Mutagenetix > Incidental Mutation

Incidental Mutation 'R0499:Psd'

47071

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Efa6, Psdl, Efa6a, 1110007H17Rik

MMRRC Submission

038695-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0499 (G1)

Quality Score

137

Status

Validated

Chromosome

Chromosomal Location

46300526-46315595 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 46310600 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 483 (E483G)

Ref Sequence

ENSEMBL: ENSMUSP00000152942 (fasta)

Gene Model

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

AlphaFold

Q5DTT2

Predicted Effect

probably damaging
Transcript: ENSMUST00000041391
AA Change: E483G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: E483G

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: E483G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: E483G

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

noncoding transcript
Transcript: ENSMUST00000224094

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224444

Predicted Effect

probably benign
Transcript: ENSMUST00000224447

Predicted Effect

probably damaging
Transcript: ENSMUST00000225323
AA Change: E483G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225072

Predicted Effect

probably benign
Transcript: ENSMUST00000224556

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225770

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225748

Predicted Effect

probably benign
Transcript: ENSMUST00000225781

Meta Mutation Damage Score

0.0620

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.2%

Validation Efficiency

99% (97/98)

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: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad9	T	C	3: 36,139,564 (GRCm39)	V388A	probably damaging	Het
Acp3	T	C	9: 104,197,201 (GRCm39)	E146G	probably damaging	Het
Adap2	A	T	11: 80,066,905 (GRCm39)	R276S	probably damaging	Het
Agbl3	A	T	6: 34,816,270 (GRCm39)	M727L	probably benign	Het
Ahnak	T	A	19: 8,977,628 (GRCm39)		probably benign	Het
Ankmy1	G	T	1: 92,813,948 (GRCm39)	D410E	probably damaging	Het
Ankra2	T	C	13: 98,402,962 (GRCm39)	S70P	probably damaging	Het
Aox4	T	C	1: 58,302,556 (GRCm39)		probably null	Het
Arl13b	G	A	16: 62,622,096 (GRCm39)	T399I	probably benign	Het
Atad2	A	T	15: 57,966,636 (GRCm39)	D652E	possibly damaging	Het
Atad2	T	G	15: 57,984,345 (GRCm39)	M328L	probably benign	Het
Ccnb1	T	C	13: 100,916,642 (GRCm39)		probably null	Het
Ccr2	G	C	9: 123,905,976 (GRCm39)	K85N	possibly damaging	Het
Ccr2	A	T	9: 123,906,163 (GRCm39)	T148S	possibly damaging	Het
Cdc20b	T	C	13: 113,192,484 (GRCm39)	V59A	probably benign	Het
Cdin1	C	T	2: 115,473,172 (GRCm39)	R101W	probably damaging	Het
Cdkl3	T	C	11: 51,923,243 (GRCm39)	S507P	possibly damaging	Het
Celf6	C	A	9: 59,510,161 (GRCm39)	T86K	probably benign	Het
Ces1g	A	G	8: 94,060,317 (GRCm39)	F101L	probably benign	Het
Cimap1d	T	C	10: 79,476,099 (GRCm39)	D155G	probably damaging	Het
Cntnap3	C	T	13: 65,006,492 (GRCm39)	D107N	probably benign	Het
Col15a1	A	T	4: 47,262,950 (GRCm39)	D534V	probably damaging	Het
Col27a1	A	G	4: 63,218,978 (GRCm39)		probably benign	Het
Csmd3	T	C	15: 47,710,527 (GRCm39)	T1687A	probably benign	Het
Cstf3	A	G	2: 104,479,950 (GRCm39)	I272M	possibly damaging	Het
Cyp2d40	T	C	15: 82,645,418 (GRCm39)	T150A	probably benign	Het
Dnah8	T	A	17: 30,934,483 (GRCm39)	F1489L	possibly damaging	Het
Dop1b	A	T	16: 93,567,325 (GRCm39)	T1251S	probably benign	Het
Dtx2	G	A	5: 136,057,957 (GRCm39)	G421R	probably damaging	Het
Epb41l3	T	A	17: 69,554,654 (GRCm39)	D251E	probably benign	Het
Erg	A	C	16: 95,161,842 (GRCm39)	Y305*	probably null	Het
Exosc4	G	A	15: 76,213,766 (GRCm39)	A197T	probably benign	Het
Fam227b	T	A	2: 125,942,829 (GRCm39)	I323L	probably benign	Het
Far1	G	T	7: 113,153,503 (GRCm39)		probably benign	Het
Fmod	A	G	1: 133,968,934 (GRCm39)	I325V	possibly damaging	Het
Fshr	C	G	17: 89,316,713 (GRCm39)	S169T	probably benign	Het
Gm4076	G	T	13: 85,275,345 (GRCm39)		noncoding transcript	Het
Gm5134	A	T	10: 75,828,359 (GRCm39)	Y313F	probably benign	Het
H2-Q6	T	A	17: 35,644,179 (GRCm39)	F54I	probably damaging	Het
Hcrtr2	C	A	9: 76,161,954 (GRCm39)	L145F	probably damaging	Het
Hepacam2	A	G	6: 3,476,121 (GRCm39)	L268P	probably damaging	Het
Herc2	C	A	7: 55,834,117 (GRCm39)	C3107*	probably null	Het
Herc4	T	C	10: 63,099,811 (GRCm39)	V78A	probably damaging	Het
Hyal5	T	C	6: 24,877,920 (GRCm39)	W339R	probably damaging	Het
Igfbp6	T	A	15: 102,056,419 (GRCm39)		probably null	Het
Il18rap	A	T	1: 40,564,218 (GRCm39)	H112L	probably benign	Het
Il1r2	T	A	1: 40,162,309 (GRCm39)	Y317*	probably null	Het
Ints8	C	A	4: 11,246,097 (GRCm39)	V190L	probably benign	Het
Ipo11	T	C	13: 107,061,595 (GRCm39)	T22A	probably benign	Het
Itgb4	C	A	11: 115,870,521 (GRCm39)	R117S	probably benign	Het
Lcorl	C	G	5: 45,891,711 (GRCm39)	G214A	probably benign	Het
Lgals3bp	T	A	11: 118,289,019 (GRCm39)		probably null	Het
Lyst	T	A	13: 13,791,298 (GRCm39)	L54I	probably damaging	Het
Mcm9	T	C	10: 53,414,250 (GRCm39)	T1015A	probably benign	Het
Mef2d	T	A	3: 88,063,825 (GRCm39)	I84N	probably damaging	Het
Mmrn2	A	G	14: 34,119,913 (GRCm39)	N261S	probably damaging	Het
Mpdz	T	C	4: 81,210,768 (GRCm39)	T1693A	probably benign	Het
Mss51	T	A	14: 20,534,756 (GRCm39)	Q338L	possibly damaging	Het
Mstn	T	A	1: 53,103,143 (GRCm39)	Y160N	probably damaging	Het
Muc6	T	C	7: 141,226,735 (GRCm39)	T1431A	probably benign	Het
Nek9	A	T	12: 85,348,657 (GRCm39)	M959K	probably benign	Het
Or2ak6	G	A	11: 58,593,069 (GRCm39)	V181I	probably benign	Het
Or4f58	A	T	2: 111,851,777 (GRCm39)	C141S	probably damaging	Het
Or8b47	A	T	9: 38,435,801 (GRCm39)	M258L	probably benign	Het
Otog	G	T	7: 45,923,256 (GRCm39)	G1044W	probably damaging	Het
Pcdh9	G	A	14: 94,123,671 (GRCm39)	T833M	probably damaging	Het
Pdcd10	T	C	3: 75,434,958 (GRCm39)	K111R	probably damaging	Het
Pde5a	A	G	3: 122,542,107 (GRCm39)	N199S	probably damaging	Het
Plekhg1	T	C	10: 3,887,971 (GRCm39)	V355A	probably damaging	Het
Podn	G	T	4: 107,878,791 (GRCm39)	L359I	probably damaging	Het
Ptch2	T	A	4: 116,968,340 (GRCm39)	L905*	probably null	Het
Rxfp2	T	A	5: 149,989,880 (GRCm39)	N420K	probably damaging	Het
Scpppq1	C	A	5: 104,222,747 (GRCm39)	G24*	probably null	Het
Sde2	T	A	1: 180,689,992 (GRCm39)	D237E	probably benign	Het
Serpina1d	A	T	12: 103,732,016 (GRCm39)	L281Q	probably damaging	Het
Serpina9	T	C	12: 103,967,729 (GRCm39)	N222S	probably benign	Het
Sh3bgrl2	A	G	9: 83,459,612 (GRCm39)	K57E	probably damaging	Het
Shc3	C	T	13: 51,634,264 (GRCm39)		probably benign	Het
Sik3	T	C	9: 46,120,038 (GRCm39)	M659T	possibly damaging	Het
Slc23a2	A	G	2: 131,913,937 (GRCm39)	L280P	probably damaging	Het
Smchd1	G	T	17: 71,694,083 (GRCm39)	Q1221K	probably benign	Het
Spmip2	T	A	3: 79,313,093 (GRCm39)	W56R	probably damaging	Het
Spocd1	A	G	4: 129,849,263 (GRCm39)	N694S	possibly damaging	Het
Styxl2	C	A	1: 165,926,670 (GRCm39)	V981L	probably benign	Het
Tecta	T	C	9: 42,263,359 (GRCm39)	D1409G	probably damaging	Het
Tmem131	A	T	1: 36,880,754 (GRCm39)	V172D	probably damaging	Het
Trpm3	T	C	19: 22,964,237 (GRCm39)	M1244T	possibly damaging	Het
Ugcg	G	C	4: 59,217,036 (GRCm39)	V187L	possibly damaging	Het
Usp17le	T	C	7: 104,417,708 (GRCm39)	N478S	probably benign	Het
Usp36	A	G	11: 118,164,397 (GRCm39)	V205A	probably damaging	Het
Vmn1r25	T	A	6: 57,955,494 (GRCm39)	Q265L	probably damaging	Het
Vwf	A	T	6: 125,615,077 (GRCm39)	H1176L	probably benign	Het
Zfyve28	C	T	5: 34,389,550 (GRCm39)	D217N	possibly damaging	Het
Zranb3	A	C	1: 127,882,817 (GRCm39)		probably null	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
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
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'- CTCTGTCCCTTAATCAGCAGTTCGG -3'
(R):5'- TGGGCTTCTCAAGTCACCAGTACC -3'

Sequencing Primer
(F):5'- AGCCCAAAGCTATCCTCAGA -3'
(R):5'- TGAAGCTATCTTGGAGTCACACC -3'

Posted On

2013-06-12