Incidental Mutation 'R5433:Cd74'
ID 428179
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 042998-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.116) question?
Stock # R5433 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 60936921-60945724 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 60940993 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 31 (A31S)
Ref Sequence ENSEMBL: ENSMUSP00000126688 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050487] [ENSMUST00000097563] [ENSMUST00000167610]
AlphaFold P04441
Predicted Effect probably benign
Transcript: ENSMUST00000050487
AA Change: A31S

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000057836
Gene: ENSMUSG00000024610
AA Change: A31S

DomainStartEndE-ValueType
Pfam:MHC2-interact 1 112 2.8e-40 PFAM
Pfam:MHCassoc_trimer 119 190 6e-36 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000097563
AA Change: A31S

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000095171
Gene: ENSMUSG00000024610
AA Change: A31S

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 probably benign
Transcript: ENSMUST00000167610
AA Change: A31S

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000126688
Gene: ENSMUSG00000024610
AA Change: A31S

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175586
Meta Mutation Damage Score 0.5540 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.8%
Validation Efficiency 100% (58/58)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700019D03Rik T C 1: 52,964,657 (GRCm39) S24G probably damaging Het
1810064F22Rik A G 9: 22,119,039 (GRCm39) noncoding transcript Het
Aacs A T 5: 125,592,078 (GRCm39) M589L probably benign Het
Adamts8 A C 9: 30,873,012 (GRCm39) H739P probably benign Het
Atp8b2 T C 3: 89,860,216 (GRCm39) probably benign Het
BC030500 A G 8: 59,366,043 (GRCm39) probably benign Het
Btnl9 T A 11: 49,066,830 (GRCm39) probably benign Het
Ceacam3 G A 7: 16,893,808 (GRCm39) A440T possibly damaging Het
Ces1d G A 8: 93,912,664 (GRCm39) T258I probably benign Het
Col10a1 A G 10: 34,266,735 (GRCm39) probably benign Het
Coro1b C T 19: 4,203,449 (GRCm39) A430V probably benign Het
Cyp2c65 A T 19: 39,081,928 (GRCm39) I485L probably benign Het
Dio1 A T 4: 107,163,977 (GRCm39) probably benign Het
Dmxl1 G A 18: 50,000,966 (GRCm39) probably null Het
Dynlt5 A G 4: 102,859,700 (GRCm39) E84G possibly damaging Het
Elp6 A G 9: 110,144,851 (GRCm39) Y136C probably damaging Het
Gon4l A T 3: 88,803,532 (GRCm39) Q1382L possibly damaging Het
Guca1a T C 17: 47,711,295 (GRCm39) E17G probably damaging Het
Gucy2d G A 7: 98,098,982 (GRCm39) G267E probably damaging Het
Gvin3 T A 7: 106,199,314 (GRCm39) noncoding transcript Het
Hspg2 T A 4: 137,256,105 (GRCm39) probably null Het
Il1a G T 2: 129,149,821 (GRCm39) D26E possibly damaging Het
Il22b T A 10: 118,130,789 (GRCm39) I36F probably damaging Het
Kcna1 A T 6: 126,620,075 (GRCm39) F82I probably damaging Het
Klhl18 G C 9: 110,265,195 (GRCm39) N335K possibly damaging Het
Lamtor5 T G 3: 107,189,323 (GRCm39) C120G probably benign Het
Lars1 A G 18: 42,384,363 (GRCm39) C72R possibly damaging Het
Lrrfip1 T G 1: 91,014,848 (GRCm39) probably null Het
Mapkapk3 T C 9: 107,133,491 (GRCm39) D349G probably damaging Het
Mknk2 A T 10: 80,503,059 (GRCm39) I421N probably benign Het
Myh6 A G 14: 55,191,381 (GRCm39) I820T probably benign Het
Notch2 T G 3: 98,033,450 (GRCm39) V1182G probably damaging Het
Or1af1 T G 2: 37,109,684 (GRCm39) F61C probably damaging Het
Or1e16 AGCGGTCGTAGGC AGC 11: 73,286,480 (GRCm39) probably null Het
Or2z2 C T 11: 58,346,680 (GRCm39) V32M probably damaging Het
Ppfia4 A T 1: 134,245,632 (GRCm39) S641T probably damaging Het
Prok1 T A 3: 107,146,949 (GRCm39) H6L probably benign Het
Ptprm A T 17: 67,000,468 (GRCm39) V1172E probably damaging Het
Rasal3 C T 17: 32,612,575 (GRCm39) R762Q probably benign Het
Rgs20 G T 1: 5,140,333 (GRCm39) A23E possibly damaging Het
Rprd1a T C 18: 24,640,288 (GRCm39) T163A probably benign Het
Rrm1 A T 7: 102,114,974 (GRCm39) N37I probably damaging Het
Shc4 T A 2: 125,481,350 (GRCm39) E520V probably damaging Het
Slc14a2 G T 18: 78,252,143 (GRCm39) P56Q probably damaging Het
Slc22a3 C T 17: 12,677,377 (GRCm39) G264S probably damaging Het
Svil A G 18: 5,059,294 (GRCm39) E770G probably damaging Het
Svop A G 5: 114,198,186 (GRCm39) V129A probably damaging Het
Szt2 A T 4: 118,232,663 (GRCm39) probably benign Het
Tcof1 T C 18: 60,951,105 (GRCm39) probably benign Het
Tmem30a T A 9: 79,687,930 (GRCm39) I80F probably damaging Het
Vmn2r16 G T 5: 109,511,708 (GRCm39) L638F probably damaging Het
Xkr7 T A 2: 152,896,244 (GRCm39) I366N probably damaging Het
Zer1 A G 2: 29,990,998 (GRCm39) 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
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
R9252:Cd74 UTSW 18 60,941,364 (GRCm39) missense possibly damaging 0.50
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'- CTGTCACTACACAGAGGAGAC -3'
(R):5'- GAGCACGCACATTTCGGAAG -3'

Sequencing Primer
(F):5'- AAGGAACGTGGCTCATCCTTC -3'
(R):5'- ACGCACATTTCGGAAGCTTCATG -3'
Posted On 2016-09-01