Incidental Mutation 'R8854:Cd1d1'
ID 675159
Institutional Source Beutler Lab
Gene Symbol Cd1d1
Ensembl Gene ENSMUSG00000028076
Gene Name CD1d1 antigen
Synonyms Cd1d, Cd1a, CD1.1, Ly-38
MMRRC Submission 068676-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.100) question?
Stock # R8854 (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 A at 86905480 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 171 (D171V)
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: D171V

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000029717
Gene: ENSMUSG00000028076
AA Change: D171V

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
SMART Domains Protein: ENSMUSP00000070616
Gene: ENSMUSG00000028076

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% (64/64)
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aldh1a1 G A 19: 20,588,297 (GRCm39) W29* probably null Het
Ankib1 C A 5: 3,777,489 (GRCm39) W467L probably null Het
Arhgef10 A G 8: 15,029,798 (GRCm39) probably null Het
Arpc1b C A 5: 145,060,405 (GRCm39) R66S probably benign Het
Atoh1 A T 6: 64,706,189 (GRCm39) probably benign Het
Bach2 T A 4: 32,575,263 (GRCm39) D619E possibly damaging Het
Bbs9 T C 9: 22,490,060 (GRCm39) I277T probably damaging Het
Cadps2 G A 6: 23,385,507 (GRCm39) P772S probably damaging Het
Cfap20dc A T 14: 8,518,638 (GRCm38) S273T probably damaging Het
Clca3a2 C T 3: 144,783,852 (GRCm39) A588T possibly damaging Het
Cps1 A G 1: 67,200,048 (GRCm39) K399E probably damaging Het
Cpt1a T C 19: 3,406,327 (GRCm39) S98P probably benign Het
Cryzl2 A G 1: 157,286,370 (GRCm39) K36R possibly damaging Het
Cxcl13 T C 5: 96,104,861 (GRCm39) L11P unknown Het
Dbf4 T A 5: 8,458,562 (GRCm39) D151V probably damaging Het
Eogt A T 6: 97,108,359 (GRCm39) C227* probably null Het
Fermt3 T A 19: 6,991,310 (GRCm39) D231V probably damaging Het
Il2rb T C 15: 78,369,953 (GRCm39) T229A probably benign Het
Ildr1 T A 16: 36,535,910 (GRCm39) Y142N probably damaging Het
Kcnv2 A T 19: 27,311,258 (GRCm39) T542S probably benign Het
Kif26b G A 1: 178,743,948 (GRCm39) G1348E possibly damaging Het
Lancl1 C T 1: 67,073,358 (GRCm39) E42K possibly damaging Het
Lrp1 T A 10: 127,378,968 (GRCm39) D4010V probably damaging Het
Mark2 A G 19: 7,258,369 (GRCm39) V640A probably benign Het
Megf6 C T 4: 154,352,469 (GRCm39) T1276M probably damaging Het
Meioc T C 11: 102,566,589 (GRCm39) M735T probably damaging Het
Mfsd4b5 C A 10: 39,846,735 (GRCm39) V282L probably damaging Het
Mlx T A 11: 100,981,951 (GRCm39) V286E Het
Ms4a18 G A 19: 10,990,887 (GRCm39) T69I probably benign Het
Muc1 C T 3: 89,139,412 (GRCm39) P604L probably damaging Het
Net1 G T 13: 3,934,214 (GRCm39) D548E probably benign Het
Ngly1 T C 14: 16,281,769 (GRCm38) S342P probably damaging Het
Niban1 A G 1: 151,584,950 (GRCm39) K516E probably damaging Het
Nipbl A T 15: 8,330,210 (GRCm39) I2405N probably damaging Het
Nkx2-1 A T 12: 56,580,206 (GRCm39) C245S probably benign Het
Or52ab7 T C 7: 102,978,023 (GRCm39) I110T probably damaging Het
Or5p76 T A 7: 108,122,936 (GRCm39) I74L probably benign Het
Pcare T C 17: 72,056,326 (GRCm39) Y1117C probably benign Het
Pcdhgb5 C T 18: 37,865,501 (GRCm39) T432I probably benign Het
Plpp4 T A 7: 128,909,362 (GRCm39) L24* probably null Het
Pnma8a T C 7: 16,695,104 (GRCm39) S320P possibly damaging Het
Sass6 C A 3: 116,399,384 (GRCm39) Q93K possibly damaging Het
Sirpb1c T C 3: 15,887,308 (GRCm39) N177S possibly damaging Het
Slc22a30 A G 19: 8,363,754 (GRCm39) probably null Het
Snd1 A G 6: 28,526,968 (GRCm39) H217R probably benign Het
Spata31d1c C A 13: 65,183,804 (GRCm39) Q449K possibly damaging Het
Spidr A G 16: 15,707,630 (GRCm39) V889A probably damaging Het
Suclg2 A T 6: 95,572,650 (GRCm39) V105D probably damaging Het
Syne1 A T 10: 5,078,503 (GRCm39) M974K probably benign Het
Tbrg4 A T 11: 6,566,691 (GRCm39) D605E probably benign Het
Tcn2 A G 11: 3,876,074 (GRCm39) F118S possibly damaging Het
Tcstv2b T A 13: 120,377,825 (GRCm39) probably benign Het
Tfap4 T C 16: 4,367,238 (GRCm39) H208R probably benign Het
Trf A G 9: 103,107,529 (GRCm39) probably benign Het
Trpc4 A T 3: 54,102,122 (GRCm39) K7* probably null Het
Uap1 G T 1: 169,976,984 (GRCm39) P405Q probably damaging Het
Usp33 C A 3: 152,073,967 (GRCm39) T271N probably benign Het
Usp42 T C 5: 143,702,632 (GRCm39) D663G possibly damaging Het
Vmn2r10 T C 5: 109,144,126 (GRCm39) D608G probably benign Het
Wfdc16 G A 2: 164,480,486 (GRCm39) P3L probably benign Het
Zfp28 T C 7: 6,397,938 (GRCm39) I791T probably benign Het
Zfp970 A T 2: 177,165,088 (GRCm39) T5S probably damaging Het
Zfy1 A T Y: 726,501 (GRCm39) H421Q possibly 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
R8957:Cd1d1 UTSW 3 86,906,140 (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'- CAAGAGTGGCTGTCAGTGAG -3'
(R):5'- CCCATTGAGATCCAGCTGTCTG -3'

Sequencing Primer
(F):5'- TGGCTGTCAGTGAGAAAATAAACCC -3'
(R):5'- CTGCGGGCTGTGAAATGTACC -3'
Posted On 2021-07-15