Mutagenetix > Incidental Mutation

Incidental Mutation 'R7318:Cd40'

565627

Institutional Source

Beutler Lab

Gene Symbol

Cd40

Ensembl Gene

ENSMUSG00000017652

Gene Name

CD40 antigen

Synonyms

Tnfrsf5, p50, Bp50, Cd40

MMRRC Submission

045414-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7318 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

164897535-164913574 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 164904255 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 34 (D34V)

Ref Sequence

ENSEMBL: ENSMUSP00000017799 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000017799] [ENSMUST00000073707] [ENSMUST00000081310] [ENSMUST00000140951] [ENSMUST00000154443] [ENSMUST00000184221]

AlphaFold

P27512

Predicted Effect

possibly damaging
Transcript: ENSMUST00000017799
AA Change: D34V

PolyPhen 2 Score 0.513 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000017799
Gene: ENSMUSG00000017652
AA Change: D34V

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

possibly damaging
Transcript: ENSMUST00000073707
AA Change: D34V

PolyPhen 2 Score 0.516 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000073386
Gene: ENSMUSG00000017652
AA Change: D34V

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

possibly damaging
Transcript: ENSMUST00000081310
AA Change: D34V

PolyPhen 2 Score 0.858 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000080059
Gene: ENSMUSG00000017652
AA Change: D34V

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 damaging
Transcript: ENSMUST00000140951
AA Change: D72V

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000122981
Gene: ENSMUSG00000017652
AA Change: D72V

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

probably benign
Transcript: ENSMUST00000154443

Predicted Effect

possibly damaging
Transcript: ENSMUST00000184221
AA Change: D34V

PolyPhen 2 Score 0.858 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000139193
Gene: ENSMUSG00000017652
AA Change: D34V

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

0.1795

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

100% (67/67)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930433I11Rik	T	C	7: 40,643,111 (GRCm39)	L260S	probably benign	Het
9130230L23Rik	A	T	5: 66,145,771 (GRCm39)	S113R	unknown	Het
Abcc5	G	A	16: 20,211,293 (GRCm39)	P557S	probably benign	Het
Acad11	A	G	9: 103,958,466 (GRCm39)	T245A	probably damaging	Het
Acap2	A	G	16: 30,946,155 (GRCm39)	F263L	probably damaging	Het
Ankle2	A	T	5: 110,385,632 (GRCm39)	N327I	probably benign	Het
Appl1	T	C	14: 26,685,617 (GRCm39)	E67G	probably benign	Het
Arfgef3	A	T	10: 18,506,211 (GRCm39)	C864S	possibly damaging	Het
Arhgap20	A	G	9: 51,751,802 (GRCm39)	I418V	probably benign	Het
Arhgef2	A	T	3: 88,539,610 (GRCm39)	N102Y	probably damaging	Het
Car9	G	T	4: 43,513,089 (GRCm39)	E431D	probably damaging	Het
Cbfa2t2	T	C	2: 154,342,374 (GRCm39)	I30T	probably benign	Het
Chrnb2	T	A	3: 89,670,674 (GRCm39)		probably null	Het
Chsy1	T	G	7: 65,759,977 (GRCm39)		probably null	Het
Cpne6	A	G	14: 55,751,751 (GRCm39)	T245A	possibly damaging	Het
Cpsf1	T	A	15: 76,481,475 (GRCm39)	K1159*	probably null	Het
Crisp1	T	A	17: 40,618,668 (GRCm39)	E64D	possibly damaging	Het
D3Ertd751e	A	G	3: 41,756,986 (GRCm39)		probably null	Het
Dennd11	A	G	6: 40,386,098 (GRCm39)	V333A	possibly damaging	Het
Dnah7b	T	A	1: 46,234,532 (GRCm39)	L1488Q	probably damaging	Het
Dnm2	G	A	9: 21,416,863 (GRCm39)	G799R	possibly damaging	Het
Elp2	G	A	18: 24,739,956 (GRCm39)	V61I	probably damaging	Het
Epb41l3	T	C	17: 69,573,135 (GRCm39)	L388P		Het
Fry	A	T	5: 150,360,458 (GRCm39)	S2035C	probably damaging	Het
Gas8	T	C	8: 124,257,707 (GRCm39)	F385L	probably benign	Het
Ghsr	T	C	3: 27,426,616 (GRCm39)	V224A	possibly damaging	Het
Gstp2	T	A	19: 4,091,065 (GRCm39)	R85W	probably benign	Het
Ighv1-20	T	A	12: 114,687,810 (GRCm39)	I6F	possibly damaging	Het
Inpp4b	T	A	8: 82,798,374 (GRCm39)	M854K	probably damaging	Het
Kif15	A	G	9: 122,817,014 (GRCm39)	E538G	probably damaging	Het
Large2	T	C	2: 92,196,373 (GRCm39)	T485A	probably benign	Het
Lmo3	T	A	6: 138,398,363 (GRCm39)		probably benign	Het
Lyg1	G	A	1: 37,988,936 (GRCm39)	P95S	probably benign	Het
Lyst	A	G	13: 13,932,028 (GRCm39)	H3552R	probably benign	Het
Mtif2	C	T	11: 29,490,115 (GRCm39)	S385L	probably benign	Het
Muc4	A	T	16: 32,575,710 (GRCm39)	I1737F	unknown	Het
Mug1	T	C	6: 121,847,611 (GRCm39)		probably null	Het
Mx1	G	T	16: 97,253,286 (GRCm39)	Q350K	probably benign	Het
Mylk3	G	T	8: 86,085,726 (GRCm39)	D269E	probably benign	Het
Myo3a	A	T	2: 22,448,332 (GRCm39)	K974*	probably null	Het
Nectin4	G	T	1: 171,208,031 (GRCm39)	R141L	probably benign	Het
Nlgn2	T	C	11: 69,716,795 (GRCm39)	H582R	probably damaging	Het
Or51ab3	T	A	7: 103,201,298 (GRCm39)	M102K	probably damaging	Het
Or51e1	T	A	7: 102,359,226 (GRCm39)	Y253*	probably null	Het
Pi16	C	A	17: 29,538,208 (GRCm39)	P7Q	possibly damaging	Het
Psmd11	C	A	11: 80,347,128 (GRCm39)	L171I	probably benign	Het
Rad54l	A	G	4: 115,967,906 (GRCm39)	V152A	possibly damaging	Het
Ranbp2	T	A	10: 58,318,909 (GRCm39)	Y2473*	probably null	Het
Sertad1	T	C	7: 27,188,910 (GRCm39)	I77T	possibly damaging	Het
Sesn3	A	T	9: 14,219,873 (GRCm39)	E87D	probably damaging	Het
Slc30a5	A	T	13: 100,950,477 (GRCm39)	S260R	probably benign	Het
Slc6a12	G	A	6: 121,328,972 (GRCm39)	G111S	probably damaging	Het
Slc6a12	T	C	6: 121,328,978 (GRCm39)	Y113H	probably benign	Het
Spag17	T	G	3: 99,847,299 (GRCm39)	M76R	probably benign	Het
Spata31f3	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	4: 42,871,823 (GRCm39)		probably benign	Het
Stard13	G	A	5: 150,986,038 (GRCm39)	Q491*	probably null	Het
Synpo2	T	C	3: 122,910,968 (GRCm39)	S226G	probably benign	Het
Tada2b	G	A	5: 36,641,331 (GRCm39)	T24I	probably benign	Het
Tafa1	T	C	6: 96,092,737 (GRCm39)		probably null	Het
Tmem51	TCCCC	TCCC	4: 141,764,996 (GRCm39)		probably null	Het
Tnnt1	T	A	7: 4,513,547 (GRCm39)		probably null	Het
Usp17lb	T	C	7: 104,490,340 (GRCm39)	I196V	probably benign	Het
Utp20	T	A	10: 88,649,811 (GRCm39)	K466N	possibly damaging	Het
Wdr46	T	C	17: 34,160,859 (GRCm39)		probably null	Het
Zfp287	T	A	11: 62,605,104 (GRCm39)	Q601L	probably damaging	Het
Zfp410	T	C	12: 84,372,464 (GRCm39)	S97P	probably benign	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
R5222:Cd40	UTSW	2	164,908,464 (GRCm39)	missense	probably benign	0.41
R5310:Cd40	UTSW	2	164,905,483 (GRCm39)	critical splice donor site	probably null
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'- AGTCCTGTGCATCTGTTCGG -3'
(R):5'- TGGGGTATTCTGGCATCAAG -3'

Sequencing Primer
(F):5'- GCTTTGGTAGATGGCAGTAAGAC -3'
(R):5'- TATTCTGGCATCAAGGAAGAGG -3'

Posted On

2019-06-26