Incidental Mutation 'R8957:Cd1d1'
ID 682080
Institutional Source Beutler Lab
Gene Symbol Cd1d1
Ensembl Gene ENSMUSG00000028076
Gene Name CD1d1 antigen
Synonyms Cd1d, Cd1a, CD1.1, Ly-38
MMRRC Submission 068793-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.100) question?
Stock # R8957 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 86903141-86906748 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 86906140 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 45 (D45G)
Ref Sequence ENSEMBL: ENSMUSP00000029717 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029717] [ENSMUST00000063869]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000029717
AA Change: D45G

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000029717
Gene: ENSMUSG00000028076
AA Change: D45G

DomainStartEndE-ValueType
Pfam:MHC_I_3 1 200 1.3e-95 PFAM
IGc1 221 291 5.35e-22 SMART
transmembrane domain 304 326 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000063869
AA Change: D45G

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000070616
Gene: ENSMUSG00000028076
AA Change: D45G

DomainStartEndE-ValueType
signal peptide 1 21 N/A INTRINSIC
PDB:4MQ7|A 23 73 2e-15 PDB
IGc1 90 160 5.35e-22 SMART
low complexity region 173 194 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.4%
Validation Efficiency 100% (66/66)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a divergent member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
PHENOTYPE: Homozygotes for targeted null mutations lack natural killer T cells, and mutant splenocytes fail to produce interleukin 4 (IL4). [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1500011B03Rik A G 5: 114,951,891 (GRCm39) V28A probably benign Het
Abca12 T A 1: 71,360,784 (GRCm39) D503V possibly damaging Het
Aco2 A T 15: 81,773,701 (GRCm39) probably benign Het
Aff1 A G 5: 103,981,634 (GRCm39) Q591R possibly damaging Het
Ankle2 G A 5: 110,379,121 (GRCm39) A7T possibly damaging Het
Ankrd12 T C 17: 66,291,491 (GRCm39) N1314S probably benign Het
Apeh A T 9: 107,969,572 (GRCm39) M216K probably benign Het
Armh1 T C 4: 117,087,104 (GRCm39) Y187C probably damaging Het
Ascc3 C A 10: 50,576,208 (GRCm39) A821E probably damaging Het
Atf7ip A G 6: 136,543,701 (GRCm39) D650G probably null Het
Cav1 T A 6: 17,339,235 (GRCm39) F107I probably benign Het
Ccdc146 A G 5: 21,514,585 (GRCm39) probably benign Het
Ccdc57 A G 11: 120,776,861 (GRCm39) I513T probably benign Het
Ccrl2 T C 9: 110,884,557 (GRCm39) R314G probably benign Het
Cfap74 G A 4: 155,521,187 (GRCm39) E620K Het
Col4a1 T A 8: 11,295,906 (GRCm39) probably benign Het
Cux2 C T 5: 121,999,011 (GRCm39) G1310R probably benign Het
Cyld G T 8: 89,432,410 (GRCm39) R136L probably damaging Het
Cyp4v3 A T 8: 45,760,018 (GRCm39) N511K probably benign Het
Dchs2 G A 3: 83,189,573 (GRCm39) V1646M Het
Des A T 1: 75,340,295 (GRCm39) I401F probably damaging Het
Dis3 T C 14: 99,337,027 (GRCm39) D28G probably damaging Het
Dnai4 T C 4: 102,953,950 (GRCm39) D83G probably damaging Het
Ehd1 A G 19: 6,344,439 (GRCm39) Y233C probably damaging Het
Fcrlb G A 1: 170,735,536 (GRCm39) A246V probably benign Het
Firrm C T 1: 163,792,335 (GRCm39) R554H probably damaging Het
Fnta T C 8: 26,489,541 (GRCm39) R357G probably benign Het
Fpgs T C 2: 32,575,354 (GRCm39) D420G probably damaging Het
Hdac4 T C 1: 91,873,757 (GRCm39) probably null Het
Hdhd5 C T 6: 120,495,404 (GRCm39) probably null Het
Iqgap2 G A 13: 95,772,154 (GRCm39) R1342C probably damaging Het
Isyna1 T G 8: 71,049,372 (GRCm39) L428R probably damaging Het
Jmjd4 C T 11: 59,340,884 (GRCm39) probably benign Het
Klra1 A G 6: 130,357,609 (GRCm39) V6A possibly damaging Het
Klrb1b T A 6: 128,795,522 (GRCm39) K124N probably benign Het
Krtap19-3 T C 16: 88,674,833 (GRCm39) probably benign Het
Lrrc74b T C 16: 17,378,976 (GRCm39) T34A probably benign Het
Map9 A G 3: 82,278,687 (GRCm39) Y229C probably benign Het
Mmp28 T C 11: 83,334,636 (GRCm39) I373V possibly damaging Het
Mpdz A T 4: 81,251,216 (GRCm39) Y1086* probably null Het
Myct1 C T 10: 5,554,208 (GRCm39) T25I probably damaging Het
Myh4 A G 11: 67,141,780 (GRCm39) K880E possibly damaging Het
Nav2 T G 7: 49,220,964 (GRCm39) V1656G probably damaging Het
Or12d13 A G 17: 37,647,382 (GRCm39) V247A probably damaging Het
Or1a1 T A 11: 74,086,772 (GRCm39) S148T probably damaging Het
Or5b101 T A 19: 13,004,881 (GRCm39) I271F probably benign Het
Pate2 T C 9: 35,596,911 (GRCm39) W100R probably benign Het
Pcdhb11 A C 18: 37,554,692 (GRCm39) K7N probably benign Het
Pcdhb11 A G 18: 37,555,872 (GRCm39) T401A probably benign Het
Pgam1 T A 19: 41,905,215 (GRCm39) I183N possibly damaging Het
Pou5f1 T G 17: 35,821,366 (GRCm39) L326R possibly damaging Het
Rbm34 A C 8: 127,692,208 (GRCm39) V178G probably benign Het
Rc3h2 A G 2: 37,289,660 (GRCm39) V384A possibly damaging Het
Sec62 T A 3: 30,864,671 (GRCm39) F178L unknown Het
Slco1a6 T C 6: 142,091,493 (GRCm39) N69S probably damaging Het
Smok2b T A 17: 13,453,873 (GRCm39) L11Q probably damaging Het
Snai2 T C 16: 14,526,113 (GRCm39) S255P probably damaging Het
Spata31h1 A G 10: 82,124,908 (GRCm39) Y2701H probably benign Het
Tesk2 T A 4: 116,659,910 (GRCm39) F343I probably benign Het
Tmem106c A T 15: 97,867,481 (GRCm39) I222F probably benign Het
Tmub1 G T 5: 24,651,775 (GRCm39) T63K probably benign Het
Tnip3 A G 6: 65,582,843 (GRCm39) T217A probably benign Het
Vmn2r10 T G 5: 109,149,780 (GRCm39) K421N possibly damaging Het
Zfp975 A T 7: 42,311,157 (GRCm39) H485Q probably damaging Het
Other mutations in Cd1d1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00588:Cd1d1 APN 3 86,905,480 (GRCm39) missense probably damaging 0.99
IGL01811:Cd1d1 APN 3 86,903,895 (GRCm39) missense possibly damaging 0.86
IGL02371:Cd1d1 APN 3 86,906,188 (GRCm39) missense probably benign 0.40
IGL03001:Cd1d1 APN 3 86,905,468 (GRCm39) missense probably benign
R0350:Cd1d1 UTSW 3 86,904,880 (GRCm39) missense probably benign 0.11
R1771:Cd1d1 UTSW 3 86,905,972 (GRCm39) missense possibly damaging 0.85
R2407:Cd1d1 UTSW 3 86,905,489 (GRCm39) missense probably damaging 1.00
R3906:Cd1d1 UTSW 3 86,906,063 (GRCm39) missense probably damaging 1.00
R4540:Cd1d1 UTSW 3 86,904,012 (GRCm39) missense probably benign 0.21
R4976:Cd1d1 UTSW 3 86,905,958 (GRCm39) missense probably benign 0.00
R5303:Cd1d1 UTSW 3 86,905,427 (GRCm39) missense probably benign 0.22
R5786:Cd1d1 UTSW 3 86,906,095 (GRCm39) missense probably benign 0.17
R6088:Cd1d1 UTSW 3 86,906,009 (GRCm39) missense probably benign 0.07
R6273:Cd1d1 UTSW 3 86,905,564 (GRCm39) missense probably benign 0.00
R7315:Cd1d1 UTSW 3 86,905,420 (GRCm39) missense possibly damaging 0.80
R7787:Cd1d1 UTSW 3 86,904,903 (GRCm39) missense probably damaging 0.98
R8854:Cd1d1 UTSW 3 86,905,480 (GRCm39) missense probably damaging 0.99
R9079:Cd1d1 UTSW 3 86,906,197 (GRCm39) missense probably benign
R9328:Cd1d1 UTSW 3 86,905,459 (GRCm39) missense possibly damaging 0.80
R9368:Cd1d1 UTSW 3 86,905,939 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- ACTCACAGTCTTCTTTAGGTGAC -3'
(R):5'- AGAACTACACTGAGCCTGCC -3'

Sequencing Primer
(F):5'- GGTGACATCATTTTGACTAATTCCTG -3'
(R):5'- CTTTCCTTCCGCAAGCGCAG -3'
Posted On 2021-08-31