Incidental Mutation 'R9252:Cd74'
ID 701632
Institutional Source Beutler Lab
Gene Symbol Cd74
Ensembl Gene ENSMUSG00000024610
Gene Name CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)
Synonyms CLIP, Ii
MMRRC Submission
Accession Numbers
Essential gene? Probably non essential (E-score: 0.114) question?
Stock # R9252 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 60936921-60945724 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 60941364 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 103 (M103K)
Ref Sequence ENSEMBL: ENSMUSP00000095171 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050487] [ENSMUST00000097563] [ENSMUST00000167610]
AlphaFold P04441
Predicted Effect possibly damaging
Transcript: ENSMUST00000050487
AA Change: M103K

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000057836
Gene: ENSMUSG00000024610
AA Change: M103K

DomainStartEndE-ValueType
Pfam:MHC2-interact 1 112 2.8e-40 PFAM
Pfam:MHCassoc_trimer 119 190 6e-36 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000097563
AA Change: M103K

PolyPhen 2 Score 0.499 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000095171
Gene: ENSMUSG00000024610
AA Change: M103K

DomainStartEndE-ValueType
Pfam:MHC2-interact 1 112 5.3e-40 PFAM
Pfam:MHCassoc_trimer 119 190 6.7e-36 PFAM
TY 212 258 8.6e-18 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000167610
AA Change: M103K

PolyPhen 2 Score 0.499 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000126688
Gene: ENSMUSG00000024610
AA Change: M103K

DomainStartEndE-ValueType
Pfam:MHC2-interact 1 112 5.8e-45 PFAM
Pfam:MHCassoc_trimer 119 187 1.7e-34 PFAM
TY 212 258 8.6e-18 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (59/59)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene associates with class II major histocompatibility complex (MHC) and is an important chaperone that regulates antigen presentation for immune response. It also serves as cell surface receptor for the cytokine macrophage migration inhibitory factor (MIF) which, when bound to the encoded protein, initiates survival pathways and cell proliferation. This protein also interacts with amyloid precursor protein (APP) and suppresses the production of amyloid beta (Abeta). Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]
PHENOTYPE: Homozygotes for targeted null mutations exhibit impaired transport of MHC class II molecules, poor antigen presentation, and deficiency of CD4+ T cell development and positive selection. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acap2 A G 16: 30,920,641 (GRCm39) probably null Het
Adgrb3 T C 1: 25,865,496 (GRCm39) N116D probably benign Het
Arfgef1 T A 1: 10,243,122 (GRCm39) R1073* probably null Het
Atp6v1d T A 12: 78,904,023 (GRCm39) Q46L probably benign Het
Brme1 A G 8: 84,898,878 (GRCm39) S589G possibly damaging Het
Car15 A T 16: 17,653,246 (GRCm39) L307* probably null Het
Catspere2 A T 1: 177,938,996 (GRCm39) H623L possibly damaging Het
Ccdc146 T C 5: 21,502,023 (GRCm39) D797G probably damaging Het
Ccdc27 A T 4: 154,125,507 (GRCm39) D112E unknown Het
Ccp110 A G 7: 118,321,673 (GRCm39) I443V probably benign Het
Cdca2 T A 14: 67,914,831 (GRCm39) R809S possibly damaging Het
Cfap46 A T 7: 139,198,165 (GRCm39) V2061E unknown Het
Cimap1b T C 15: 89,262,601 (GRCm39) S119G probably benign Het
Ddx11 G A 17: 66,457,807 (GRCm39) E873K probably benign Het
Gucy2d G A 7: 98,116,979 (GRCm39) probably null Het
Herc1 T A 9: 66,309,834 (GRCm39) S1061R probably damaging Het
Ildr1 G A 16: 36,536,574 (GRCm39) R201H probably damaging Het
Jakmip2 T A 18: 43,715,194 (GRCm39) I111F possibly damaging Het
Kcnj2 A G 11: 110,963,355 (GRCm39) D249G probably damaging Het
Kif1a T A 1: 93,002,776 (GRCm39) T208S probably damaging Het
Mgam T G 6: 40,706,577 (GRCm39) M76R probably damaging Het
Mib1 T G 18: 10,800,088 (GRCm39) I809S probably benign Het
Myh8 G T 11: 67,177,302 (GRCm39) R456L probably damaging Het
Mzf1 T C 7: 12,777,647 (GRCm39) T665A probably benign Het
Nfya T C 17: 48,699,943 (GRCm39) H27R Het
Nhsl3 A G 4: 129,117,269 (GRCm39) V510A probably benign Het
Nktr T C 9: 121,579,415 (GRCm39) M1161T unknown Het
Nox4 G A 7: 87,025,448 (GRCm39) R525Q probably benign Het
Or13c7b C T 4: 43,821,109 (GRCm39) G84D probably benign Het
Pde8b C T 13: 95,169,424 (GRCm39) D567N probably damaging Het
Pik3cd A G 4: 149,740,087 (GRCm39) I491T possibly damaging Het
Plcd3 G T 11: 102,968,380 (GRCm39) Y392* probably null Het
Plcd4 A G 1: 74,588,359 (GRCm39) I69M probably damaging Het
Plekhm2 T C 4: 141,356,443 (GRCm39) Y799C probably damaging Het
Pnlip T A 19: 58,669,273 (GRCm39) I424N possibly damaging Het
Prlr A G 15: 10,326,550 (GRCm39) probably benign Het
Ptprq A G 10: 107,522,247 (GRCm39) V568A probably benign Het
Rtkn A G 6: 83,125,143 (GRCm39) E201G probably damaging Het
Scg2 C T 1: 79,414,069 (GRCm39) R218H probably damaging Het
Shank2 A G 7: 143,622,535 (GRCm39) H223R possibly damaging Het
Slc23a2 A T 2: 131,913,842 (GRCm39) F312I probably damaging Het
Slc24a1 T A 9: 64,835,394 (GRCm39) E911V probably damaging Het
St8sia4 CCTCT CCT 1: 95,555,232 (GRCm39) probably null Het
Stat1 C A 1: 52,174,831 (GRCm39) Q178K probably benign Het
Stat6 A C 10: 127,483,661 (GRCm39) N75T probably benign Het
Stk10 G T 11: 32,538,915 (GRCm39) K251N Het
Sult1e1 G T 5: 87,737,973 (GRCm39) A36E probably damaging Het
Tbc1d12 A G 19: 38,899,477 (GRCm39) S466G probably benign Het
Thsd4 C A 9: 59,964,230 (GRCm39) A421S probably benign Het
Tsga10 T A 1: 37,873,364 (GRCm39) I172L probably benign Het
Ttn A T 2: 76,600,856 (GRCm39) M18842K probably benign Het
Ttpal T G 2: 163,449,105 (GRCm39) probably benign Het
Twf2 A G 9: 106,088,999 (GRCm39) D62G probably benign Het
Ube3d C A 9: 86,254,501 (GRCm39) V327F probably damaging Het
Ugt1a8 T C 1: 88,015,706 (GRCm39) S40P probably benign Het
Unc13c A T 9: 73,424,553 (GRCm39) I2021N possibly damaging Het
Vmn2r97 A T 17: 19,167,849 (GRCm39) Y701F probably benign Het
Other mutations in Cd74
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00980:Cd74 APN 18 60,944,398 (GRCm39) missense probably benign 0.02
IGL01475:Cd74 APN 18 60,943,393 (GRCm39) unclassified probably benign
IGL01867:Cd74 APN 18 60,941,352 (GRCm39) missense probably benign 0.03
IGL03207:Cd74 APN 18 60,944,996 (GRCm39) unclassified probably benign
R0010:Cd74 UTSW 18 60,936,968 (GRCm39) start gained probably benign
R0010:Cd74 UTSW 18 60,942,143 (GRCm39) missense probably benign 0.06
R0010:Cd74 UTSW 18 60,942,143 (GRCm39) missense probably benign 0.06
R0416:Cd74 UTSW 18 60,944,486 (GRCm39) missense possibly damaging 0.90
R0652:Cd74 UTSW 18 60,944,957 (GRCm39) missense probably damaging 1.00
R1433:Cd74 UTSW 18 60,937,064 (GRCm39) missense probably benign 0.04
R1490:Cd74 UTSW 18 60,944,438 (GRCm39) missense probably damaging 1.00
R1762:Cd74 UTSW 18 60,944,390 (GRCm39) missense probably benign 0.00
R1869:Cd74 UTSW 18 60,943,484 (GRCm39) missense probably benign 0.18
R4957:Cd74 UTSW 18 60,942,109 (GRCm39) missense probably benign 0.01
R5433:Cd74 UTSW 18 60,940,993 (GRCm39) missense probably benign 0.21
R5513:Cd74 UTSW 18 60,944,377 (GRCm39) missense probably damaging 1.00
R6073:Cd74 UTSW 18 60,944,558 (GRCm39) critical splice donor site probably null
R6381:Cd74 UTSW 18 60,944,435 (GRCm39) missense probably damaging 1.00
R7394:Cd74 UTSW 18 60,936,965 (GRCm39) start gained probably benign
R8944:Cd74 UTSW 18 60,943,127 (GRCm39) missense probably damaging 1.00
R9256:Cd74 UTSW 18 60,944,366 (GRCm39) missense probably benign 0.03
X0011:Cd74 UTSW 18 60,944,559 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- TTCCGAAATGTGCGTGCTCC -3'
(R):5'- TAAGAGTTCTGGCCTCCTCAG -3'

Sequencing Primer
(F):5'- AAATGTGCGTGCTCCACCTG -3'
(R):5'- CTTGGCAAACACCAGCTA -3'
Posted On 2022-03-25