Incidental Mutation 'R8163:Cd3d'
ID 633626
Institutional Source Beutler Lab
Gene Symbol Cd3d
Ensembl Gene ENSMUSG00000032094
Gene Name CD3 antigen, delta polypeptide
Synonyms T3d
MMRRC Submission 067589-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.134) question?
Stock # R8163 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 44893067-44898350 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 44896952 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 109 (F109L)
Ref Sequence ENSEMBL: ENSMUSP00000034602 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034602]
AlphaFold P04235
Predicted Effect probably benign
Transcript: ENSMUST00000034602
AA Change: F109L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000034602
Gene: ENSMUSG00000032094
AA Change: F109L

DomainStartEndE-ValueType
signal peptide 1 21 N/A INTRINSIC
Pfam:Ig_4 30 103 5.9e-23 PFAM
transmembrane domain 105 127 N/A INTRINSIC
ITAM 146 166 2.41e-4 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.4%
  • 20x: 98.2%
Validation Efficiency 100% (53/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is part of the T-cell receptor/CD3 complex (TCR/CD3 complex) and is involved in T-cell development and signal transduction. The encoded membrane protein represents the delta subunit of the CD3 complex, and along with four other CD3 subunits, binds either TCR alpha/beta or TCR gamma/delta to form the TCR/CD3 complex on the surface of T-cells. Defects in this gene are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (SCIDBNK). Two transcript variants encoding different isoforms have been found for this gene. Other variants may also exist, but the full-length natures of their transcripts has yet to be defined. [provided by RefSeq, Feb 2009]
PHENOTYPE: Homozygotes for targeted null mutations exhibit impaired early thymic development, small numbers of peripheral TCR-alpha/beta+ T cells, and failure of T lymphocyte transition from double-positive to single-positive developmental stages. [provided by MGI curators]
Allele List at MGI

All alleles(9) : Targeted, knock-out(2) Targeted, other(2) Gene trapped(5)
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930022D16Rik A G 11: 109,304,883 (GRCm39) I11V unknown Het
Ago3 G T 4: 126,262,377 (GRCm39) T391K probably benign Het
Asap1 A G 15: 63,963,899 (GRCm39) W1100R probably damaging Het
Bbof1 T C 12: 84,473,536 (GRCm39) S289P possibly damaging Het
Cebpd A T 16: 15,705,841 (GRCm39) E218V probably damaging Het
Cfl1 T C 19: 5,543,528 (GRCm39) probably benign Het
Cpa2 A C 6: 30,564,350 (GRCm39) I394L probably damaging Het
Ddx50 C A 10: 62,475,678 (GRCm39) V348F possibly damaging Het
Dnajc28 G A 16: 91,413,795 (GRCm39) R150* probably null Het
Echs1 A G 7: 139,692,357 (GRCm39) V130A possibly damaging Het
Eif2s2 A G 2: 154,734,621 (GRCm39) S2P probably benign Het
Fastk A G 5: 24,649,273 (GRCm39) I38T probably benign Het
Fat3 G A 9: 15,871,055 (GRCm39) R3779C probably damaging Het
Fat4 A T 3: 39,033,881 (GRCm39) N2511I possibly damaging Het
Fbxw13 G A 9: 109,012,122 (GRCm39) T315I probably benign Het
Fzd5 A T 1: 64,774,352 (GRCm39) Y470N probably damaging Het
G530012D18Rik C G 1: 85,504,935 (GRCm39) D113E unknown Het
Gpr25 T C 1: 136,187,596 (GRCm39) D339G probably damaging Het
Igsf9b T A 9: 27,233,907 (GRCm39) probably null Het
Il5 T A 11: 53,614,813 (GRCm39) M125K possibly damaging Het
Iqub G A 6: 24,449,714 (GRCm39) T717I probably benign Het
Katnb1 T C 8: 95,823,014 (GRCm39) F403S probably damaging Het
Krt26 T C 11: 99,220,498 (GRCm39) I451V probably benign Het
Krt88 T C 15: 101,351,389 (GRCm39) L132P probably damaging Het
Kynu G T 2: 43,518,966 (GRCm39) G245V probably damaging Het
Lap3 C T 5: 45,669,389 (GRCm39) R513* probably null Het
Lin9 C T 1: 180,486,691 (GRCm39) R126W probably damaging Het
Lrrc37 A T 11: 103,506,688 (GRCm39) I1760K unknown Het
Lrrtm2 C T 18: 35,346,777 (GRCm39) R175H probably damaging Het
N4bp2l2 A G 5: 150,584,774 (GRCm39) L60P probably damaging Het
Ncr1 T C 7: 4,343,828 (GRCm39) F142S probably damaging Het
Nktr TAGAAG TAG 9: 121,579,929 (GRCm39) probably benign Het
Or5b95 A G 19: 12,657,552 (GRCm39) I27V probably benign Het
Parp16 T A 9: 65,137,231 (GRCm39) H152Q probably damaging Het
Plaa C G 4: 94,457,640 (GRCm39) V777L probably benign Het
Prnp A G 2: 131,778,908 (GRCm39) T187A probably benign Het
Pzp T G 6: 128,489,157 (GRCm39) I485L probably benign Het
Rc3h1 T A 1: 160,782,629 (GRCm39) Y703N probably damaging Het
Rngtt G A 4: 33,325,109 (GRCm39) C110Y probably damaging Het
Rps10 G A 17: 27,853,085 (GRCm39) R95C probably benign Het
Scn9a T A 2: 66,314,745 (GRCm39) I1658F probably damaging Het
Sec16a A T 2: 26,306,433 (GRCm39) W702R Het
Taf6 G T 5: 138,180,238 (GRCm39) Q339K possibly damaging Het
Tbcd C T 11: 121,384,711 (GRCm39) T315M probably benign Het
Tmem198 C T 1: 75,459,671 (GRCm39) P209S possibly damaging Het
Vmn2r78 G A 7: 86,603,660 (GRCm39) A613T probably damaging Het
Vps13c G A 9: 67,857,720 (GRCm39) E2651K probably benign Het
Wdfy4 C T 14: 32,873,545 (GRCm39) V255I Het
Zfhx3 A G 8: 109,675,925 (GRCm39) D2325G probably damaging Het
Zfp36l2 T C 17: 84,494,551 (GRCm39) N29D possibly damaging Het
Zfp692 T A 11: 58,201,199 (GRCm39) probably null Het
Other mutations in Cd3d
AlleleSourceChrCoordTypePredicted EffectPPH Score
3-1:Cd3d UTSW 9 44,896,295 (GRCm39) missense probably damaging 1.00
R1992:Cd3d UTSW 9 44,896,299 (GRCm39) nonsense probably null
R4989:Cd3d UTSW 9 44,896,296 (GRCm39) missense probably damaging 1.00
R5133:Cd3d UTSW 9 44,896,296 (GRCm39) missense probably damaging 1.00
R5134:Cd3d UTSW 9 44,896,296 (GRCm39) missense probably damaging 1.00
R6362:Cd3d UTSW 9 44,897,589 (GRCm39) missense probably damaging 1.00
R6857:Cd3d UTSW 9 44,896,902 (GRCm39) missense probably damaging 1.00
R6923:Cd3d UTSW 9 44,897,157 (GRCm39) intron probably benign
R7040:Cd3d UTSW 9 44,896,991 (GRCm39) missense probably damaging 1.00
R7711:Cd3d UTSW 9 44,897,634 (GRCm39) missense probably benign 0.00
R9071:Cd3d UTSW 9 44,896,340 (GRCm39) missense probably benign
Z1176:Cd3d UTSW 9 44,896,926 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCACAAAGCTGAAGTGTGTC -3'
(R):5'- ATCCCACATCTTTCAGCCAG -3'

Sequencing Primer
(F):5'- CCACAAAGCTGAAGTGTGTCATGTC -3'
(R):5'- GCCAGTTTATGAGTTCACACAC -3'
Posted On 2020-07-13