Mutagenetix > Incidental Mutation

Incidental Mutation 'R6860:Psd'

535485

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Efa6, Psdl, Efa6a, 1110007H17Rik

MMRRC Submission

045025-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6860 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

46300526-46315595 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 46310858 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 397 (D397V)

Ref Sequence

ENSEMBL: ENSMUSP00000152942 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041391] [ENSMUST00000096029] [ENSMUST00000223903] [ENSMUST00000223917] [ENSMUST00000224447] [ENSMUST00000224556] [ENSMUST00000225323] [ENSMUST00000225781]

AlphaFold

Q5DTT2

Predicted Effect

probably damaging
Transcript: ENSMUST00000041391
AA Change: D397V

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

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: D397V

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 damaging
Transcript: ENSMUST00000096029
AA Change: D397V

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

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: D397V

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: ENSMUST00000223903

Predicted Effect

probably benign
Transcript: ENSMUST00000223917

Predicted Effect

probably benign
Transcript: ENSMUST00000224447

Predicted Effect

probably benign
Transcript: ENSMUST00000224556

Predicted Effect

probably damaging
Transcript: ENSMUST00000225323
AA Change: D397V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000225781

Meta Mutation Damage Score

0.1729

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.3%

Validation Efficiency

100% (86/86)

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	T	C	11: 72,080,412 (GRCm39)	E418G	probably damaging	Het
9930012K11Rik	C	A	14: 70,395,071 (GRCm39)	V28L	possibly damaging	Het
Abtb2	C	T	2: 103,539,770 (GRCm39)	R712*	probably null	Het
Acvr1c	C	T	2: 58,177,717 (GRCm39)	G171S	probably damaging	Het
Ahctf1	G	T	1: 179,580,853 (GRCm39)	A1783E	probably benign	Het
Anapc4	A	T	5: 53,006,170 (GRCm39)	Q149L	probably damaging	Het
Ankrd27	T	C	7: 35,327,952 (GRCm39)	V824A	possibly damaging	Het
Ankrd31	G	C	13: 96,968,094 (GRCm39)	C577S	probably benign	Het
Apol7c	T	C	15: 77,410,274 (GRCm39)	N224S	probably benign	Het
Arl14	A	T	3: 69,130,029 (GRCm39)	T59S	probably benign	Het
Astn1	T	A	1: 158,440,042 (GRCm39)	I870K	probably damaging	Het
B4galt1	A	T	4: 40,807,796 (GRCm39)	V335E	probably benign	Het
C2cd3	C	T	7: 100,039,448 (GRCm39)	P216S	probably benign	Het
Cchcr1	C	A	17: 35,840,015 (GRCm39)	N711K	possibly damaging	Het
Chd2	A	G	7: 73,147,558 (GRCm39)	F467L	possibly damaging	Het
Cntn6	A	T	6: 104,838,907 (GRCm39)	E987V	possibly damaging	Het
Col11a2	T	A	17: 34,272,572 (GRCm39)	L286H	probably damaging	Het
Cwc22	C	T	2: 77,759,792 (GRCm39)	R85Q	possibly damaging	Het
Cyp7a1	A	C	4: 6,272,587 (GRCm39)	F209V	probably damaging	Het
Dmtn	T	C	14: 70,852,322 (GRCm39)	T189A	possibly damaging	Het
Dnhd1	C	G	7: 105,327,473 (GRCm39)	N777K	probably benign	Het
Dusp16	A	T	6: 134,702,842 (GRCm39)	C216*	probably null	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Fbn1	T	C	2: 125,170,078 (GRCm39)	N1993S	probably damaging	Het
Fbxw22	A	G	9: 109,213,030 (GRCm39)	S306P	probably benign	Het
Ferd3l	T	C	12: 33,978,651 (GRCm39)	S55P	probably benign	Het
Fpr-rs3	A	G	17: 20,844,560 (GRCm39)	S194P	possibly damaging	Het
Gm19965	G	A	1: 116,748,609 (GRCm39)	D97N	probably benign	Het
Gtpbp2	A	G	17: 46,478,914 (GRCm39)		probably benign	Het
H3c7	G	T	13: 23,728,760 (GRCm39)	V36L	probably benign	Het
Hcn3	A	C	3: 89,067,152 (GRCm39)	I72S	possibly damaging	Het
Hk3	T	A	13: 55,162,278 (GRCm39)	N109Y	probably damaging	Het
Iqub	T	C	6: 24,505,737 (GRCm39)	E57G	possibly damaging	Het
Kcnk3	T	A	5: 30,779,397 (GRCm39)	M149K	possibly damaging	Het
Kcp	C	T	6: 29,505,719 (GRCm39)	G51D	probably benign	Het
Kif26a	C	A	12: 112,113,263 (GRCm39)	A53D	probably damaging	Het
Lifr	T	A	15: 7,202,418 (GRCm39)	I353K	probably benign	Het
Llph	A	T	10: 120,067,189 (GRCm39)	N102I	probably damaging	Het
Lmo3	C	A	6: 138,393,566 (GRCm39)	R18L	possibly damaging	Het
Lrrc46	T	C	11: 96,926,371 (GRCm39)	E175G	probably benign	Het
Ltk	A	T	2: 119,585,075 (GRCm39)	C128*	probably null	Het
Map1b	T	C	13: 99,571,275 (GRCm39)	E482G	probably damaging	Het
Mapk8ip2	T	C	15: 89,344,655 (GRCm39)	V740A	probably damaging	Het
Miga2	T	C	2: 30,261,175 (GRCm39)	W157R	probably benign	Het
Mlip	A	G	9: 77,009,675 (GRCm39)	*837Q	probably null	Het
Mroh2a	G	T	1: 88,182,657 (GRCm39)	R1195L	possibly damaging	Het
Myl1	T	C	1: 66,984,217 (GRCm39)		probably benign	Het
Or1l4	T	C	2: 37,092,189 (GRCm39)	L312P	possibly damaging	Het
Or2a5	T	C	6: 42,873,750 (GRCm39)	Y122H	probably benign	Het
Or51ab3	A	G	7: 103,201,075 (GRCm39)	I28V	probably benign	Het
P3h3	A	T	6: 124,834,331 (GRCm39)	V107D	probably benign	Het
Papolb	A	T	5: 142,514,651 (GRCm39)	S331T	possibly damaging	Het
Pars2	T	G	4: 106,511,700 (GRCm39)	V494G	probably benign	Het
Pcdhb3	C	A	18: 37,434,763 (GRCm39)	T243K	probably benign	Het
Pde9a	T	A	17: 31,689,698 (GRCm39)	M415K	probably damaging	Het
Ppp1r9b	G	A	11: 94,882,974 (GRCm39)	A201T	probably benign	Het
Prl	A	G	13: 27,248,942 (GRCm39)	N197S	possibly damaging	Het
Prl2c1	T	A	13: 28,035,724 (GRCm39)	M32K	probably benign	Het
Prrt4	T	C	6: 29,170,737 (GRCm39)	S572G	possibly damaging	Het
Psme2b	A	T	11: 48,836,307 (GRCm39)	Y213*	probably null	Het
Ptcd3	T	A	6: 71,874,094 (GRCm39)		probably null	Het
Ptprk	T	G	10: 28,210,480 (GRCm39)	F167L	probably damaging	Het
Rfx7	T	C	9: 72,524,226 (GRCm39)	V472A	probably damaging	Het
Sanbr	A	G	11: 23,575,100 (GRCm39)	L58P	probably damaging	Het
Scnn1g	T	C	7: 121,339,576 (GRCm39)	L125S	probably damaging	Het
Sec16a	T	C	2: 26,320,124 (GRCm39)	Y1438C	probably damaging	Het
Serinc3	C	T	2: 163,476,366 (GRCm39)	S155N	probably benign	Het
Slc3a2	A	T	19: 8,690,996 (GRCm39)	V78E	probably damaging	Het
Slc44a4	T	A	17: 35,140,044 (GRCm39)	L23Q	probably damaging	Het
Slco5a1	C	T	1: 12,951,420 (GRCm39)		probably benign	Het
Slit1	A	G	19: 41,605,154 (GRCm39)	M899T	probably benign	Het
Sorl1	A	G	9: 41,933,688 (GRCm39)	I1094T	probably benign	Het
Spag9	T	A	11: 93,972,196 (GRCm39)	L258Q	probably benign	Het
Strip1	T	C	3: 107,526,252 (GRCm39)	E488G	possibly damaging	Het
Stx18	G	A	5: 38,262,235 (GRCm39)	D30N	possibly damaging	Het
Sync	T	C	4: 129,181,583 (GRCm39)		probably null	Het
Syncrip	A	G	9: 88,358,849 (GRCm39)	V220A	probably damaging	Het
Tagln2	T	C	1: 172,333,476 (GRCm39)	I110T	probably benign	Het
Taok1	T	C	11: 77,432,627 (GRCm39)	T729A	probably benign	Het
Tgfbrap1	C	T	1: 43,106,759 (GRCm39)	V75I	possibly damaging	Het
Tnfrsf21	A	G	17: 43,327,957 (GRCm39)	T24A	probably benign	Het
Tnxb	T	A	17: 34,932,131 (GRCm39)	D2221E	probably damaging	Het
Triml1	A	G	8: 43,583,603 (GRCm39)	S333P	probably damaging	Het
Trp53bp1	C	A	2: 121,029,594 (GRCm39)	R1862L	probably damaging	Het
Tsc22d1	T	G	14: 76,655,732 (GRCm39)	I737S	possibly damaging	Het
U2af2	A	T	7: 5,082,273 (GRCm39)	K462N	possibly damaging	Het
Ubap2	A	C	4: 41,233,631 (GRCm39)	N86K	probably damaging	Het
Uso1	A	G	5: 92,343,207 (GRCm39)	K764E	probably benign	Het
Vmn1r192	T	A	13: 22,372,122 (GRCm39)	M33L	probably benign	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
R0894:Psd	UTSW	19	46,301,880 (GRCm39)	missense	probably damaging	1.00
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
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'- TGCCAGAATCAGGTTCAAGAGG -3'
(R):5'- GGGACACTGAACTTCATGAGG -3'

Sequencing Primer
(F):5'- CAGGTGCAGGTGGGTCAG -3'
(R):5'- CACTGAACTTCATGAGGTTTTGGATC -3'

Posted On

2018-09-12