Mutagenetix > Incidental Mutations

Incidental Mutation 'R7326:Psd'

568963

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Psdl, Efa6a, Efa6, 1110007H17Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7326 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

46312087-46327156 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 46324454 bp

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 159 (L159P)

Ref Sequence

ENSEMBL: ENSMUSP00000039728 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026256] [ENSMUST00000041391] [ENSMUST00000096029] [ENSMUST00000177667] [ENSMUST00000223903] [ENSMUST00000223917] [ENSMUST00000224447] [ENSMUST00000225323] [ENSMUST00000225781]

Predicted Effect

probably benign
Transcript: ENSMUST00000026256

SMART Domains

Protein: ENSMUSP00000026256
Gene: ENSMUSG00000025226

Domain	Start	End	E-Value	Type
Pfam:F-box	18	63	1.9e-6	PFAM
low complexity region	76	84	N/A	INTRINSIC
LRR	113	138	1.01e1	SMART
LRR	139	164	1.89e-1	SMART
LRR	165	190	2.27e-4	SMART
LRR	192	217	3.47e0	SMART
LRR	218	243	2.57e-3	SMART
LRR	244	269	2.05e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000041391
AA Change: L159P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: L159P

Domain	Start	End	E-Value	Type
low complexity region	48	63	N/A	INTRINSIC
low complexity region	79	99	N/A	INTRINSIC
low complexity region	329	368	N/A	INTRINSIC
low complexity region	419	431	N/A	INTRINSIC
low complexity region	445	466	N/A	INTRINSIC
Sec7	519	708	5.08e-75	SMART
low complexity region	714	724	N/A	INTRINSIC
low complexity region	736	744	N/A	INTRINSIC
PH	757	871	1.87e-13	SMART
Blast:Sec7	900	952	1e-6	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000096029
AA Change: L159P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: L159P

Domain	Start	End	E-Value	Type
low complexity region	48	63	N/A	INTRINSIC
low complexity region	79	99	N/A	INTRINSIC
low complexity region	329	368	N/A	INTRINSIC
low complexity region	419	431	N/A	INTRINSIC
low complexity region	445	466	N/A	INTRINSIC
Sec7	520	709	5.08e-75	SMART
low complexity region	715	725	N/A	INTRINSIC
low complexity region	737	745	N/A	INTRINSIC
PH	758	872	1.87e-13	SMART
Blast:Sec7	901	953	1e-6	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000177667

SMART Domains

Protein: ENSMUSP00000137489
Gene: ENSMUSG00000025226

Domain	Start	End	E-Value	Type
Pfam:F-box	18	63	2.1e-6	PFAM
low complexity region	76	84	N/A	INTRINSIC
LRR	113	138	1.01e1	SMART
LRR	139	164	1.89e-1	SMART
LRR	165	190	2.27e-4	SMART
LRR	192	217	3.47e0	SMART
LRR	218	243	2.57e-3	SMART
LRR	244	269	2.05e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000223903

Predicted Effect

probably benign
Transcript: ENSMUST00000223917

Predicted Effect

probably benign
Transcript: ENSMUST00000224447

Predicted Effect

probably benign
Transcript: ENSMUST00000225323
AA Change: L159P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

Predicted Effect

probably benign
Transcript: ENSMUST00000225781

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

Allele List at MGI

Other mutations in this stock

Total: 112 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6430531B16Rik	A	T	7: 139,978,545		probably null	Het
Abcb4	T	C	5: 8,934,226	V652A	probably benign	Het
Acvrl1	G	T	15: 101,141,072	V417L	probably damaging	Het
Add1	A	G	5: 34,619,371	R479G	probably benign	Het
Adgb	A	T	10: 10,400,574	L350Q	possibly damaging	Het
Adgrl2	A	T	3: 148,846,870	S666T	probably benign	Het
Akap9	T	A	5: 4,045,930	D2268E	possibly damaging	Het
Amigo3	C	A	9: 108,054,066	H229Q	probably benign	Het
Ano6	G	C	15: 95,864,244	Q31H	possibly damaging	Het
Ap4m1	G	A	5: 138,175,019	D180N	probably damaging	Het
Apc2	A	T	10: 80,311,740	D876V	probably damaging	Het
Apcdd1	T	A	18: 62,952,188	Y485*	probably null	Het
Aqp1	G	T	6: 55,336,851	D121Y	probably benign	Het
Bicd2	C	A	13: 49,369,609	R141S	probably benign	Het
Brpf3	C	A	17: 28,806,293	H113Q	probably benign	Het
Cacng2	A	T	15: 78,013,320	Y96*	probably null	Het
Catsperg1	G	T	7: 29,210,759	N52K	possibly damaging	Het
Celsr2	A	C	3: 108,394,995	F2606V	possibly damaging	Het
Cerkl	A	T	2: 79,332,605	N516K	probably benign	Het
Ciita	G	A	16: 10,512,288	R812H	probably damaging	Het
Cldn3	T	A	5: 134,986,983	L180Q	probably damaging	Het
Cnot6l	T	C	5: 96,077,299	I512V	probably benign	Het
Col5a2	A	T	1: 45,442,867	D32E	unknown	Het
Coro7	A	G	16: 4,632,048	V616A	probably damaging	Het
Cyp4f18	T	C	8: 71,988,654	D494G	probably benign	Het
Ddx39	T	A	8: 83,722,471	V296E	probably benign	Het
Dgkg	A	T	16: 22,548,690	H593Q	probably damaging	Het
Dhx16	T	C	17: 35,886,160	L645P	probably damaging	Het
Dnah14	A	G	1: 181,598,403	M171V	probably benign	Het
Dnhd1	G	A	7: 105,720,930	V4521I	probably damaging	Het
Dok7	A	T	5: 35,064,522	M60L	probably benign	Het
Donson	A	T	16: 91,688,711	M1K	probably null	Het
Dsp	C	T	13: 38,192,883	T1548M	probably benign	Het
Dyrk1a	A	G	16: 94,692,043	T712A	probably damaging	Het
Eef2	A	G	10: 81,181,282	T708A	probably benign	Het
Epn3	G	A	11: 94,493,780	T289I	probably benign	Het
Fam171a1	C	T	2: 3,226,472	R881*	probably null	Het
Fam71a	G	A	1: 191,164,353	T31M	probably benign	Het
Fat2	T	A	11: 55,282,304	R2528W	probably damaging	Het
Fgfr1	T	G	8: 25,573,839	F707C	probably damaging	Het
Frem2	G	C	3: 53,654,753	P778A	probably damaging	Het
Ganc	A	G	2: 120,430,599	Y255C	probably damaging	Het
Ginm1	A	T	10: 7,777,850	Y65*	probably null	Het
Gm11559	T	A	11: 99,864,881	C119S	unknown	Het
Gnai1	T	A	5: 18,289,551	H188L		Het
H6pd	C	T	4: 149,996,350	A13T	probably benign	Het
Hist1h2be	T	C	13: 23,585,923	K12E	probably benign	Het
Hoxd12	A	T	2: 74,675,246	T54S	possibly damaging	Het
Hs3st5	T	A	10: 36,833,194	L242M	probably damaging	Het
Il9r	C	A	11: 32,194,389	V139L	possibly damaging	Het
Immt	A	G	6: 71,846,369	D68G	probably damaging	Het
Itsn2	A	G	12: 4,632,985	I304V	unknown	Het
Lgr4	G	A	2: 109,996,629	W159*	probably null	Het
Lin52	G	A	12: 84,457,954	G38S	probably damaging	Het
Lpgat1	A	T	1: 191,719,453	M64L	probably benign	Het
Lrrc10b	G	T	19: 10,456,778	R180S	possibly damaging	Het
Lrrc29	T	C	8: 105,312,898	D127G	probably damaging	Het
Lrrc36	A	T	8: 105,449,769	L258F	possibly damaging	Het
Ltbp4	T	A	7: 27,329,755	Q235L	unknown	Het
Maml2	A	G	9: 13,621,607	M706V		Het
Mc5r	G	T	18: 68,339,668	C366F	probably damaging	Het
Mlip	T	C	9: 77,164,842	R244G	probably benign	Het
Muc16	T	A	9: 18,585,013	R6658S	probably benign	Het
Mup4	G	T	4: 59,960,046	H73N	possibly damaging	Het
Nf1	A	G	11: 79,564,943	M565V	probably benign	Het
Nphp1	G	A	2: 127,761,217	T382I	possibly damaging	Het
Nrcam	C	T	12: 44,564,026	T503I	possibly damaging	Het
Nwd2	A	T	5: 63,800,409	N361Y	probably damaging	Het
Olfr1045	A	G	2: 86,198,573	Y60H	probably damaging	Het
Olfr1309	A	T	2: 111,983,327	L249*	probably null	Het
Olfr308	A	G	7: 86,321,574	I126T	probably damaging	Het
Olfr461	G	T	6: 40,544,895	A28E	probably damaging	Het
Olfr518	A	T	7: 108,880,816	H263Q	probably damaging	Het
Olfr836	A	G	9: 19,121,669	Y235C	probably benign	Het
Olfr993	A	T	2: 85,414,444	V145E	probably damaging	Het
Orc5	A	G	5: 22,523,584	F308L	probably benign	Het
Padi1	T	A	4: 140,832,404	Y54F	probably benign	Het
Parp1	A	G	1: 180,569,100	K23E	possibly damaging	Het
Pate1	A	T	9: 35,685,972	V79D	possibly damaging	Het
Pcdh18	T	C	3: 49,756,860	H2R	probably benign	Het
Pcnx2	G	A	8: 125,887,083	S543F	probably damaging	Het
Pcp4l1	G	A	1: 171,174,465	A42V	possibly damaging	Het
Pnkp	T	A	7: 44,859,734	F169L	probably damaging	Het
Ppp6r3	A	T	19: 3,507,325	N254K	probably damaging	Het
Ptprf	A	G	4: 118,231,669	Y646H	probably damaging	Het
Rab3ip	A	T	10: 116,937,633	S92T	probably benign	Het
Rabgef1	A	G	5: 130,187,351		probably benign	Het
Ralgapa1	C	A	12: 55,709,004	W1129L	probably damaging	Het
Rhpn2	T	A	7: 35,385,463	L594Q	probably benign	Het
Rnf38	C	A	4: 44,158,989		probably benign	Het
Ryr2	T	A	13: 11,738,194	H1747L	possibly damaging	Het
Sec16a	A	G	2: 26,439,717	L13P	unknown	Het
Sppl3	C	A	5: 115,082,335	T102K	probably damaging	Het
Srgap2	A	T	1: 131,291,613	Y264*	probably null	Het
Stxbp2	T	C	8: 3,641,151	M465T		Het
Sumf2	A	G	5: 129,862,710	K305R	probably benign	Het
Susd2	T	A	10: 75,642,565	Y59F	probably benign	Het
Taco1	T	C	11: 106,072,617	V198A	probably benign	Het
Tas2r136	A	T	6: 132,777,906	M86K	possibly damaging	Het
Tbc1d10c	T	C	19: 4,184,898	E388G	possibly damaging	Het
Tmem132c	C	T	5: 127,564,059	T1098I	possibly damaging	Het
Trim3	G	T	7: 105,617,800	Y457*	probably null	Het
Ttc38	A	G	15: 85,852,861	T316A	probably benign	Het
Ubqln4	T	A	3: 88,555,910	N127K	probably benign	Het
Wdr91	A	T	6: 34,904,626	F262Y	probably damaging	Het
Zdhhc6	A	T	19: 55,302,755	C343S	possibly damaging	Het
Zfp248	A	G	6: 118,430,209	C140R	probably damaging	Het
Zfp266	T	C	9: 20,502,095	T90A	probably benign	Het
Zfp407	A	T	18: 84,559,042	D1315E	possibly damaging	Het
Zfp644	T	C	5: 106,638,277	S135G	probably benign	Het
Zscan29	A	T	2: 121,160,988	I773N	probably damaging	Het
Zswim5	T	A	4: 116,980,834	V787E	possibly damaging	Het

Other mutations in Psd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01291:Psd	APN	19	46314747	missense	possibly damaging	0.77
IGL01307:Psd	APN	19	46314658	missense	probably damaging	1.00
IGL02329:Psd	APN	19	46319659	missense	possibly damaging	0.66
IGL02423:Psd	APN	19	46314504	missense	possibly damaging	0.95
IGL02644:Psd	APN	19	46323395	missense	probably damaging	1.00
IGL02724:Psd	APN	19	46319545	missense	probably benign	0.04
IGL03117:Psd	APN	19	46323122	unclassified	probably benign
ANU05:Psd	UTSW	19	46314747	missense	possibly damaging	0.77
P0035:Psd	UTSW	19	46320961	missense	possibly damaging	0.56
R0054:Psd	UTSW	19	46323342	missense	probably damaging	1.00
R0054:Psd	UTSW	19	46323342	missense	probably damaging	1.00
R0403:Psd	UTSW	19	46320972	unclassified	probably benign
R0499:Psd	UTSW	19	46322161	missense	probably damaging	0.98
R0542:Psd	UTSW	19	46314210	missense	probably damaging	1.00
R0543:Psd	UTSW	19	46319517	missense	possibly damaging	0.62
R0894:Psd	UTSW	19	46313441	missense	probably damaging	1.00
R1449:Psd	UTSW	19	46324811	missense	probably damaging	0.99
R1586:Psd	UTSW	19	46314798	missense	probably damaging	0.98
R2096:Psd	UTSW	19	46324649	splice site	probably null
R2504:Psd	UTSW	19	46324913	missense	possibly damaging	0.90
R2857:Psd	UTSW	19	46324420	missense	probably benign	0.00
R2863:Psd	UTSW	19	46314762	missense	probably damaging	0.97
R3897:Psd	UTSW	19	46324585	missense	possibly damaging	0.93
R3967:Psd	UTSW	19	46324406	missense	probably benign
R3970:Psd	UTSW	19	46324406	missense	probably benign
R4435:Psd	UTSW	19	46314494	missense	probably damaging	1.00
R4612:Psd	UTSW	19	46313339	missense	probably benign	0.15
R4940:Psd	UTSW	19	46322417	missense	probably damaging	1.00
R5055:Psd	UTSW	19	46322468	missense	probably benign	0.00
R5485:Psd	UTSW	19	46316089	splice site	probably null
R5768:Psd	UTSW	19	46312739	missense	possibly damaging	0.84
R5775:Psd	UTSW	19	46314772	nonsense	probably null
R6057:Psd	UTSW	19	46323314	missense	possibly damaging	0.77
R6349:Psd	UTSW	19	46313387	splice site	probably null
R6496:Psd	UTSW	19	46320314	missense	probably damaging	1.00
R6614:Psd	UTSW	19	46313412	missense	probably benign	0.11
R6820:Psd	UTSW	19	46320844	missense	probably damaging	1.00
R6849:Psd	UTSW	19	46317746	missense	probably damaging	0.97
R6860:Psd	UTSW	19	46322419	missense	probably damaging	1.00
R7286:Psd	UTSW	19	46314801	missense	probably damaging	0.98
R7351:Psd	UTSW	19	46322430	missense	probably benign	0.27
R7593:Psd	UTSW	19	46312913	missense	possibly damaging	0.47
R7614:Psd	UTSW	19	46313438	missense	probably damaging	1.00
R7943:Psd	UTSW	19	46324730	missense	possibly damaging	0.54
R8301:Psd	UTSW	19	46321102	intron	probably benign
R8498:Psd	UTSW	19	46324349	missense	probably damaging	1.00
Z1177:Psd	UTSW	19	46324661	missense	probably benign	0.16

Predicted Primers

PCR Primer
(F):5'- ATTTGTCCCTTAGCTGAGGTAC -3'
(R):5'- CGTTTTGTGGAGAAGGCCAG -3'

Sequencing Primer
(F):5'- CCAAGGCAGATTTCATACCTGG -3'
(R):5'- CCAGTGTGAGGCCACTGAATG -3'

Posted On

2019-09-13