Mutagenetix > Incidental Mutation

Incidental Mutation 'R4612:Psd'

344901

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Efa6, Psdl, Efa6a, 1110007H17Rik

MMRRC Submission

041823-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4612 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

46300526-46315595 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 46301778 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 937 (D937V)

Ref Sequence

ENSEMBL: ENSMUSP00000152942 (fasta)

Gene Model

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

AlphaFold

Q5DTT2

Predicted Effect

probably benign
Transcript: ENSMUST00000041391
AA Change: D936V

PolyPhen 2 Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: D936V

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 benign
Transcript: ENSMUST00000096029
AA Change: D937V

PolyPhen 2 Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: D937V

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: D305V

PolyPhen 2 Score 0.107 (Sensitivity: 0.93; Specificity: 0.86)

Predicted Effect

probably benign
Transcript: ENSMUST00000225323
AA Change: D937V

PolyPhen 2 Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225748

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226062

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.3%

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: 109 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700019D03Rik	T	C	1: 52,964,635 (GRCm39)	D31G	probably benign	Het
5730455P16Rik	A	T	11: 80,268,806 (GRCm39)	M1K	probably null	Het
Abca15	A	G	7: 119,934,384 (GRCm39)	D120G	probably benign	Het
Adam26a	A	T	8: 44,021,830 (GRCm39)	N553K	probably damaging	Het
Adam32	A	T	8: 25,362,752 (GRCm39)	C558S	probably damaging	Het
Adam34l	A	T	8: 44,079,587 (GRCm39)	F212L	probably benign	Het
Adam39	A	T	8: 41,278,958 (GRCm39)	S450C	probably damaging	Het
Agap2	A	T	10: 126,915,965 (GRCm39)	T159S	unknown	Het
Ahnak	G	A	19: 8,981,088 (GRCm39)	V791I	probably benign	Het
Ak7	T	G	12: 105,727,772 (GRCm39)	L468R	probably damaging	Het
Akap12	A	G	10: 4,304,456 (GRCm39)	D422G	probably damaging	Het
Antxr1	T	A	6: 87,265,155 (GRCm39)	I129F	probably damaging	Het
Arhgap32	G	A	9: 32,170,775 (GRCm39)	G1185D	probably damaging	Het
Atf7ip2	A	T	16: 10,059,427 (GRCm39)	E322D	probably benign	Het
Atg4b	T	C	1: 93,714,263 (GRCm39)	F349L	probably damaging	Het
Atp6v1c1	A	G	15: 38,677,856 (GRCm39)	K127R	probably damaging	Het
Atxn1l	C	T	8: 110,458,736 (GRCm39)	V509M	possibly damaging	Het
B3glct	T	A	5: 149,663,022 (GRCm39)	I260N	probably damaging	Het
Bcl2l12	G	A	7: 44,646,009 (GRCm39)	P70L	probably damaging	Het
Bok	T	A	1: 93,621,900 (GRCm39)	F157L	probably damaging	Het
Bves	G	A	10: 45,215,373 (GRCm39)	G16D	probably benign	Het
Cacna1b	T	A	2: 24,516,864 (GRCm39)	K65*	probably null	Het
Casc3	A	G	11: 98,713,784 (GRCm39)	T339A	probably benign	Het
Ccdc18	C	T	5: 108,283,307 (GRCm39)	S6L	probably benign	Het
Cd86	A	G	16: 36,435,692 (GRCm39)	Y242H	probably benign	Het
Chd3	A	C	11: 69,244,035 (GRCm39)	Y1249*	probably null	Het
Chrne	T	C	11: 70,507,848 (GRCm39)	T284A	probably damaging	Het
Col12a1	T	C	9: 79,523,339 (GRCm39)	D2746G	probably damaging	Het
Cryaa	T	A	17: 31,897,448 (GRCm39)	M72K	probably benign	Het
Csmd1	G	T	8: 15,971,908 (GRCm39)		probably null	Het
Det1	A	T	7: 78,493,454 (GRCm39)	N183K	probably damaging	Het
Dis3	C	A	14: 99,328,871 (GRCm39)	V294L	probably benign	Het
Dnah2	G	A	11: 69,374,193 (GRCm39)	L1493F	possibly damaging	Het
Dsc2	A	T	18: 20,174,876 (GRCm39)	D466E	probably damaging	Het
Dsg4	T	A	18: 20,595,470 (GRCm39)	S558T	probably benign	Het
Dzip3	A	T	16: 48,772,403 (GRCm39)	L422*	probably null	Het
Elp6	T	C	9: 110,143,087 (GRCm39)	F100S	probably damaging	Het
Epg5	C	T	18: 78,025,629 (GRCm39)	T1224I	possibly damaging	Het
Exoc1l	A	T	5: 76,664,345 (GRCm39)	N145Y	probably damaging	Het
F830016B08Rik	T	A	18: 60,434,087 (GRCm39)	I390N	probably benign	Het
Fam110c	A	G	12: 31,124,655 (GRCm39)	T206A	unknown	Het
Fam187b	G	A	7: 30,676,518 (GRCm39)	G9D	possibly damaging	Het
Fat1	A	G	8: 45,478,184 (GRCm39)	D2410G	probably damaging	Het
Fbln1	T	A	15: 85,122,760 (GRCm39)	F390Y	probably benign	Het
Fgg	A	G	3: 82,917,397 (GRCm39)	N142S	probably damaging	Het
Fhip1a	G	A	3: 85,637,679 (GRCm39)	R207*	probably null	Het
Flcn	T	C	11: 59,683,513 (GRCm39)	T555A	probably damaging	Het
Foxq1	G	T	13: 31,742,808 (GRCm39)		probably benign	Het
Gm3233	A	T	10: 77,595,498 (GRCm39)		probably benign	Het
Gprc5a	G	A	6: 135,055,927 (GRCm39)	V125I	probably damaging	Het
Gria2	T	C	3: 80,639,358 (GRCm39)	D218G	probably damaging	Het
Gtf3c5	C	T	2: 28,469,596 (GRCm39)	A103T	probably benign	Het
Hspg2	C	T	4: 137,246,251 (GRCm39)	R1010C	probably damaging	Het
Hspg2	A	G	4: 137,266,886 (GRCm39)	T1964A	possibly damaging	Het
Htatip2	G	T	7: 49,422,345 (GRCm39)	E188*	probably null	Het
Ifna13	T	G	4: 88,562,113 (GRCm39)	E170D	probably damaging	Het
Il4ra	A	G	7: 125,175,255 (GRCm39)	T488A	probably benign	Het
Jup	G	T	11: 100,272,660 (GRCm39)	H251N	probably damaging	Het
Kif21a	A	T	15: 90,852,426 (GRCm39)		probably null	Het
Klhl28	T	A	12: 65,004,034 (GRCm39)	I160L	probably damaging	Het
Klk1b5	A	T	7: 43,494,696 (GRCm39)	T60S	possibly damaging	Het
Kntc1	A	G	5: 123,950,706 (GRCm39)	R1995G	probably damaging	Het
Lrig2	A	C	3: 104,370,099 (GRCm39)	I844M	probably damaging	Het
Lrp2	C	T	2: 69,288,771 (GRCm39)	W3698*	probably null	Het
Lyar	T	A	5: 38,382,053 (GRCm39)	S12T	possibly damaging	Het
Map3k19	T	C	1: 127,743,037 (GRCm39)	K1507E	probably benign	Het
Mre11a	G	A	9: 14,714,199 (GRCm39)	G267R	probably damaging	Het
Mthfd1l	A	G	10: 3,980,717 (GRCm39)	Q473R	probably damaging	Het
Ncald	T	A	15: 37,397,593 (GRCm39)	E29V	probably benign	Het
Neb	T	C	2: 52,177,255 (GRCm39)	D1362G	probably damaging	Het
Nme2	T	C	11: 93,846,428 (GRCm39)	T7A	possibly damaging	Het
Nod2	T	A	8: 89,391,664 (GRCm39)	L657Q	possibly damaging	Het
Nrm	T	A	17: 36,174,421 (GRCm39)	V75E	probably benign	Het
Ogfod1	A	C	8: 94,763,975 (GRCm39)	K20T	possibly damaging	Het
Omp	T	C	7: 97,794,348 (GRCm39)	N93S	probably damaging	Het
Or10h28	T	A	17: 33,488,454 (GRCm39)	V252E	probably benign	Het
Or14a256	T	A	7: 86,264,944 (GRCm39)	Q303L	probably benign	Het
Or5h27	T	C	16: 59,006,674 (GRCm39)	I57M	probably damaging	Het
Pcdhb15	A	C	18: 37,608,648 (GRCm39)	T627P	probably damaging	Het
Pld1	A	G	3: 28,185,882 (GRCm39)	T1036A	possibly damaging	Het
Pogk	C	A	1: 166,226,334 (GRCm39)	E606*	probably null	Het
Ppp1r10	T	A	17: 36,238,823 (GRCm39)	L292Q	probably damaging	Het
Prpf6	T	C	2: 181,273,872 (GRCm39)	C339R	possibly damaging	Het
Rbak	T	C	5: 143,160,222 (GRCm39)	Q277R	probably benign	Het
Sbno1	T	A	5: 124,542,087 (GRCm39)	Y355F	probably damaging	Het
Sec23ip	C	T	7: 128,352,226 (GRCm39)	Q201*	probably null	Het
Serpinb3a	T	C	1: 106,975,337 (GRCm39)	K157E	probably damaging	Het
Slc22a28	A	T	19: 8,078,770 (GRCm39)	N306K	probably damaging	Het
Smarca2	C	A	19: 26,753,625 (GRCm39)	D1584E	possibly damaging	Het
Snx29	C	A	16: 11,265,359 (GRCm39)	Q530K	probably damaging	Het
Stard10	C	A	7: 100,994,877 (GRCm39)	Q278K	possibly damaging	Het
Tgm2	C	T	2: 157,966,124 (GRCm39)	C510Y	probably benign	Het
Tlr9	C	T	9: 106,101,006 (GRCm39)	P99L	probably damaging	Het
Tmco4	T	C	4: 138,717,871 (GRCm39)	W4R	probably benign	Het
Tmem151a	T	A	19: 5,121,862 (GRCm39)		probably benign	Het
Tmem255b	T	C	8: 13,504,228 (GRCm39)	V140A	probably benign	Het
Trbj1-2	C	T	6: 41,510,950 (GRCm39)		probably benign	Het
Trpm2	T	C	10: 77,781,750 (GRCm39)	T290A	probably damaging	Het
Tsc22d1	G	A	14: 76,656,445 (GRCm39)	E120K	possibly damaging	Het
Ttc29	A	G	8: 79,052,175 (GRCm39)	D352G	probably benign	Het
Usp25	A	T	16: 76,830,833 (GRCm39)	I30F	possibly damaging	Het
Usp34	A	C	11: 23,382,268 (GRCm39)	N1993T	probably damaging	Het
Vmn2r124	A	C	17: 18,283,284 (GRCm39)	H326P	probably benign	Het
Vmn2r92	C	A	17: 18,387,132 (GRCm39)	T157K	probably benign	Het
Vstm5	A	T	9: 15,168,789 (GRCm39)	I118F	probably benign	Het
Vwa7	T	C	17: 35,242,426 (GRCm39)	V510A	probably damaging	Het
Zfhx4	G	A	3: 5,462,123 (GRCm39)	S1266N	probably damaging	Het
Zfp763	T	A	17: 33,237,922 (GRCm39)	N408Y	probably benign	Het
Zswim5	C	T	4: 116,843,901 (GRCm39)	H980Y	probably 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
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
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'- TAACAGACGTGTCACCTGACCC -3'
(R):5'- AGGCAGCCCCTTGATAAAATTTG -3'

Sequencing Primer
(F):5'- ACGTGTCACCTGACCCTAGTG -3'
(R):5'- CCCCTTGATAAAATTTGCACGAAGG -3'

Posted On

2015-09-25