Incidental Mutation 'R9177:Cd40'
ID 696730
Institutional Source Beutler Lab
Gene Symbol Cd40
Ensembl Gene ENSMUSG00000017652
Gene Name CD40 antigen
Synonyms Tnfrsf5, p50, Bp50, Cd40
MMRRC Submission 068949-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9177 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 164897535-164913574 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 164905465 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Arginine at position 161 (C161R)
Ref Sequence ENSEMBL: ENSMUSP00000017799 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000017799] [ENSMUST00000073707] [ENSMUST00000081310] [ENSMUST00000140951] [ENSMUST00000154443] [ENSMUST00000184221]
AlphaFold P27512
Predicted Effect probably damaging
Transcript: ENSMUST00000017799
AA Change: C161R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000017799
Gene: ENSMUSG00000017652
AA Change: C161R

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 damaging
Transcript: ENSMUST00000073707
AA Change: C161R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000073386
Gene: ENSMUSG00000017652
AA Change: C161R

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 damaging
Transcript: ENSMUST00000081310
AA Change: C161R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000080059
Gene: ENSMUSG00000017652
AA Change: C161R

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 probably benign
Transcript: ENSMUST00000154443
Predicted Effect probably damaging
Transcript: ENSMUST00000184221
AA Change: C161R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000139193
Gene: ENSMUSG00000017652
AA Change: C161R

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik T A 3: 137,775,677 (GRCm39) V1622D probably damaging Het
Acadsb C T 7: 131,033,763 (GRCm39) T260I probably damaging Het
Acap2 A T 16: 30,955,392 (GRCm39) V161E probably damaging Het
Alk T C 17: 72,181,190 (GRCm39) T1367A probably damaging Het
Atg2a A C 19: 6,291,905 (GRCm39) H27P probably damaging Het
Atp2c1 C T 9: 105,336,858 (GRCm39) probably null Het
C1s1 T G 6: 124,508,362 (GRCm39) K542N probably damaging Het
Camk1d A G 2: 5,303,901 (GRCm39) S351P probably benign Het
Carf C A 1: 60,148,558 (GRCm39) Q85K possibly damaging Het
Caskin2 T C 11: 115,698,683 (GRCm39) N43S probably damaging Het
Cdh19 A G 1: 110,877,111 (GRCm39) F76S probably damaging Het
Cdkl1 T C 12: 69,794,100 (GRCm39) N346D probably benign Het
Cdon A G 9: 35,381,230 (GRCm39) D540G probably benign Het
Cep164 T A 9: 45,691,060 (GRCm39) E379V probably damaging Het
Clock T C 5: 76,377,256 (GRCm39) N681S probably benign Het
Col15a1 G C 4: 47,288,200 (GRCm39) probably benign Het
Col6a5 T G 9: 105,808,152 (GRCm39) K965N unknown Het
Dctn4 T A 18: 60,659,304 (GRCm39) M1K probably null Het
Dhx30 T C 9: 109,915,750 (GRCm39) D741G probably damaging Het
Dhx37 A G 5: 125,507,958 (GRCm39) V104A probably benign Het
Dnah12 A G 14: 26,571,255 (GRCm39) K2788R possibly damaging Het
Egfr T A 11: 16,855,410 (GRCm39) D898E probably damaging Het
Eif2ak4 G C 2: 118,271,701 (GRCm39) probably null Het
Eif6 A G 2: 155,665,852 (GRCm39) L101P probably damaging Het
Etaa1 A T 11: 17,896,419 (GRCm39) V566E probably damaging Het
Far2 C T 6: 148,060,418 (GRCm39) T257I probably benign Het
Fuca2 G A 10: 13,390,563 (GRCm39) W453* probably null Het
Galntl6 A T 8: 58,310,590 (GRCm39) Y370* probably null Het
Gcn1 T C 5: 115,719,867 (GRCm39) V374A probably benign Het
Hjv T C 3: 96,435,881 (GRCm39) F380L probably benign Het
Hycc2 T C 1: 58,591,361 (GRCm39) D94G probably damaging Het
Ifi202b A T 1: 173,804,949 (GRCm39) M1K probably null Het
Lama4 A G 10: 38,950,688 (GRCm39) Y997C probably damaging Het
Lepr T A 4: 101,602,798 (GRCm39) C195* probably null Het
Lrrc37 T A 11: 103,508,263 (GRCm39) H1235L unknown Het
Lrrc73 T C 17: 46,565,535 (GRCm39) S89P probably benign Het
Macf1 T C 4: 123,367,582 (GRCm39) E2393G probably damaging Het
Mdga2 T A 12: 66,517,481 (GRCm39) T118S possibly damaging Het
Msantd5f3 T C 4: 73,575,373 (GRCm39) S351P probably damaging Het
Mtf2 A G 5: 108,234,949 (GRCm39) K124R probably benign Het
Muc5b T C 7: 141,399,075 (GRCm39) Y339H unknown Het
Nes G A 3: 87,887,012 (GRCm39) G1757E probably damaging Het
Nfatc4 A T 14: 56,064,685 (GRCm39) I391F probably damaging Het
Nup93 A T 8: 94,954,371 (GRCm39) I23F probably benign Het
Or4a27 A C 2: 88,559,174 (GRCm39) Y256* probably null Het
Or5h17 T G 16: 58,820,083 (GRCm39) F12V probably damaging Het
Or6y1 A C 1: 174,276,923 (GRCm39) T245P probably damaging Het
Or7g16 G T 9: 18,726,742 (GRCm39) Q283K probably damaging Het
Or9i14 A T 19: 13,792,388 (GRCm39) C189S probably damaging Het
Pak5 A C 2: 135,943,126 (GRCm39) M338R probably benign Het
Papola A G 12: 105,766,032 (GRCm39) E44G probably benign Het
Pcdh15 A T 10: 74,479,455 (GRCm39) E522V probably benign Het
Peli2 A G 14: 48,518,927 (GRCm39) E225G probably benign Het
Pla2g1b T G 5: 115,612,595 (GRCm39) I117S probably damaging Het
Plxnd1 G T 6: 115,943,469 (GRCm39) Q1246K probably benign Het
Pole A G 5: 110,480,288 (GRCm39) E1953G probably benign Het
Pus7l T C 15: 94,431,445 (GRCm39) I395V probably benign Het
Shisa7 T G 7: 4,837,333 (GRCm39) D244A probably damaging Het
Slco3a1 T C 7: 73,952,946 (GRCm39) T538A probably benign Het
Syk T A 13: 52,766,480 (GRCm39) N188K probably benign Het
Tcf20 A G 15: 82,740,705 (GRCm39) S249P probably benign Het
Tmem25 T C 9: 44,709,529 (GRCm39) T91A possibly damaging Het
Trank1 T C 9: 111,221,579 (GRCm39) V2772A probably benign Het
Ttn A T 2: 76,596,447 (GRCm39) Y20155* probably null Het
Uchl4 C T 9: 64,142,986 (GRCm39) H156Y probably benign Het
Ulbp1 A T 10: 7,396,392 (GRCm39) L295Q unknown Het
Vwf G A 6: 125,581,254 (GRCm39) A631T Het
Zfp810 C T 9: 22,189,936 (GRCm39) C324Y probably damaging Het
Zswim8 T C 14: 20,761,908 (GRCm39) L227P probably 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
R5310:Cd40 UTSW 2 164,905,483 (GRCm39) critical splice donor site probably null
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
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'- ACCAACAGGCTTCTATTAACTAAGC -3'

Sequencing Primer
(F):5'- CTTGGGGTAAGAAGCTGAGGGC -3'
(R):5'- CAGGCTTCTATTAACTAAGCAGAAG -3'
Posted On 2022-02-07