Incidental Mutation 'R9079:Cd1d1'
ID 689886
Institutional Source Beutler Lab
Gene Symbol Cd1d1
Ensembl Gene ENSMUSG00000028076
Gene Name CD1d1 antigen
Synonyms Cd1d, Cd1a, CD1.1, Ly-38
MMRRC Submission 068899-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.100) question?
Stock # R9079 (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 86906197 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 26 (Y26F)
Ref Sequence ENSEMBL: ENSMUSP00000029717 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029717] [ENSMUST00000063869]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000029717
AA Change: Y26F

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000029717
Gene: ENSMUSG00000028076
AA Change: Y26F

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: Y26F

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000070616
Gene: ENSMUSG00000028076
AA Change: Y26F

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: 100.0%
  • 10x: 99.8%
  • 20x: 99.4%
Validation Efficiency 98% (51/52)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atad2 A T 15: 57,989,223 (GRCm39) S212R probably benign Het
Bcl9 A T 3: 97,112,816 (GRCm39) V1213E probably damaging Het
Brd1 T C 15: 88,598,153 (GRCm39) D531G probably damaging Het
Cep83 T C 10: 94,564,541 (GRCm39) F160S possibly damaging Het
Cfap61 G T 2: 145,781,859 (GRCm39) V31F probably benign Het
Cox11 G A 11: 90,535,246 (GRCm39) M232I probably damaging Het
Cpne7 C T 8: 123,856,951 (GRCm39) P402L probably damaging Het
Cubn A G 2: 13,291,914 (GRCm39) S3304P probably benign Het
Eif4b T A 15: 102,003,177 (GRCm39) D549E unknown Het
Extl1 T A 4: 134,089,975 (GRCm39) N378Y probably damaging Het
Fbxo4 C T 15: 3,998,388 (GRCm39) probably null Het
Fhip1a C A 3: 85,579,590 (GRCm39) G872* probably null Het
G430095P16Rik A T 8: 85,453,412 (GRCm39) H133L unknown Het
Gm8138 A T 14: 43,272,502 (GRCm39) N104K Het
Gzma A G 13: 113,232,858 (GRCm39) F78S probably benign Het
Hars2 T C 18: 36,923,190 (GRCm39) S400P possibly damaging Het
Hnrnpm G T 17: 33,868,775 (GRCm39) R551S probably damaging Het
Htr5b T A 1: 121,455,816 (GRCm39) T35S probably benign Het
Jak3 A C 8: 72,131,898 (GRCm39) E158A probably benign Het
Kctd16 A G 18: 40,390,080 (GRCm39) probably benign Het
Kdm4c C A 4: 74,277,738 (GRCm39) D797E probably benign Het
Klhl31 T A 9: 77,558,151 (GRCm39) V289E probably damaging Het
Loxhd1 T C 18: 77,490,593 (GRCm39) S1398P probably benign Het
Matn4 A T 2: 164,235,473 (GRCm39) probably benign Het
Mrps28 A G 3: 8,867,308 (GRCm39) *187Q probably null Het
Myh7b G A 2: 155,465,174 (GRCm39) V677I probably damaging Het
Naip1 A T 13: 100,559,727 (GRCm39) D1092E probably benign Het
Nicn1 C T 9: 108,171,708 (GRCm39) R163C possibly damaging Het
Notch3 A T 17: 32,383,033 (GRCm39) probably benign Het
Nr1h2 C A 7: 44,199,430 (GRCm39) E440D possibly damaging Het
Or1l4b T C 2: 37,036,989 (GRCm39) V255A probably damaging Het
Or6c207 A T 10: 129,104,466 (GRCm39) M242K possibly damaging Het
Or7g16 A T 9: 18,726,731 (GRCm39) N286K probably damaging Het
Or8g2b T A 9: 39,750,769 (GRCm39) I13N probably benign Het
Osbpl9 A T 4: 108,920,644 (GRCm39) V543D possibly damaging Het
Pcgf6 T C 19: 47,039,053 (GRCm39) E69G possibly damaging Het
Piezo2 A G 18: 63,157,537 (GRCm39) L2391P probably damaging Het
Rcn2 T A 9: 55,952,393 (GRCm39) probably benign Het
Ripor2 G A 13: 24,915,637 (GRCm39) R1069H probably benign Het
Ro60 A C 1: 143,641,519 (GRCm39) L314R probably damaging Het
Rsf1 ATGGCG ATGGCGACGGTGGCG 7: 97,229,111 (GRCm39) probably benign Het
Senp5 A T 16: 31,787,718 (GRCm39) I635N probably damaging Het
Slc30a9 A T 5: 67,484,241 (GRCm39) K126M possibly damaging Het
Slc9b2 A T 3: 135,042,150 (GRCm39) R476S probably damaging Het
Sptb G T 12: 76,677,454 (GRCm39) R127S probably damaging Het
Svil T C 18: 5,056,308 (GRCm39) S394P probably benign Het
Tjp1 A T 7: 64,950,966 (GRCm39) I1636N possibly damaging Het
Tlcd5 C T 9: 43,022,664 (GRCm39) R230Q probably benign Het
Trio T C 15: 27,733,023 (GRCm39) I2953V possibly damaging Het
Ttn A G 2: 76,632,734 (GRCm39) F14107L probably damaging Het
Usp20 A G 2: 30,895,120 (GRCm39) probably benign Het
Vmn1r123 A T 7: 20,896,979 (GRCm39) L290F probably benign Het
Vmn1r202 T C 13: 22,685,602 (GRCm39) M272V probably benign Het
Vmn2r97 A T 17: 19,149,640 (GRCm39) N343Y probably benign Het
Wdr90 A T 17: 26,076,403 (GRCm39) W45R 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
R8957:Cd1d1 UTSW 3 86,906,140 (GRCm39) missense probably damaging 0.99
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'- AGCTGACTCGATAGACTTGAAAC -3'
(R):5'- CTTGCAACAACAGTGGGAGG -3'

Sequencing Primer
(F):5'- CTCGATAGACTTGAAACATATGCTGC -3'
(R):5'- GAGCAATGTATGGCTGCGGC -3'
Posted On 2021-11-19