Incidental Mutation 'IGL03001:Cd1d1'
ID 407337
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Cd1d1
Ensembl Gene ENSMUSG00000028076
Gene Name CD1d1 antigen
Synonyms Cd1d, Cd1a, CD1.1, Ly-38
Accession Numbers
Essential gene? Probably non essential (E-score: 0.100) question?
Stock # IGL03001
Quality Score
Status
Chromosome 3
Chromosomal Location 86903141-86906748 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 86905468 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Asparagine at position 175 (S175N)
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: S175N

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000029717
Gene: ENSMUSG00000028076
AA Change: S175N

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000107620
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132131
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142793
Coding Region Coverage
Validation Efficiency
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
Acan A C 7: 78,761,042 (GRCm39) D1918A probably damaging Het
Ahcy C A 2: 154,906,748 (GRCm39) D182Y probably damaging Het
Aldob T G 4: 49,542,844 (GRCm39) D110A probably damaging Het
Alkbh8 A T 9: 3,344,602 (GRCm39) M53L probably benign Het
Aqr T C 2: 113,977,400 (GRCm39) D363G probably benign Het
Asxl3 A G 18: 22,650,455 (GRCm39) R815G probably damaging Het
Atf4 T A 15: 80,140,858 (GRCm39) W83R probably damaging Het
Baz1a A T 12: 54,969,896 (GRCm39) M587K possibly damaging Het
Btbd8 T C 5: 107,645,708 (GRCm39) I9T probably damaging Het
Cactin T A 10: 81,161,568 (GRCm39) I700N probably damaging Het
Catsperg2 T C 7: 29,424,504 (GRCm39) S95G probably benign Het
Chd4 C A 6: 125,078,529 (GRCm39) A217E possibly damaging Het
Cnbd2 T C 2: 156,175,554 (GRCm39) probably null Het
Cntnap5c G A 17: 58,362,634 (GRCm39) C329Y probably damaging Het
Col12a1 C T 9: 79,540,955 (GRCm39) G2391R probably damaging Het
Col5a3 T A 9: 20,719,040 (GRCm39) D238V unknown Het
Cuedc1 T C 11: 88,073,315 (GRCm39) V160A probably benign Het
Depdc5 T C 5: 33,102,434 (GRCm39) V342A possibly damaging Het
Dnah6 T C 6: 73,126,123 (GRCm39) D1338G probably benign Het
Dpyd T C 3: 118,710,891 (GRCm39) V433A probably benign Het
Epb41l5 T C 1: 119,545,374 (GRCm39) H179R probably damaging Het
Fbf1 T C 11: 116,056,712 (GRCm39) probably benign Het
Flnb T C 14: 7,934,680 (GRCm38) S2251P probably damaging Het
Fsip2 A T 2: 82,820,968 (GRCm39) probably benign Het
Grin2b C T 6: 135,716,113 (GRCm39) V735M probably damaging Het
Itpr3 T G 17: 27,308,586 (GRCm39) probably benign Het
Lingo4 C T 3: 94,309,703 (GRCm39) R214C probably damaging Het
Lrp1b C T 2: 40,817,901 (GRCm39) R2329H probably damaging Het
Lrrc47 T C 4: 154,100,450 (GRCm39) L342P probably damaging Het
Mmp15 T C 8: 96,094,845 (GRCm39) S240P probably damaging Het
Ndufaf4 T A 4: 24,901,747 (GRCm39) N95K probably benign Het
Nms C T 1: 38,980,993 (GRCm39) P60S probably benign Het
Npas3 A T 12: 53,547,975 (GRCm39) Y77F probably damaging Het
Or2ak7 T G 11: 58,574,702 (GRCm39) M1R probably null Het
Or51f5 G T 7: 102,424,460 (GRCm39) C243F probably damaging Het
Or5d43 T A 2: 88,105,189 (GRCm39) D68V probably damaging Het
Or8d2b A G 9: 38,789,374 (GRCm39) M301V probably benign Het
Or9m2 T A 2: 87,820,493 (GRCm39) Y13N probably benign Het
Or9s27 T A 1: 92,516,273 (GRCm39) S74T probably damaging Het
Picalm T C 7: 89,831,454 (GRCm39) V429A probably benign Het
Pkhd1l1 T A 15: 44,421,400 (GRCm39) I3056N probably damaging Het
Pomt1 G T 2: 32,134,338 (GRCm39) M286I probably benign Het
Popdc2 A T 16: 38,189,881 (GRCm39) Y176F probably benign Het
Psg21 A T 7: 18,386,410 (GRCm39) M192K probably benign Het
Psma1 C A 7: 113,865,674 (GRCm39) A219S probably benign Het
Rad21l T G 2: 151,510,389 (GRCm39) H22P probably damaging Het
Rnf213 A G 11: 119,370,767 (GRCm39) T4791A probably damaging Het
Sdk2 A G 11: 113,712,452 (GRCm39) V1609A probably benign Het
Sema3e T A 5: 14,291,057 (GRCm39) S606T probably benign Het
Slc16a4 A T 3: 107,218,858 (GRCm39) R486S possibly damaging Het
Slc17a3 T C 13: 24,040,767 (GRCm39) L331P probably damaging Het
Slc38a11 A T 2: 65,184,159 (GRCm39) V164D probably damaging Het
Slc38a6 A G 12: 73,383,827 (GRCm39) I173V probably benign Het
Synpo2 T C 3: 122,873,604 (GRCm39) T1121A probably benign Het
Tfcp2 T C 15: 100,426,302 (GRCm39) D83G possibly damaging Het
Thnsl1 A G 2: 21,216,455 (GRCm39) T70A probably damaging Het
Tnfrsf21 A G 17: 43,398,786 (GRCm39) I631V probably damaging Het
Tor2a C A 2: 32,647,329 (GRCm39) H6Q possibly damaging Het
Ttn T C 2: 76,565,267 (GRCm39) N19993S probably benign Het
Vps53 T C 11: 76,029,150 (GRCm39) E119G probably damaging Het
Zkscan6 T C 11: 65,705,495 (GRCm39) W69R probably damaging Het
Zng1 T C 19: 24,900,002 (GRCm39) K301E probably benign Het
Zswim8 T C 14: 20,764,459 (GRCm39) S610P 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
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
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
Posted On 2016-08-02