Incidental Mutation 'R5222:Cd40'
| ID |
402357 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Cd40
|
| Ensembl Gene |
ENSMUSG00000017652 |
| Gene Name |
CD40 antigen |
| Synonyms |
Tnfrsf5, p50, Bp50, Cd40 |
| MMRRC Submission |
042795-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5222 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
164897535-164913574 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to C
at 164908464 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 180
(S180T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000139193
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000017799]
[ENSMUST00000073707]
[ENSMUST00000081310]
[ENSMUST00000140951]
[ENSMUST00000154443]
[ENSMUST00000184221]
|
| AlphaFold |
P27512 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000017799
AA Change: S180T
PolyPhen 2
Score 0.415 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000017799
Gene: ENSMUSG00000017652
AA Change: S180T
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
TNFR
|
26 |
59 |
9.45e-6 |
SMART |
|
TNFR
|
62 |
103 |
2.38e-11 |
SMART |
|
TNFR
|
105 |
143 |
4.55e-8 |
SMART |
|
TNFR
|
146 |
186 |
2.42e-3 |
SMART |
|
transmembrane domain
|
193 |
215 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000073707
AA Change: S180T
PolyPhen 2
Score 0.415 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000073386
Gene: ENSMUSG00000017652
AA Change: S180T
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
TNFR
|
26 |
59 |
9.45e-6 |
SMART |
|
TNFR
|
62 |
103 |
2.38e-11 |
SMART |
|
TNFR
|
105 |
143 |
4.55e-8 |
SMART |
|
TNFR
|
146 |
186 |
2.42e-3 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000081310
|
| SMART Domains |
Protein: ENSMUSP00000080059
Gene: ENSMUSG00000017652
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
TNFR
|
26 |
59 |
9.45e-6 |
SMART |
|
TNFR
|
62 |
103 |
2.38e-11 |
SMART |
|
TNFR
|
105 |
143 |
4.55e-8 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000140951
|
| SMART Domains |
Protein: ENSMUSP00000122981
Gene: ENSMUSG00000017652
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
TNFR
|
64 |
97 |
9.45e-6 |
SMART |
|
Blast:TNFR
|
100 |
121 |
1e-8 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153105
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154443
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000184221
AA Change: S180T
PolyPhen 2
Score 0.415 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000139193
Gene: ENSMUSG00000017652
AA Change: S180T
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
TNFR
|
26 |
59 |
9.45e-6 |
SMART |
|
TNFR
|
62 |
103 |
2.38e-11 |
SMART |
|
TNFR
|
105 |
143 |
4.55e-8 |
SMART |
|
TNFR
|
146 |
186 |
2.42e-3 |
SMART |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
| Validation Efficiency |
98% (52/53) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the TNF-receptor superfamily. The encoded protein is a receptor on antigen-presenting cells of the immune system and is essential for mediating a broad variety of immune and inflammatory responses including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. AT-hook transcription factor AKNA is reported to coordinately regulate the expression of this receptor and its ligand, which may be important for homotypic cell interactions. Adaptor protein TNFR2 interacts with this receptor and serves as a mediator of the signal transduction. The interaction of this receptor and its ligand is found to be necessary for amyloid-beta-induced microglial activation, and thus is thought to be an early event in Alzheimer disease pathogenesis. Mutations affecting this gene are the cause of autosomal recessive hyper-IgM immunodeficiency type 3 (HIGM3). Multiple alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Nov 2014]
PHENOTYPE: Homozygous inactivation of this gene may cause impaired immunoglobulin class switching and germinal center formation, reduced susceptibility to type II hypersensitivity reaction, impaired priming of T cells and control of M. tuberculosis infection, and altered response to transplant. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930523C07Rik |
C |
A |
1: 159,872,178 (GRCm39) |
|
noncoding transcript |
Het |
| Acad11 |
G |
A |
9: 103,974,576 (GRCm39) |
A515T |
probably damaging |
Het |
| Angpt1 |
T |
C |
15: 42,539,730 (GRCm39) |
Y43C |
probably damaging |
Het |
| Arhgef33 |
A |
G |
17: 80,644,743 (GRCm39) |
Y24C |
probably damaging |
Het |
| Cenpc1 |
A |
T |
5: 86,185,606 (GRCm39) |
S302T |
possibly damaging |
Het |
| Cit |
C |
A |
5: 116,090,602 (GRCm39) |
T932K |
probably benign |
Het |
| Col19a1 |
A |
C |
1: 24,598,721 (GRCm39) |
|
probably null |
Het |
| Dapk3 |
A |
G |
10: 81,028,294 (GRCm39) |
E288G |
probably damaging |
Het |
| Ddx60 |
T |
C |
8: 62,437,192 (GRCm39) |
F1002S |
probably damaging |
Het |
| Dgke |
G |
T |
11: 88,941,220 (GRCm39) |
T321K |
probably benign |
Het |
| Ebf2 |
T |
G |
14: 67,551,043 (GRCm39) |
|
probably benign |
Het |
| Enpp7 |
A |
G |
11: 118,881,788 (GRCm39) |
D311G |
probably benign |
Het |
| Epm2a |
A |
G |
10: 11,324,493 (GRCm39) |
E194G |
probably damaging |
Het |
| Esf1 |
A |
G |
2: 140,000,503 (GRCm39) |
Y428H |
possibly damaging |
Het |
| Esyt2 |
T |
C |
12: 116,282,446 (GRCm39) |
F132S |
probably damaging |
Het |
| Gm5455 |
T |
C |
13: 110,441,494 (GRCm39) |
|
noncoding transcript |
Het |
| Gria1 |
T |
A |
11: 57,080,623 (GRCm39) |
V202E |
probably benign |
Het |
| Lin9 |
T |
A |
1: 180,496,763 (GRCm39) |
L351I |
probably benign |
Het |
| Mark1 |
A |
T |
1: 184,660,288 (GRCm39) |
F123I |
probably damaging |
Het |
| Nectin4 |
T |
A |
1: 171,212,825 (GRCm39) |
|
probably null |
Het |
| Obscn |
T |
A |
11: 58,934,971 (GRCm39) |
T5220S |
possibly damaging |
Het |
| Or1e16 |
AGCGGTCGTAGGC |
AGC |
11: 73,286,480 (GRCm39) |
|
probably null |
Het |
| Or2l13 |
A |
C |
16: 19,305,680 (GRCm39) |
I31L |
probably benign |
Het |
| Or2p2 |
T |
A |
13: 21,256,739 (GRCm39) |
H244L |
probably damaging |
Het |
| Pdcd1 |
A |
T |
1: 93,980,175 (GRCm39) |
V14E |
probably damaging |
Het |
| Pmel |
A |
G |
10: 128,554,853 (GRCm39) |
|
probably null |
Het |
| Pramel28 |
T |
A |
4: 143,691,362 (GRCm39) |
I454F |
possibly damaging |
Het |
| Prrx1 |
C |
T |
1: 163,089,542 (GRCm39) |
R95Q |
probably damaging |
Het |
| Pstpip2 |
T |
A |
18: 77,962,032 (GRCm39) |
Y267* |
probably null |
Het |
| Ptprq |
A |
G |
10: 107,498,425 (GRCm39) |
I884T |
probably damaging |
Het |
| Rad17 |
G |
A |
13: 100,770,399 (GRCm39) |
T216I |
possibly damaging |
Het |
| Rif1 |
T |
C |
2: 51,967,032 (GRCm39) |
I107T |
probably benign |
Het |
| Rpp14 |
T |
C |
14: 8,087,513 (GRCm38) |
L69P |
probably damaging |
Het |
| Rtel1 |
G |
T |
2: 180,988,776 (GRCm39) |
|
probably benign |
Het |
| Sap130 |
C |
T |
18: 31,799,756 (GRCm39) |
T362M |
probably damaging |
Het |
| Scn11a |
A |
G |
9: 119,644,268 (GRCm39) |
|
probably null |
Het |
| Sec31a |
G |
T |
5: 100,530,754 (GRCm39) |
T243N |
probably benign |
Het |
| Slc5a9 |
T |
A |
4: 111,755,808 (GRCm39) |
H30L |
possibly damaging |
Het |
| Slco6b1 |
T |
A |
1: 96,925,216 (GRCm39) |
|
noncoding transcript |
Het |
| Smarca4 |
A |
G |
9: 21,567,002 (GRCm39) |
D694G |
probably benign |
Het |
| Spaca6 |
A |
G |
17: 18,058,367 (GRCm39) |
T213A |
probably benign |
Het |
| Tagap |
C |
A |
17: 8,152,473 (GRCm39) |
Q553K |
possibly damaging |
Het |
| Tagap |
A |
T |
17: 8,152,474 (GRCm39) |
Q553L |
possibly damaging |
Het |
| Tcf7l2 |
A |
G |
19: 55,887,044 (GRCm39) |
Q19R |
probably benign |
Het |
| Ttn |
A |
G |
2: 76,709,197 (GRCm39) |
|
probably benign |
Het |
| Ubr7 |
A |
T |
12: 102,741,964 (GRCm39) |
R399S |
probably benign |
Het |
| Uspl1 |
C |
A |
5: 149,150,911 (GRCm39) |
Q690K |
possibly damaging |
Het |
| Vps8 |
T |
A |
16: 21,400,298 (GRCm39) |
Y853* |
probably null |
Het |
| Vrk3 |
A |
T |
7: 44,409,220 (GRCm39) |
Q129L |
possibly damaging |
Het |
| Wapl |
T |
A |
14: 34,458,642 (GRCm39) |
C901* |
probably null |
Het |
|
| Other mutations in Cd40 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
bluebonnet
|
UTSW |
2 |
164,904,221 (GRCm39) |
missense |
probably benign |
0.23 |
|
noelle
|
UTSW |
2 |
164,905,483 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0553:Cd40
|
UTSW |
2 |
164,912,661 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1115:Cd40
|
UTSW |
2 |
164,912,681 (GRCm39) |
missense |
possibly damaging |
0.59 |
|
R1134:Cd40
|
UTSW |
2 |
164,912,738 (GRCm39) |
missense |
probably benign |
0.44 |
|
R2036:Cd40
|
UTSW |
2 |
164,904,221 (GRCm39) |
missense |
probably benign |
0.23 |
|
R2938:Cd40
|
UTSW |
2 |
164,911,622 (GRCm39) |
missense |
probably benign |
0.01 |
|
R3034:Cd40
|
UTSW |
2 |
164,904,235 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4690:Cd40
|
UTSW |
2 |
164,911,615 (GRCm39) |
missense |
possibly damaging |
0.68 |
|
R5310:Cd40
|
UTSW |
2 |
164,905,483 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7318:Cd40
|
UTSW |
2 |
164,904,255 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R7833:Cd40
|
UTSW |
2 |
164,908,431 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7905:Cd40
|
UTSW |
2 |
164,904,245 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8069:Cd40
|
UTSW |
2 |
164,898,695 (GRCm39) |
missense |
unknown |
|
|
R8371:Cd40
|
UTSW |
2 |
164,908,458 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9177:Cd40
|
UTSW |
2 |
164,905,465 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9224:Cd40
|
UTSW |
2 |
164,898,716 (GRCm39) |
missense |
unknown |
|
|
R9311:Cd40
|
UTSW |
2 |
164,912,667 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R9419:Cd40
|
UTSW |
2 |
164,904,162 (GRCm39) |
intron |
probably benign |
|
|
R9625:Cd40
|
UTSW |
2 |
164,905,061 (GRCm39) |
missense |
probably benign |
|
|
Z1088:Cd40
|
UTSW |
2 |
164,904,960 (GRCm39) |
missense |
probably damaging |
0.96 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAGGACTTGCTGCTTGCTG -3'
(R):5'- ACCTGAACCTCAAGCAAGGG -3'
Sequencing Primer
(F):5'- CTGCTTGCTGGGGGACTC -3'
(R):5'- AAGGGATGTGACTTACCCAGCTC -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation