Mutagenetix > Incidental Mutation

Incidental Mutation 'R8039:Pik3cd'

618391

Institutional Source

Beutler Lab

Gene Symbol

Pik3cd

Ensembl Gene

ENSMUSG00000039936

Gene Name

phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta

Synonyms

2410099E07Rik, p110delta, 2610208K16Rik

MMRRC Submission

067476-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R8039 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

149649168-149702571 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 149659866 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 143 (M143L)

Ref Sequence

ENSEMBL: ENSMUSP00000101315 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038859] [ENSMUST00000105688] [ENSMUST00000105689] [ENSMUST00000105690] [ENSMUST00000118704] [ENSMUST00000122059] [ENSMUST00000127273] [ENSMUST00000131224] [ENSMUST00000134534] [ENSMUST00000146612] [ENSMUST00000156309] [ENSMUST00000177654]

AlphaFold

O35904

Predicted Effect

probably benign
Transcript: ENSMUST00000038859
AA Change: M143L

PolyPhen 2 Score 0.382 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000036434
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	685	8.56e-87	SMART
PI3Kc	776	1042	5.65e-128	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105688
AA Change: M143L

PolyPhen 2 Score 0.757 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000101313
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	685	8.56e-87	SMART
PI3Kc	775	1041	5.65e-128	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105689
AA Change: M143L

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000101314
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	684	1.35e-84	SMART
PI3Kc	774	1040	5.65e-128	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105690
AA Change: M143L

PolyPhen 2 Score 0.909 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000101315
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	688	1.22e-82	SMART
PI3Kc	778	1044	5.65e-128	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000118704
AA Change: M143L

PolyPhen 2 Score 0.909 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000112863
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	687	1.8e-80	SMART
PI3Kc	777	1043	5.65e-128	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000122059
AA Change: M143L

PolyPhen 2 Score 0.757 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000113844
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	408	6.47e-23	SMART
PI3Ka	492	681	8.56e-87	SMART
PI3Kc	771	1037	5.65e-128	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000127273
AA Change: M143L

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000119858
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
Blast:PI3K_rbd	126	171	1e-15	BLAST

Predicted Effect

possibly damaging
Transcript: ENSMUST00000131224
AA Change: M143L

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000115542
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000134534

SMART Domains

Protein: ENSMUSP00000118988
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
Pfam:PI3K_p85B	31	62	1.9e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000146612

SMART Domains

Protein: ENSMUSP00000121843
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000156309

Predicted Effect

possibly damaging
Transcript: ENSMUST00000177654
AA Change: M143L

PolyPhen 2 Score 0.909 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000136045
Gene: ENSMUSG00000039936
AA Change: M143L

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	688	1.22e-82	SMART
PI3Kc	778	1044	5.65e-128	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.5%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Phosphoinositide 3-kinases (PI3Ks) phosphorylate inositol lipids and are involved in the immune response. The protein encoded by this gene is a class I PI3K found primarily in leukocytes. Like other class I PI3Ks (p110-alpha p110-beta, and p110-gamma), the encoded protein binds p85 adapter proteins and GTP-bound RAS. However, unlike the other class I PI3Ks, this protein phosphorylates itself, not p85 protein.[provided by RefSeq, Jul 2010]
PHENOTYPE: Homozygotes for targeted null mutations exhibit impaired B and T cell antigen receptor signaling, reduced or ablated immune responses and decreased immunoglobulin levels. Mutants also develop inflammatory bowel disease. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932438A13Rik	T	A	3: 36,943,214	V1140E	probably benign	Het
Abca17	T	C	17: 24,328,725	H225R	probably damaging	Het
Adgrb2	T	A	4: 130,022,268	L1451Q	probably damaging	Het
Afdn	T	C	17: 13,899,141	L1713P	probably damaging	Het
Agr2	A	T	12: 35,995,559	I15F	probably benign	Het
Agrn	T	C	4: 156,169,011	T1808A	probably benign	Het
Akap6	A	G	12: 53,141,676	I1958V	probably benign	Het
Ankrd60	C	A	2: 173,572,491		probably null	Het
Anpep	A	G	7: 79,839,400		probably null	Het
Apoa4	A	T	9: 46,242,293	D64V	possibly damaging	Het
Arhgef26	C	A	3: 62,339,930	T145N	probably benign	Het
Art1	A	T	7: 102,106,845	Q81L	probably benign	Het
Astl	A	T	2: 127,343,983	S71C	probably damaging	Het
Atp2a1	A	G	7: 126,448,805	I611T	probably damaging	Het
Cacna2d2	T	A	9: 107,527,433	V1139D	possibly damaging	Het
Chst10	T	A	1: 38,866,031	K198*	probably null	Het
Ckmt2	G	A	13: 91,863,312	H60Y	possibly damaging	Het
Coq7	G	C	7: 118,533,246	S2R	possibly damaging	Het
Cspp1	T	A	1: 10,113,013	D814E	probably benign	Het
Cyp2c54	CCTCTTTCATAGCTCT	CCTCT	19: 40,073,732		probably null	Het
Daam2	C	A	17: 49,464,538	G860V	probably damaging	Het
Ecm2	A	T	13: 49,514,850	I10F	probably benign	Het
Epb41l1	A	T	2: 156,506,412	D312V	probably damaging	Het
Epsti1	G	A	14: 77,931,301	R126H	probably damaging	Het
Erc1	A	T	6: 119,773,665	Y367*	probably null	Het
Erh	T	A	12: 80,637,578	R42W	probably damaging	Het
Fam124a	C	T	14: 62,605,876	Q278*	probably null	Het
Fam155a	T	C	8: 9,207,892	T419A	probably benign	Het
Fbxo3	T	A	2: 104,054,941	L385Q	probably damaging	Het
Fbxo31	T	A	8: 121,559,055	T219S	probably damaging	Het
Fstl5	T	G	3: 76,648,418	V534G	possibly damaging	Het
Gatsl3	G	T	11: 4,221,639	A288S	probably damaging	Het
Gbp2b	A	T	3: 142,618,164	I577F	probably benign	Het
Gbp8	A	T	5: 105,050,917	L44*	probably null	Het
Gck	C	T	11: 5,910,301	A114T	probably benign	Het
Gm16486	T	C	8: 70,710,906	V916A	probably benign	Het
Gtf2i	A	G	5: 134,255,834	V537A	possibly damaging	Het
Iqcm	C	A	8: 75,763,105	H400Q	probably damaging	Het
Itpr1	T	C	6: 108,386,628	L737P	probably damaging	Het
Jakmip1	A	G	5: 37,100,772	E254G	probably damaging	Het
Kif15	A	T	9: 123,007,425	R1095W	possibly damaging	Het
Klhdc8a	G	A	1: 132,303,108	R237Q	probably benign	Het
Klhl38	T	C	15: 58,322,862	E157G	probably benign	Het
Klrk1	T	A	6: 129,612,823	N221I	probably benign	Het
Lhx8	A	T	3: 154,306,939	H345Q	probably damaging	Het
Lims1	T	A	10: 58,409,672	N174K	probably benign	Het
Madd	T	A	2: 91,167,061	Q754L	probably benign	Het
Mau2	T	C	8: 70,019,790	D581G	probably damaging	Het
Miga1	A	T	3: 152,276,756	I561N	probably benign	Het
Mmp1a	TG	TGG	9: 7,465,083		probably null	Het
Mob3c	T	C	4: 115,831,687	V139A	probably benign	Het
Nadk	G	T	4: 155,577,067	D17Y	probably benign	Het
Ncapd2	C	T	6: 125,181,026	V380I	probably damaging	Het
Nes	G	A	3: 87,977,008	R858K	probably benign	Het
Nphp3	T	C	9: 104,031,963	S791P	probably benign	Het
Nup210	T	C	6: 91,070,233	T496A	probably benign	Het
Ogfr	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	2: 180,595,266		probably benign	Het
Olfr1186	C	T	2: 88,525,871	T96I	probably benign	Het
Olfr220	T	A	1: 174,449,596	S324R	unknown	Het
Olfr914	T	A	9: 38,607,389	M308K	probably benign	Het
Ovgp1	T	A	3: 105,976,023	S105T	probably benign	Het
Pbld2	T	A	10: 63,047,992	C79S	probably damaging	Het
Plat	G	T	8: 22,772,232	G91W	probably damaging	Het
Poln	A	G	5: 34,122,672	V282A	probably benign	Het
Ppp1r11	T	C	17: 36,951,446	T21A	probably damaging	Het
Prpf8	T	A	11: 75,502,542	I1664N	possibly damaging	Het
Prr29	C	T	11: 106,376,912	A161V	probably benign	Het
Rasa3	T	C	8: 13,588,931	D292G	probably damaging	Het
Rnf25	T	C	1: 74,593,964	T411A	probably damaging	Het
Rraga	C	T	4: 86,575,980	T21I	probably damaging	Het
Setdb2	T	A	14: 59,402,375	Y673F	probably damaging	Het
Sf3a1	C	T	11: 4,167,787	T183I	probably damaging	Het
Shank3	A	T	15: 89,505,439	H413L	probably damaging	Het
Slc30a5	A	G	13: 100,813,681		probably null	Het
Slc6a18	T	C	13: 73,665,626	S523G	probably benign	Het
Spaca1	C	T	4: 34,044,207	V96I	probably damaging	Het
Sycp2	C	T	2: 178,374,585	A695T	probably benign	Het
Tnrc18	C	A	5: 142,732,052	G2216C	unknown	Het
Trak2	T	C	1: 58,946,288	N17S	probably benign	Het
Ttn	T	A	2: 76,878,432	N8792I	unknown	Het
Ttyh1	T	C	7: 4,122,541	V64A	probably benign	Het
Usb1	T	A	8: 95,333,413	S50R	probably damaging	Het
Ush2a	T	A	1: 188,957,373	I5044N	probably damaging	Het
Vmn1r84	A	T	7: 12,362,008	F253I	possibly damaging	Het
Vmn2r99	T	C	17: 19,380,040	I442T	probably benign	Het
Vsig1	C	T	X: 140,933,126	H232Y	probably benign	Het

Other mutations in Pik3cd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01308:Pik3cd	APN	4	149657460	missense	probably damaging	1.00
IGL01536:Pik3cd	APN	4	149652666	missense	probably damaging	1.00
IGL01636:Pik3cd	APN	4	149654315	missense	possibly damaging	0.82
IGL02794:Pik3cd	APN	4	149654571	missense	probably benign
grand_tetons	UTSW	4	149652699	missense	probably damaging	1.00
Helena	UTSW	4	149651820	missense	probably damaging	1.00
stinger	UTSW	4	149657319	missense	probably damaging	1.00
F5770:Pik3cd	UTSW	4	149657319	missense	probably damaging	1.00
R0003:Pik3cd	UTSW	4	149656379	critical splice donor site	probably null
R0309:Pik3cd	UTSW	4	149663220	missense	probably damaging	1.00
R1246:Pik3cd	UTSW	4	149659800	missense	probably damaging	1.00
R1259:Pik3cd	UTSW	4	149650648	nonsense	probably null
R1533:Pik3cd	UTSW	4	149655196	missense	probably damaging	1.00
R1756:Pik3cd	UTSW	4	149658750	missense	probably benign	0.02
R1796:Pik3cd	UTSW	4	149654119	missense	possibly damaging	0.83
R1887:Pik3cd	UTSW	4	149652634	missense	probably damaging	1.00
R1988:Pik3cd	UTSW	4	149663203	missense	probably damaging	1.00
R2089:Pik3cd	UTSW	4	149652699	missense	probably damaging	1.00
R2091:Pik3cd	UTSW	4	149652699	missense	probably damaging	1.00
R4997:Pik3cd	UTSW	4	149658984	missense	probably damaging	1.00
R5391:Pik3cd	UTSW	4	149659131	missense	probably damaging	0.98
R5603:Pik3cd	UTSW	4	149658855	missense	probably benign
R6282:Pik3cd	UTSW	4	149659743	missense	probably benign	0.00
R6453:Pik3cd	UTSW	4	149652302	missense	probably damaging	1.00
R7286:Pik3cd	UTSW	4	149659714	missense	probably benign	0.08
R7423:Pik3cd	UTSW	4	149651763	critical splice donor site	probably null
R7508:Pik3cd	UTSW	4	149654583	missense	possibly damaging	0.78
R7665:Pik3cd	UTSW	4	149654050	missense	possibly damaging	0.70
R7897:Pik3cd	UTSW	4	149657269	missense	probably benign	0.06
R8476:Pik3cd	UTSW	4	149651820	missense	probably damaging	1.00
R9015:Pik3cd	UTSW	4	149655598	missense	probably benign	0.06
R9252:Pik3cd	UTSW	4	149655630	missense	possibly damaging	0.88
R9704:Pik3cd	UTSW	4	149655382	missense	probably benign	0.17
V7580:Pik3cd	UTSW	4	149657319	missense	probably damaging	1.00
V7581:Pik3cd	UTSW	4	149657319	missense	probably damaging	1.00
V7582:Pik3cd	UTSW	4	149657319	missense	probably damaging	1.00
V7583:Pik3cd	UTSW	4	149657319	missense	probably damaging	1.00
X0023:Pik3cd	UTSW	4	149660034	missense	probably benign	0.04
Z1176:Pik3cd	UTSW	4	149654847	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TGCCCTCATATGCTACTGGG -3'
(R):5'- CGTGAAGAAGCTCATTAACTCCC -3'

Sequencing Primer
(F):5'- CCCTCATATGCTACTGGGAGAAG -3'
(R):5'- CAGATCAGCCTCCTCATTGG -3'

Posted On

2020-01-23