Incidental Mutation 'R4540:Cd1d1'
| ID |
333481 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Cd1d1
|
| Ensembl Gene |
ENSMUSG00000028076 |
| Gene Name |
CD1d1 antigen |
| Synonyms |
Cd1d, Cd1a, CD1.1, Ly-38 |
| MMRRC Submission |
041776-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.100)
|
| Stock # |
R4540 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
86903141-86906748 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 86904012 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 194
(I194T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000070616
(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: I325T
PolyPhen 2
Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000029717
Gene: ENSMUSG00000028076
AA Change: I325T
| Domain | Start | End | E-Value | Type |
|---|
|
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: I194T
PolyPhen 2
Score 0.207 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000070616
Gene: ENSMUSG00000028076
AA Change: I194T
| Domain | Start | End | E-Value | Type |
|---|
|
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
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
| Validation Efficiency |
100% (43/43) |
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam6a |
A |
T |
12: 113,508,119 (GRCm39) |
H164L |
probably damaging |
Het |
| Arrdc3 |
C |
A |
13: 81,038,790 (GRCm39) |
R31S |
possibly damaging |
Het |
| Baiap3 |
C |
T |
17: 25,465,644 (GRCm39) |
V585M |
probably damaging |
Het |
| Braf |
A |
G |
6: 39,621,267 (GRCm39) |
S391P |
probably damaging |
Het |
| Ccdc51 |
T |
C |
9: 108,921,288 (GRCm39) |
F392L |
possibly damaging |
Het |
| Cep162 |
T |
C |
9: 87,094,992 (GRCm39) |
K806E |
probably damaging |
Het |
| Cntn4 |
A |
G |
6: 106,652,709 (GRCm39) |
E726G |
probably damaging |
Het |
| Col11a1 |
A |
G |
3: 113,890,815 (GRCm39) |
Y384C |
unknown |
Het |
| Cops3 |
A |
T |
11: 59,720,980 (GRCm39) |
L145H |
probably damaging |
Het |
| Cul9 |
C |
T |
17: 46,814,015 (GRCm39) |
M2286I |
probably null |
Het |
| Echdc1 |
G |
A |
10: 29,220,578 (GRCm39) |
V245I |
probably benign |
Het |
| Fsip2 |
A |
T |
2: 82,782,009 (GRCm39) |
M261L |
probably benign |
Het |
| Gm4353 |
A |
G |
7: 115,683,212 (GRCm39) |
L123P |
probably benign |
Het |
| Hcfc2 |
G |
C |
10: 82,568,481 (GRCm39) |
E42Q |
probably benign |
Het |
| Hfm1 |
A |
C |
5: 107,022,087 (GRCm39) |
Y199* |
probably null |
Het |
| Iba57 |
G |
A |
11: 59,053,904 (GRCm39) |
|
probably benign |
Het |
| Ihh |
T |
A |
1: 74,987,558 (GRCm39) |
N161I |
possibly damaging |
Het |
| Kcnh7 |
A |
G |
2: 62,569,530 (GRCm39) |
S789P |
probably damaging |
Het |
| Kndc1 |
C |
A |
7: 139,501,343 (GRCm39) |
C877* |
probably null |
Het |
| Lhcgr |
A |
G |
17: 89,063,036 (GRCm39) |
I212T |
probably benign |
Het |
| Lrrtm2 |
T |
A |
18: 35,346,199 (GRCm39) |
T368S |
probably benign |
Het |
| Mag |
A |
C |
7: 30,600,154 (GRCm39) |
V500G |
probably damaging |
Het |
| Nadsyn1 |
A |
G |
7: 143,356,960 (GRCm39) |
V512A |
probably damaging |
Het |
| Nlrp3 |
G |
A |
11: 59,442,725 (GRCm39) |
C759Y |
possibly damaging |
Het |
| Nup107 |
T |
C |
10: 117,597,925 (GRCm39) |
|
probably null |
Het |
| Or4c3d |
T |
C |
2: 89,882,494 (GRCm39) |
Y58C |
probably damaging |
Het |
| Or4f56 |
T |
C |
2: 111,703,546 (GRCm39) |
Y218C |
probably damaging |
Het |
| Pcdha1 |
A |
C |
18: 37,064,680 (GRCm39) |
D448A |
probably damaging |
Het |
| Pitrm1 |
T |
A |
13: 6,605,506 (GRCm39) |
|
probably null |
Het |
| Pth2r |
A |
G |
1: 65,321,360 (GRCm39) |
N13S |
probably benign |
Het |
| Rae1 |
G |
T |
2: 172,857,185 (GRCm39) |
|
probably benign |
Het |
| Selenoi |
A |
G |
5: 30,461,085 (GRCm39) |
D107G |
probably damaging |
Het |
| Sost |
G |
A |
11: 101,857,670 (GRCm39) |
P44S |
probably damaging |
Het |
| Spag17 |
C |
T |
3: 99,995,697 (GRCm39) |
P1779S |
probably damaging |
Het |
| Supt3 |
T |
C |
17: 45,347,662 (GRCm39) |
V208A |
probably benign |
Het |
| Tbc1d30 |
T |
C |
10: 121,115,063 (GRCm39) |
E365G |
probably damaging |
Het |
| Tnxb |
C |
T |
17: 34,922,309 (GRCm39) |
T2374I |
possibly damaging |
Het |
| Trip12 |
A |
G |
1: 84,726,997 (GRCm39) |
I1T |
probably damaging |
Het |
|
| Other mutations in Cd1d1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TTCATCCCCAGATCCTGAGC -3'
(R):5'- GCCAGATCCTGATCATGAGAAATGG -3'
Sequencing Primer
(F):5'- ACTGAAGTCCTAGAGCCTGG -3'
(R):5'- TCCTGATCATGAGAAATGGAATGG -3'
|
| Posted On |
2015-08-18 |
Incidental Mutation