Mutagenetix > Incidental Mutation

Incidental Mutation 'R4997:Pik3cd'

385330

Institutional Source

Beutler Lab

Gene Symbol

Pik3cd

Ensembl Gene

ENSMUSG00000039936

Gene Name

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

Synonyms

2610208K16Rik, 2410099E07Rik, p110delta

MMRRC Submission

042591-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.959) question?

Stock #

R4997 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

149733625-149787023 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 149743441 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Arginine at position 256 (L256R)

Ref Sequence

ENSEMBL: ENSMUSP00000113844 (fasta)

Gene Model

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

AlphaFold

O35904

Predicted Effect

probably damaging
Transcript: ENSMUST00000038859
AA Change: L256R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000036434
Gene: ENSMUSG00000039936
AA Change: L256R

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

probably damaging
Transcript: ENSMUST00000105688
AA Change: L256R

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000101313
Gene: ENSMUSG00000039936
AA Change: L256R

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

probably damaging
Transcript: ENSMUST00000105689
AA Change: L256R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000101314
Gene: ENSMUSG00000039936
AA Change: L256R

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

probably damaging
Transcript: ENSMUST00000105690
AA Change: L256R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000101315
Gene: ENSMUSG00000039936
AA Change: L256R

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

probably damaging
Transcript: ENSMUST00000118704
AA Change: L256R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000112863
Gene: ENSMUSG00000039936
AA Change: L256R

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

probably damaging
Transcript: ENSMUST00000122059
AA Change: L256R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000113844
Gene: ENSMUSG00000039936
AA Change: L256R

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

probably benign
Transcript: ENSMUST00000127273

SMART Domains

Protein: ENSMUSP00000119858
Gene: ENSMUSG00000039936

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000177654
AA Change: L256R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000136045
Gene: ENSMUSG00000039936
AA Change: L256R

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

noncoding transcript
Transcript: ENSMUST00000185093

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: ENSMUST00000131224

SMART Domains

Protein: ENSMUSP00000115542
Gene: ENSMUSG00000039936

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

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

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.1%

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630023A22Rik	A	T	14: 33,775,623 (GRCm39)	M1L	probably benign	Het
Abca7	C	A	10: 79,843,154 (GRCm39)	Q1210K	possibly damaging	Het
Abcc4	C	T	14: 118,753,915 (GRCm39)	W1024*	probably null	Het
Accs	A	T	2: 93,672,228 (GRCm39)	Y213*	probably null	Het
Adam6a	G	T	12: 113,508,991 (GRCm39)	G455C	probably damaging	Het
Adcy1	A	C	11: 7,111,298 (GRCm39)	Y863S	probably benign	Het
Adgrg1	A	G	8: 95,736,148 (GRCm39)	D434G	probably damaging	Het
Afap1l1	C	T	18: 61,884,879 (GRCm39)	R202Q	probably benign	Het
Aldh3a1	T	C	11: 61,103,137 (GRCm39)	V27A	probably benign	Het
Antxr2	A	G	5: 98,125,553 (GRCm39)	F235L	probably benign	Het
Arhgap23	T	A	11: 97,342,846 (GRCm39)	V376E	probably damaging	Het
Brca1	A	C	11: 101,415,159 (GRCm39)	S992A	probably damaging	Het
Brcc3dc	A	G	10: 108,535,649 (GRCm39)	I102T	probably benign	Het
Calcrl	A	T	2: 84,181,592 (GRCm39)	C185*	probably null	Het
Cep152	T	C	2: 125,428,271 (GRCm39)	T787A	probably benign	Het
Coch	T	A	12: 51,649,964 (GRCm39)		probably null	Het
Col5a1	T	A	2: 27,922,794 (GRCm39)	Y287*	probably null	Het
Dis3l	A	G	9: 64,219,224 (GRCm39)	S569P	possibly damaging	Het
Dnai1	A	G	4: 41,597,919 (GRCm39)	I74V	possibly damaging	Het
Dpy19l4	A	G	4: 11,287,493 (GRCm39)	V394A	probably benign	Het
Egfem1	A	G	3: 29,207,739 (GRCm39)	H122R	probably benign	Het
Endou	A	G	15: 97,617,458 (GRCm39)	L164P	probably damaging	Het
Epgn	A	G	5: 91,180,098 (GRCm39)	E80G	possibly damaging	Het
Fcgbpl1	T	G	7: 27,843,349 (GRCm39)	S746A	possibly damaging	Het
Fitm1	T	C	14: 55,814,364 (GRCm39)	S287P	probably benign	Het
Foxm1	A	G	6: 128,342,731 (GRCm39)	N22D	probably benign	Het
Gsdmc	A	T	15: 63,648,629 (GRCm39)	M426K	probably damaging	Het
Hmcn2	T	A	2: 31,291,720 (GRCm39)	V2418D	probably damaging	Het
Hs3st2	T	A	7: 121,099,679 (GRCm39)	L175Q	possibly damaging	Het
Il1r2	T	C	1: 40,160,206 (GRCm39)		probably null	Het
Il27ra	A	T	8: 84,766,156 (GRCm39)	Y209*	probably null	Het
Inpp5a	A	T	7: 138,980,654 (GRCm39)	S31C	probably benign	Het
Invs	A	G	4: 48,396,332 (GRCm39)	D335G	probably damaging	Het
Isg15	C	T	4: 156,284,154 (GRCm39)	E125K	possibly damaging	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Lama4	C	A	10: 38,968,262 (GRCm39)	T1468K	probably damaging	Het
Lce1a2	A	G	3: 92,576,395 (GRCm39)	S56P	unknown	Het
Llgl1	C	T	11: 60,600,394 (GRCm39)	P581L	probably benign	Het
Lmf1	G	A	17: 25,807,650 (GRCm39)	W164*	probably null	Het
Mad2l1bp	G	T	17: 46,463,804 (GRCm39)	C73*	probably null	Het
Mpzl1	A	C	1: 165,429,350 (GRCm39)	V230G	probably damaging	Het
Myo3b	A	G	2: 70,088,427 (GRCm39)	T869A	possibly damaging	Het
Ncor2	T	C	5: 125,111,074 (GRCm39)	H1316R	probably damaging	Het
Nlrp1b	T	A	11: 71,109,160 (GRCm39)	I114F	probably damaging	Het
Nsun7	A	G	5: 66,453,182 (GRCm39)	I632M	probably benign	Het
Nubp1	T	C	16: 10,239,185 (GRCm39)	I234T	probably benign	Het
Olfml1	A	G	7: 107,170,413 (GRCm39)	D100G	probably damaging	Het
Or1e1b-ps1	T	A	11: 73,845,612 (GRCm39)	L32Q	probably damaging	Het
Or5p73	C	A	7: 108,064,701 (GRCm39)	Q57K	probably benign	Het
Or7g23	A	T	9: 19,086,627 (GRCm39)	L115Q	probably damaging	Het
Osmr	G	T	15: 6,845,120 (GRCm39)	P882Q	probably benign	Het
Peg10	TCAGGATCC	TCAGGATCCCCAGCAGGATCC	6: 4,756,457 (GRCm39)		probably benign	Het
Per2	T	A	1: 91,378,505 (GRCm39)	T15S	probably benign	Het
Piezo2	A	G	18: 63,216,184 (GRCm39)	Y1184H	probably damaging	Het
Pik3c2b	C	T	1: 133,032,819 (GRCm39)	A1560V	probably damaging	Het
Ppl	C	A	16: 4,907,235 (GRCm39)	R1020L	probably damaging	Het
Ppp1r10	A	G	17: 36,234,976 (GRCm39)	N60S	probably damaging	Het
Prkcg	T	C	7: 3,371,097 (GRCm39)		probably null	Het
Prkci	T	C	3: 31,085,375 (GRCm39)		probably null	Het
Prrc2b	A	G	2: 32,112,323 (GRCm39)	Y1929C	probably damaging	Het
Prss12	T	C	3: 123,240,857 (GRCm39)	V17A	probably benign	Het
Qtrt1	A	G	9: 21,328,654 (GRCm39)	N206S	probably benign	Het
Rad54l2	A	C	9: 106,600,108 (GRCm39)	S50A	possibly damaging	Het
Rhov	C	T	2: 119,100,949 (GRCm39)	R96H	probably damaging	Het
Rph3a	A	T	5: 121,101,906 (GRCm39)	V110E	probably damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Ryr2	A	T	13: 11,610,192 (GRCm39)	N646K	probably benign	Het
Scn8a	A	G	15: 100,854,935 (GRCm39)	T141A	probably damaging	Het
Serping1	T	C	2: 84,600,629 (GRCm39)	R238G	possibly damaging	Het
Shank3	T	A	15: 89,433,901 (GRCm39)	W1474R	probably damaging	Het
Slc16a12	T	A	19: 34,652,358 (GRCm39)	M263L	probably benign	Het
Spata13	T	C	14: 60,946,908 (GRCm39)	V652A	probably damaging	Het
Spata31	G	A	13: 65,067,537 (GRCm39)	M66I	probably benign	Het
Spem2	T	C	11: 69,708,558 (GRCm39)	I136V	probably benign	Het
Supt5	T	C	7: 28,015,462 (GRCm39)	H925R	probably benign	Het
Syk	A	T	13: 52,766,484 (GRCm39)	K190*	probably null	Het
Thsd1	T	A	8: 22,733,340 (GRCm39)	V129D	probably damaging	Het
Tiprl	A	G	1: 165,047,759 (GRCm39)	V174A	possibly damaging	Het
Tmed4	T	A	11: 6,224,500 (GRCm39)		probably null	Het
Tnfrsf19	T	C	14: 61,208,658 (GRCm39)	T288A	probably benign	Het
Tnfrsf25	T	C	4: 152,202,153 (GRCm39)		probably null	Het
Tpd52	A	G	3: 9,000,056 (GRCm39)	L121S	probably damaging	Het
Trim30a	T	A	7: 104,060,827 (GRCm39)	K316N	probably benign	Het
Ttc3	T	G	16: 94,253,841 (GRCm39)	D1221E	probably damaging	Het
Ttn	C	T	2: 76,714,403 (GRCm39)		probably benign	Het
Ttn	T	C	2: 76,776,615 (GRCm39)	I1514V	probably benign	Het
Ulk2	T	C	11: 61,689,982 (GRCm39)	T671A	probably benign	Het
Wasf1	C	T	10: 40,810,600 (GRCm39)	P281S	probably damaging	Het
Wnt10b	C	A	15: 98,672,084 (GRCm39)	R211L	probably damaging	Het
Xpnpep3	T	A	15: 81,332,577 (GRCm39)	C371*	probably null	Het
Zfp41	C	T	15: 75,490,617 (GRCm39)		probably benign	Het
Zfp553	T	A	7: 126,834,683 (GRCm39)	N79K	probably benign	Het
Zmynd8	G	T	2: 165,634,736 (GRCm39)	D1096E	probably benign	Het

Other mutations in Pik3cd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01308:Pik3cd	APN	4	149,741,917 (GRCm39)	missense	probably damaging	1.00
IGL01536:Pik3cd	APN	4	149,737,123 (GRCm39)	missense	probably damaging	1.00
IGL01636:Pik3cd	APN	4	149,738,772 (GRCm39)	missense	possibly damaging	0.82
IGL02794:Pik3cd	APN	4	149,739,028 (GRCm39)	missense	probably benign
grand_tetons	UTSW	4	149,737,156 (GRCm39)	missense	probably damaging	1.00
Helena	UTSW	4	149,736,277 (GRCm39)	missense	probably damaging	1.00
stinger	UTSW	4	149,741,776 (GRCm39)	missense	probably damaging	1.00
F5770:Pik3cd	UTSW	4	149,741,776 (GRCm39)	missense	probably damaging	1.00
R0003:Pik3cd	UTSW	4	149,740,836 (GRCm39)	critical splice donor site	probably null
R0309:Pik3cd	UTSW	4	149,747,677 (GRCm39)	missense	probably damaging	1.00
R1246:Pik3cd	UTSW	4	149,744,257 (GRCm39)	missense	probably damaging	1.00
R1259:Pik3cd	UTSW	4	149,735,105 (GRCm39)	nonsense	probably null
R1533:Pik3cd	UTSW	4	149,739,653 (GRCm39)	missense	probably damaging	1.00
R1756:Pik3cd	UTSW	4	149,743,207 (GRCm39)	missense	probably benign	0.02
R1796:Pik3cd	UTSW	4	149,738,576 (GRCm39)	missense	possibly damaging	0.83
R1887:Pik3cd	UTSW	4	149,737,091 (GRCm39)	missense	probably damaging	1.00
R1988:Pik3cd	UTSW	4	149,747,660 (GRCm39)	missense	probably damaging	1.00
R2089:Pik3cd	UTSW	4	149,737,156 (GRCm39)	missense	probably damaging	1.00
R2091:Pik3cd	UTSW	4	149,737,156 (GRCm39)	missense	probably damaging	1.00
R5391:Pik3cd	UTSW	4	149,743,588 (GRCm39)	missense	probably damaging	0.98
R5603:Pik3cd	UTSW	4	149,743,312 (GRCm39)	missense	probably benign
R6282:Pik3cd	UTSW	4	149,744,200 (GRCm39)	missense	probably benign	0.00
R6453:Pik3cd	UTSW	4	149,736,759 (GRCm39)	missense	probably damaging	1.00
R7286:Pik3cd	UTSW	4	149,744,171 (GRCm39)	missense	probably benign	0.08
R7423:Pik3cd	UTSW	4	149,736,220 (GRCm39)	critical splice donor site	probably null
R7508:Pik3cd	UTSW	4	149,739,040 (GRCm39)	missense	possibly damaging	0.78
R7665:Pik3cd	UTSW	4	149,738,507 (GRCm39)	missense	possibly damaging	0.70
R7897:Pik3cd	UTSW	4	149,741,726 (GRCm39)	missense	probably benign	0.06
R8039:Pik3cd	UTSW	4	149,744,323 (GRCm39)	missense	possibly damaging	0.91
R8476:Pik3cd	UTSW	4	149,736,277 (GRCm39)	missense	probably damaging	1.00
R9015:Pik3cd	UTSW	4	149,740,055 (GRCm39)	missense	probably benign	0.06
R9252:Pik3cd	UTSW	4	149,740,087 (GRCm39)	missense	possibly damaging	0.88
R9704:Pik3cd	UTSW	4	149,739,839 (GRCm39)	missense	probably benign	0.17
V7580:Pik3cd	UTSW	4	149,741,776 (GRCm39)	missense	probably damaging	1.00
V7581:Pik3cd	UTSW	4	149,741,776 (GRCm39)	missense	probably damaging	1.00
V7582:Pik3cd	UTSW	4	149,741,776 (GRCm39)	missense	probably damaging	1.00
V7583:Pik3cd	UTSW	4	149,741,776 (GRCm39)	missense	probably damaging	1.00
X0023:Pik3cd	UTSW	4	149,744,491 (GRCm39)	missense	probably benign	0.04
Z1176:Pik3cd	UTSW	4	149,739,304 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- AGGATTGCTCTGCTCATCCC -3'
(R):5'- TCCTTCTTCCTACAGGAGAGC -3'

Sequencing Primer
(F):5'- CATCCCGCATAGCAAGGATGG -3'
(R):5'- AGGAGAGCTTCACCTTCCAG -3'

Posted On

2016-05-10