Mutagenetix > Incidental Mutation

Incidental Mutation 'R0894:Psd'

83730

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Efa6, Psdl, Efa6a, 1110007H17Rik

MMRRC Submission

039057-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0894 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

46300526-46315595 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 46301880 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 903 (E903G)

Ref Sequence

ENSEMBL: ENSMUSP00000152942 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041391] [ENSMUST00000073116] [ENSMUST00000096029] [ENSMUST00000111881] [ENSMUST00000224556] [ENSMUST00000225323]

AlphaFold

Q5DTT2

Predicted Effect

probably damaging
Transcript: ENSMUST00000041391
AA Change: E902G

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

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: E902G

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: ENSMUST00000073116

SMART Domains

Protein: ENSMUSP00000072859
Gene: ENSMUSG00000025225

Domain	Start	End	E-Value	Type
Pfam:RHD_DNA_bind	40	220	1.3e-67	PFAM
IPT	227	326	3.48e-27	SMART
low complexity region	351	382	N/A	INTRINSIC
low complexity region	391	409	N/A	INTRINSIC
ANK	487	522	5.58e1	SMART
ANK	526	555	9.78e-4	SMART
ANK	559	591	3.74e0	SMART
ANK	599	628	3.36e-2	SMART
ANK	633	663	1.3e1	SMART
ANK	667	696	4.26e-4	SMART
low complexity region	707	721	N/A	INTRINSIC
ANK	729	758	2.35e3	SMART
DEATH	764	851	5.52e-16	SMART
low complexity region	879	894	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000096029
AA Change: E903G

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

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: E903G

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: ENSMUST00000111881

SMART Domains

Protein: ENSMUSP00000107512
Gene: ENSMUSG00000025225

Domain	Start	End	E-Value	Type
Pfam:RHD	40	220	1.3e-67	PFAM
IPT	227	326	3.48e-27	SMART
low complexity region	351	382	N/A	INTRINSIC
low complexity region	391	409	N/A	INTRINSIC
ANK	487	522	5.58e1	SMART
ANK	526	555	9.78e-4	SMART
ANK	559	591	3.74e0	SMART
ANK	599	628	3.36e-2	SMART
ANK	633	663	1.3e1	SMART
ANK	667	696	4.26e-4	SMART
low complexity region	707	721	N/A	INTRINSIC
ANK	729	758	2.35e3	SMART
DEATH	764	851	5.52e-16	SMART
low complexity region	879	894	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000224556
AA Change: E271G

PolyPhen 2 Score 0.161 (Sensitivity: 0.92; Specificity: 0.87)

Predicted Effect

probably damaging
Transcript: ENSMUST00000225323
AA Change: E903G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225748

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226062

Meta Mutation Damage Score

0.2014

Coding Region Coverage

1x: 99.5%
3x: 99.0%
10x: 97.7%
20x: 95.8%

Validation Efficiency

97% (102/105)

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: 104 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	A	G	13: 77,471,726 (GRCm39)	S1044G	probably benign	Het
Aanat	A	G	11: 116,487,730 (GRCm39)	H143R	probably benign	Het
Abca8a	A	G	11: 109,941,792 (GRCm39)	I1159T	probably benign	Het
Abcb1a	G	T	5: 8,724,856 (GRCm39)		probably benign	Het
Abcc1	T	C	16: 14,283,001 (GRCm39)	V1159A	possibly damaging	Het
Akr1e1	T	A	13: 4,645,071 (GRCm39)	Q204L	probably damaging	Het
Alk	T	C	17: 72,202,930 (GRCm39)	Y1135C	probably damaging	Het
Atad2b	C	T	12: 5,015,915 (GRCm39)	T547I	probably damaging	Het
Brd10	T	C	19: 29,697,974 (GRCm39)		probably benign	Het
C030005K15Rik	A	T	10: 97,561,648 (GRCm39)	S28T	unknown	Het
Cdk5rap3	A	G	11: 96,799,654 (GRCm39)	L387P	probably damaging	Het
Cfap95	T	C	19: 23,630,062 (GRCm39)	E10G	unknown	Het
Cfap96	A	G	8: 46,409,497 (GRCm39)	F274S	probably damaging	Het
Clec4f	T	A	6: 83,629,979 (GRCm39)	N193I	probably damaging	Het
Col4a4	A	T	1: 82,507,377 (GRCm39)		probably null	Het
Cplx4	T	G	18: 66,090,116 (GRCm39)	D101A	possibly damaging	Het
Cpne8	A	T	15: 90,533,474 (GRCm39)	D50E	probably damaging	Het
Csmd3	G	T	15: 47,721,316 (GRCm39)	D1542E	possibly damaging	Het
Ctdp1	A	G	18: 80,512,736 (GRCm39)	V9A	probably benign	Het
Ctnnd2	A	T	15: 30,332,301 (GRCm39)		probably benign	Het
Cyp7b1	C	T	3: 18,151,674 (GRCm39)	A180T	probably benign	Het
Dcun1d5	C	T	9: 7,203,379 (GRCm39)		probably benign	Het
Dgat1	G	T	15: 76,387,199 (GRCm39)	L363I	possibly damaging	Het
Dipk2b	T	A	X: 18,289,791 (GRCm39)	I224F	possibly damaging	Het
Dlg1	T	A	16: 31,561,965 (GRCm39)	H120Q	probably benign	Het
Dnah6	T	C	6: 73,101,740 (GRCm39)	N1928S	probably benign	Het
Dnai4	T	C	4: 102,906,583 (GRCm39)		probably benign	Het
Dync2h1	A	T	9: 7,041,734 (GRCm39)		probably benign	Het
Ednra	T	G	8: 78,446,649 (GRCm39)		probably benign	Het
Efcab6	A	T	15: 83,802,493 (GRCm39)	C845S	probably benign	Het
Egln1	A	T	8: 125,642,435 (GRCm39)	C303S	probably damaging	Het
Eomes	T	C	9: 118,311,368 (GRCm39)		probably null	Het
Epha1	A	G	6: 42,340,756 (GRCm39)	V568A	probably benign	Het
Ercc6	T	A	14: 32,238,985 (GRCm39)	N24K	probably benign	Het
Esco2	T	C	14: 66,064,726 (GRCm39)	Q338R	probably benign	Het
Fbxo46	T	C	7: 18,869,654 (GRCm39)	V91A	probably damaging	Het
Fryl	A	T	5: 73,198,675 (GRCm39)		probably benign	Het
Gab3	A	C	X: 74,077,024 (GRCm39)	D43E	probably damaging	Het
Gltpd2	T	A	11: 70,410,535 (GRCm39)		probably benign	Het
Gm17333	G	T	16: 77,649,711 (GRCm39)		noncoding transcript	Het
Gm7353	T	C	7: 3,160,570 (GRCm39)		noncoding transcript	Het
Grik4	T	C	9: 42,599,405 (GRCm39)		probably benign	Het
Gtpbp2	G	T	17: 46,476,895 (GRCm39)	A358S	possibly damaging	Het
Hyls1	C	T	9: 35,472,528 (GRCm39)	C296Y	probably damaging	Het
Igf2r	C	T	17: 12,910,988 (GRCm39)	M1943I	probably benign	Het
Iqca1l	T	C	5: 24,755,731 (GRCm39)		probably null	Het
Ireb2	T	A	9: 54,803,861 (GRCm39)	N517K	probably damaging	Het
Itga10	A	G	3: 96,560,976 (GRCm39)	S614G	possibly damaging	Het
Kdm2b	A	G	5: 123,122,523 (GRCm39)		probably null	Het
Kif17	T	C	4: 138,025,542 (GRCm39)	M948T	possibly damaging	Het
Klhl33	A	T	14: 51,129,583 (GRCm39)	N347K	probably damaging	Het
Llph	T	A	10: 120,064,086 (GRCm39)	C67*	probably null	Het
Lrrn3	T	C	12: 41,504,033 (GRCm39)	T95A	probably damaging	Het
Map3k12	C	A	15: 102,410,613 (GRCm39)	A455S	probably damaging	Het
Mex3d	T	C	10: 80,217,376 (GRCm39)	T149A	probably benign	Het
Myo7b	A	G	18: 32,133,123 (GRCm39)	W409R	probably damaging	Het
Nbea	A	G	3: 55,916,761 (GRCm39)	M833T	possibly damaging	Het
Ncapg	A	G	5: 45,837,236 (GRCm39)	T436A	probably null	Het
Nkx1-2	C	A	7: 132,201,042 (GRCm39)	D72Y	probably null	Het
Or11g27	T	C	14: 50,771,159 (GRCm39)	S97P	possibly damaging	Het
Or2d3b	T	A	7: 106,514,317 (GRCm39)	I304K	probably benign	Het
Or6c217	T	A	10: 129,737,751 (GRCm39)	N276I	probably damaging	Het
Pcdh15	A	G	10: 74,460,087 (GRCm39)	Y1308C	probably damaging	Het
Pcnx2	A	G	8: 126,613,665 (GRCm39)		probably benign	Het
Pcsk1	G	A	13: 75,246,096 (GRCm39)	G158D	probably damaging	Het
Phkb	A	T	8: 86,744,070 (GRCm39)	D573V	probably damaging	Het
Pik3r4	A	G	9: 105,544,970 (GRCm39)	K150E	possibly damaging	Het
Ppp2r5e	C	G	12: 75,516,341 (GRCm39)	A239P	probably damaging	Het
Ppp4r4	C	T	12: 103,566,754 (GRCm39)	A67V	probably damaging	Het
Prex2	A	G	1: 11,252,122 (GRCm39)	T1056A	probably benign	Het
Prkca	A	T	11: 107,903,518 (GRCm39)	Y285N	possibly damaging	Het
Psg19	T	C	7: 18,527,987 (GRCm39)	E252G	probably benign	Het
Psg20	T	A	7: 18,414,969 (GRCm39)	K306*	probably null	Het
Pygl	T	G	12: 70,241,148 (GRCm39)		probably benign	Het
Rasgrf2	A	G	13: 92,130,890 (GRCm39)	S724P	probably damaging	Het
Reck	C	A	4: 43,922,967 (GRCm39)	A414D	probably damaging	Het
Scn10a	C	A	9: 119,459,213 (GRCm39)	V1150L	probably damaging	Het
Shc2	A	T	10: 79,465,751 (GRCm39)	I187N	probably damaging	Het
Sipa1l3	T	A	7: 29,086,716 (GRCm39)	K625*	probably null	Het
Slc44a4	T	C	17: 35,147,466 (GRCm39)	L583P	possibly damaging	Het
Slc5a11	G	C	7: 122,857,643 (GRCm39)	R244P	possibly damaging	Het
Slfn8	T	A	11: 82,894,407 (GRCm39)	Q744L	probably benign	Het
Snx2	G	T	18: 53,309,488 (GRCm39)	V13L	probably benign	Het
Spmip5	A	T	19: 58,776,015 (GRCm39)	L138Q	probably damaging	Het
Spsb1	C	T	4: 149,990,872 (GRCm39)		probably null	Het
Stfa2l1	A	T	16: 35,977,228 (GRCm39)	I8L	probably benign	Het
Svil	G	T	18: 5,097,494 (GRCm39)	R1659L	probably damaging	Het
Tbccd1	A	T	16: 22,640,995 (GRCm39)	L461M	probably benign	Het
Tmem9	A	T	1: 135,961,926 (GRCm39)	T174S	possibly damaging	Het
Tnks2	T	C	19: 36,867,450 (GRCm39)		probably null	Het
Tnrc18	C	A	5: 142,800,869 (GRCm39)	V30L	probably benign	Het
Tomm7	A	G	5: 24,049,025 (GRCm39)	F16S	probably damaging	Het
Ttf2	A	G	3: 100,876,865 (GRCm39)		probably benign	Het
Ubr7	C	A	12: 102,735,450 (GRCm39)	T303N	probably damaging	Het
Ushbp1	A	T	8: 71,842,868 (GRCm39)		probably null	Het
Vmn1r177	C	A	7: 23,565,475 (GRCm39)	V134F	probably benign	Het
Vmn2r12	A	G	5: 109,235,716 (GRCm39)		probably null	Het
Vmn2r53	T	G	7: 12,335,141 (GRCm39)	H173P	probably benign	Het
Yars1	A	T	4: 129,090,948 (GRCm39)	M119L	probably damaging	Het
Zcrb1	A	T	15: 93,295,038 (GRCm39)		probably benign	Het
Zfp267	T	A	3: 36,218,935 (GRCm39)	Y319*	probably null	Het
Zfp319	C	A	8: 96,056,250 (GRCm39)		probably benign	Het
Zfp783	C	G	6: 47,920,320 (GRCm39)		noncoding transcript	Het
Zfyve26	A	G	12: 79,320,372 (GRCm39)	I1024T	possibly damaging	Het

Other mutations in Psd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01291:Psd	APN	19	46,303,186 (GRCm39)	missense	possibly damaging	0.77
IGL01307:Psd	APN	19	46,303,097 (GRCm39)	missense	probably damaging	1.00
IGL02329:Psd	APN	19	46,308,098 (GRCm39)	missense	possibly damaging	0.66
IGL02423:Psd	APN	19	46,302,943 (GRCm39)	missense	possibly damaging	0.95
IGL02644:Psd	APN	19	46,311,834 (GRCm39)	missense	probably damaging	1.00
IGL02724:Psd	APN	19	46,307,984 (GRCm39)	missense	probably benign	0.04
IGL03117:Psd	APN	19	46,311,561 (GRCm39)	unclassified	probably benign
ANU05:Psd	UTSW	19	46,303,186 (GRCm39)	missense	possibly damaging	0.77
G1Funyon:Psd	UTSW	19	46,309,541 (GRCm39)	intron	probably benign
P0035:Psd	UTSW	19	46,309,400 (GRCm39)	missense	possibly damaging	0.56
R0054:Psd	UTSW	19	46,311,781 (GRCm39)	missense	probably damaging	1.00
R0054:Psd	UTSW	19	46,311,781 (GRCm39)	missense	probably damaging	1.00
R0403:Psd	UTSW	19	46,309,411 (GRCm39)	unclassified	probably benign
R0499:Psd	UTSW	19	46,310,600 (GRCm39)	missense	probably damaging	0.98
R0542:Psd	UTSW	19	46,302,649 (GRCm39)	missense	probably damaging	1.00
R0543:Psd	UTSW	19	46,307,956 (GRCm39)	missense	possibly damaging	0.62
R1449:Psd	UTSW	19	46,313,250 (GRCm39)	missense	probably damaging	0.99
R1586:Psd	UTSW	19	46,303,237 (GRCm39)	missense	probably damaging	0.98
R2096:Psd	UTSW	19	46,313,088 (GRCm39)	splice site	probably null
R2504:Psd	UTSW	19	46,313,352 (GRCm39)	missense	possibly damaging	0.90
R2857:Psd	UTSW	19	46,312,859 (GRCm39)	missense	probably benign	0.00
R2863:Psd	UTSW	19	46,303,201 (GRCm39)	missense	probably damaging	0.97
R3897:Psd	UTSW	19	46,313,024 (GRCm39)	missense	possibly damaging	0.93
R3967:Psd	UTSW	19	46,312,845 (GRCm39)	missense	probably benign
R3970:Psd	UTSW	19	46,312,845 (GRCm39)	missense	probably benign
R4435:Psd	UTSW	19	46,302,933 (GRCm39)	missense	probably damaging	1.00
R4612:Psd	UTSW	19	46,301,778 (GRCm39)	missense	probably benign	0.15
R4940:Psd	UTSW	19	46,310,856 (GRCm39)	missense	probably damaging	1.00
R5055:Psd	UTSW	19	46,310,907 (GRCm39)	missense	probably benign	0.00
R5485:Psd	UTSW	19	46,304,528 (GRCm39)	splice site	probably null
R5768:Psd	UTSW	19	46,301,178 (GRCm39)	missense	possibly damaging	0.84
R5775:Psd	UTSW	19	46,303,211 (GRCm39)	nonsense	probably null
R6057:Psd	UTSW	19	46,311,753 (GRCm39)	missense	possibly damaging	0.77
R6349:Psd	UTSW	19	46,301,826 (GRCm39)	splice site	probably null
R6496:Psd	UTSW	19	46,308,753 (GRCm39)	missense	probably damaging	1.00
R6614:Psd	UTSW	19	46,301,851 (GRCm39)	missense	probably benign	0.11
R6820:Psd	UTSW	19	46,309,283 (GRCm39)	missense	probably damaging	1.00
R6849:Psd	UTSW	19	46,306,185 (GRCm39)	missense	probably damaging	0.97
R6860:Psd	UTSW	19	46,310,858 (GRCm39)	missense	probably damaging	1.00
R7286:Psd	UTSW	19	46,303,240 (GRCm39)	missense	probably damaging	0.98
R7326:Psd	UTSW	19	46,312,893 (GRCm39)	missense	probably benign	0.01
R7351:Psd	UTSW	19	46,310,869 (GRCm39)	missense	probably benign	0.27
R7593:Psd	UTSW	19	46,301,352 (GRCm39)	missense	possibly damaging	0.47
R7614:Psd	UTSW	19	46,301,877 (GRCm39)	missense	probably damaging	1.00
R7943:Psd	UTSW	19	46,313,169 (GRCm39)	missense	possibly damaging	0.54
R8301:Psd	UTSW	19	46,309,541 (GRCm39)	intron	probably benign
R8498:Psd	UTSW	19	46,312,788 (GRCm39)	missense	probably damaging	1.00
R8712:Psd	UTSW	19	46,301,775 (GRCm39)	missense	probably damaging	1.00
R8952:Psd	UTSW	19	46,310,900 (GRCm39)	missense	probably damaging	1.00
R8980:Psd	UTSW	19	46,310,657 (GRCm39)	missense	possibly damaging	0.95
R9168:Psd	UTSW	19	46,309,233 (GRCm39)	missense	probably damaging	1.00
R9322:Psd	UTSW	19	46,301,880 (GRCm39)	missense	probably damaging	1.00
R9512:Psd	UTSW	19	46,306,154 (GRCm39)	missense	possibly damaging	0.79
R9569:Psd	UTSW	19	46,308,717 (GRCm39)	missense	possibly damaging	0.94
R9638:Psd	UTSW	19	46,301,841 (GRCm39)	frame shift	probably null
R9645:Psd	UTSW	19	46,301,841 (GRCm39)	frame shift	probably null
R9721:Psd	UTSW	19	46,311,628 (GRCm39)	missense	probably benign	0.00
Z1177:Psd	UTSW	19	46,313,100 (GRCm39)	missense	probably benign	0.16

Predicted Primers

PCR Primer
(F):5'- TGGGTTCCAGGCTTAGCTATCAGAC -3'
(R):5'- AAGAAATTCAGCCGCCCTCTGC -3'

Sequencing Primer
(F):5'- AGGCTTAGCTATCAGACCCTTATC -3'
(R):5'- CAGGTAGTTCCAAGTGGCTCAG -3'

Posted On

2013-11-08