C 11: 104,315,684 (GRCm39) Y118C possibly damaging Het
Khk G A 5: 31,084,373 (GRCm39) V118M probably benign Het
Klra17 T A 6: 129,845,671 (GRCm39) K181M probably damaging Het
Lbh T C 17: 73,228,287 (GRCm39) probably null Het
Lmo2 T C 2: 103,806,445 (GRCm39) I108T probably damaging Het
Maco1 T C 4: 134,564,330 (GRCm39) probably benign Het
Mgat5 T A 1: 127,315,251 (GRCm39) probably null Het
Mink1 T C 11: 70,498,169 (GRCm39) V525A probably benign Het
Myo10 C A 15: 25,778,164 (GRCm39) probably null Het
Nlrp2 T C 7: 5,328,007 (GRCm39) N682S probably benign Het
Nr2e3 G A 9: 59,856,617 (GRCm39) probably benign Het
Or5p5 T C 7: 107,414,171 (GRCm39) C129R probably damaging Het
Or6b2b T C 1: 92,418,758 (GRCm39) T240A probably damaging Het
Pabpc4l T C 3: 46,401,276 (GRCm39) T123A probably benign Het
Pfas G A 11: 68,878,847 (GRCm39) S1319F probably damaging Het
Phf3 T C 1: 30,842,887 (GRCm39) K2024R probably damaging Het
Pld4 G A 12: 112,735,046 (GRCm39) C501Y probably damaging Het
Psg16 C T 7: 16,824,560 (GRCm39) R115W probably damaging Het
Rab3gap1 G A 1: 127,870,110 (GRCm39) probably null Het
Rimkla C A 4: 119,335,049 (GRCm39) K111N probably damaging Het
Rrm2b T C 15: 37,927,571 (GRCm39) E113G probably damaging Het
Rspry1 C T 8: 95,349,813 (GRCm39) T67I probably benign Het
Skint6 C A 4: 113,041,965 (GRCm39) E292* probably null Het
Skint8 C A 4: 111,807,390 (GRCm39) L359M probably damaging Het
Slc13a1 A G 6: 24,134,373 (GRCm39) M170T probably benign Het
Slc15a5 T C 6: 138,050,034 (GRCm39) N127S probably benign Het
Slc39a10 G A 1: 46,875,285 (GRCm39) H6Y probably damaging Het
Spata31e2 A C 1: 26,724,169 (GRCm39) V337G probably benign Het
Sugct A T 13: 17,427,145 (GRCm39) C338* probably null Het
Tbk1 A T 10: 121,391,956 (GRCm39) M486K probably benign Het
Terf1 A T 1: 15,875,909 (GRCm39) E3V probably damaging Het
Thoc5 T A 11: 4,860,648 (GRCm39) Y246N probably damaging Het
Tmem167b G A 3: 108,469,415 (GRCm39) probably benign Het
Tmtc1 T A 6: 148,256,910 (GRCm39) probably benign Het
Zfp322a A T 13: 23,541,532 (GRCm39) M70K possibly damaging Het
Zfp979 A T 4: 147,698,375 (GRCm39) H111Q possibly damaging Het
Other mutations in Cd40
AlleleSourceChrCoordTypePredicted EffectPPH Score
bluebonnet UTSW 2 164,904,221 (GRCm39) missense probably benign 0.23
noelle UTSW 2 164,905,483 (GRCm39) critical splice donor site probably null
R0553:Cd40 UTSW 2 164,912,661 (GRCm39) missense probably benign 0.01
R1115:Cd40 UTSW 2 164,912,681 (GRCm39) missense possibly damaging 0.59
R1134:Cd40 UTSW 2 164,912,738 (GRCm39) missense probably benign 0.44
R2036:Cd40 UTSW 2 164,904,221 (GRCm39) missense probably benign 0.23
R2938:Cd40 UTSW 2 164,911,622 (GRCm39) missense probably benign 0.01
R3034:Cd40 UTSW 2 164,904,235 (GRCm39) missense probably benign 0.02
R4690:Cd40 UTSW 2 164,911,615 (GRCm39) missense possibly damaging 0.68
R5222:Cd40 UTSW 2 164,908,464 (GRCm39) missense probably benign 0.41
R7318:Cd40 UTSW 2 164,904,255 (GRCm39) missense possibly damaging 0.51
R7833:Cd40 UTSW 2 164,908,431 (GRCm39) missense probably benign 0.01
R7905:Cd40 UTSW 2 164,904,245 (GRCm39) missense probably damaging 1.00
R8069:Cd40 UTSW 2 164,898,695 (GRCm39) missense unknown
R8371:Cd40 UTSW 2 164,908,458 (GRCm39) missense probably damaging 1.00
R9177:Cd40 UTSW 2 164,905,465 (GRCm39) missense probably damaging 1.00
R9224:Cd40 UTSW 2 164,898,716 (GRCm39) missense unknown
R9311:Cd40 UTSW 2 164,912,667 (GRCm39) missense possibly damaging 0.87
R9419:Cd40 UTSW 2 164,904,162 (GRCm39) intron probably benign
R9625:Cd40 UTSW 2 164,905,061 (GRCm39) missense probably benign
Z1088:Cd40 UTSW 2 164,904,960 (GRCm39) missense probably damaging 0.96
Predicted Primers PCR Primer
(F):5'- TGCCTTGGGGTAAGAAGCTG -3'
(R):5'- CCAACAGGCTTCTATTAACTAAGC -3'

Sequencing Primer
(F):5'- AGGTGTTCTGTCCTGCCCTG -3'
(R):5'- CAGGCTTCTATTAACTAAGCAGAAG -3'
Posted On 2016-07-22