Mutagenetix > Incidental Mutation

Incidental Mutation 'R7286:Psd'

566063

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Efa6, Psdl, Efa6a, 1110007H17Rik

MMRRC Submission

045394-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7286 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

46300526-46315595 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 46303240 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 713 (D713V)

Ref Sequence

ENSEMBL: ENSMUSP00000039728 (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: D713V

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: D713V

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: D714V

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: D714V

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 damaging
Transcript: ENSMUST00000224556
AA Change: D82V

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

Predicted Effect

probably damaging
Transcript: ENSMUST00000225323
AA Change: D714V

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930550C14Rik	A	T	9: 53,334,317 (GRCm39)	M187L	possibly damaging	Het
9930012K11Rik	T	C	14: 70,394,686 (GRCm39)	E156G	possibly damaging	Het
Acad9	C	T	3: 36,130,139 (GRCm39)	A194V	probably damaging	Het
Agps	T	A	2: 75,683,128 (GRCm39)	V151E	probably benign	Het
Ak9	A	T	10: 41,283,367 (GRCm39)	I1273L		Het
Akr1c19	T	A	13: 4,296,818 (GRCm39)	L288Q	probably damaging	Het
Carmil1	T	G	13: 24,197,377 (GRCm39)	D1353A	probably damaging	Het
Ccz1	T	A	5: 143,949,897 (GRCm39)	I43F	probably damaging	Het
Cep70	G	A	9: 99,157,638 (GRCm39)	C179Y	probably damaging	Het
Comt	A	T	16: 18,229,440 (GRCm39)	L196H	probably damaging	Het
Cspg5	A	T	9: 110,076,023 (GRCm39)	D253V	probably damaging	Het
Dars2	A	G	1: 160,874,378 (GRCm39)	V437A	possibly damaging	Het
Dcaf5	A	G	12: 80,395,164 (GRCm39)	I335T	probably damaging	Het
Ddn	T	C	15: 98,703,906 (GRCm39)	K462R	possibly damaging	Het
Dscaml1	T	C	9: 45,654,044 (GRCm39)		probably null	Het
Eef1ece2	T	C	16: 20,451,341 (GRCm39)	S325P	probably benign	Het
Ethe1	A	G	7: 24,307,377 (GRCm39)	Y197C	probably damaging	Het
Evc	A	T	5: 37,479,527 (GRCm39)	L269*	probably null	Het
Fam161a	T	C	11: 22,970,001 (GRCm39)	S60P	possibly damaging	Het
Fam20b	A	G	1: 156,509,012 (GRCm39)	V400A	probably benign	Het
Fam53b	T	A	7: 132,361,390 (GRCm39)	S213C	possibly damaging	Het
Flot2	A	G	11: 77,945,612 (GRCm39)	I45V	probably benign	Het
Gemin4	A	C	11: 76,103,579 (GRCm39)	L394R	probably damaging	Het
Glis2	T	G	16: 4,429,182 (GRCm39)	S128R	possibly damaging	Het
Gm3696	A	G	14: 18,435,009 (GRCm39)	Y92H	probably damaging	Het
Gpbp1l1	T	C	4: 116,447,442 (GRCm39)	V374A	probably benign	Het
Grm1	T	C	10: 10,565,440 (GRCm39)	N956S	probably benign	Het
Hbb-bh1	T	C	7: 103,492,238 (GRCm39)	E27G	probably damaging	Het
Hmcn1	A	T	1: 150,458,088 (GRCm39)	C5233S	probably damaging	Het
Hmgcr	C	T	13: 96,803,105 (GRCm39)	C30Y	probably damaging	Het
Hoxb6	A	G	11: 96,183,651 (GRCm39)		probably benign	Het
Igf2	T	C	7: 142,209,555 (GRCm39)	Q35R	possibly damaging	Het
Ighv1-4	C	T	12: 114,450,941 (GRCm39)	V56I	probably benign	Het
Kif13a	C	T	13: 46,905,931 (GRCm39)	V671M	possibly damaging	Het
Lmtk2	C	T	5: 144,111,178 (GRCm39)	Q633*	probably null	Het
Mesd	T	C	7: 83,544,957 (GRCm39)	Y136H	probably damaging	Het
Mga	T	A	2: 119,795,269 (GRCm39)	S2984R	possibly damaging	Het
Mkrn3	T	C	7: 62,068,675 (GRCm39)	N372S	probably benign	Het
Mtpap	A	G	18: 4,387,068 (GRCm39)	I373V	probably benign	Het
Mycbp2	G	A	14: 103,358,027 (GRCm39)	T4589M	probably damaging	Het
Myh2	A	G	11: 67,079,195 (GRCm39)	Q921R	probably benign	Het
Myom1	A	G	17: 71,352,544 (GRCm39)	D324G	possibly damaging	Het
Nat10	T	C	2: 103,584,514 (GRCm39)	K88E	probably benign	Het
Ncapd3	A	G	9: 26,981,254 (GRCm39)	R915G	probably damaging	Het
Nek4	T	C	14: 30,679,249 (GRCm39)	Y190H	probably damaging	Het
Nfasc	A	C	1: 132,529,790 (GRCm39)	Y797D	probably damaging	Het
Ngp	A	G	9: 110,249,978 (GRCm39)	D92G	probably benign	Het
Nos2	A	C	11: 78,820,680 (GRCm39)	H95P	probably damaging	Het
Nr3c1	ACGTC	ACGTCGTC	18: 39,619,513 (GRCm39)		probably benign	Het
Or10ag59	C	T	2: 87,405,863 (GRCm39)	T145I	probably benign	Het
Or5bw2	C	A	7: 6,573,715 (GRCm39)	H242N	probably damaging	Het
Or5p73	T	C	7: 108,064,642 (GRCm39)	I37T	possibly damaging	Het
Or5t18	A	T	2: 86,636,967 (GRCm39)	H125Q	possibly damaging	Het
Otogl	T	A	10: 107,606,471 (GRCm39)	D2154V	probably benign	Het
Pdss1	T	A	2: 22,825,653 (GRCm39)		probably null	Het
Pex5	A	T	6: 124,375,022 (GRCm39)	L609*	probably null	Het
Pglyrp4	C	A	3: 90,640,281 (GRCm39)	A177D	probably damaging	Het
Phactr4	A	G	4: 132,104,489 (GRCm39)		probably null	Het
Phf8-ps	T	C	17: 33,284,501 (GRCm39)	D767G	probably benign	Het
Pik3cd	G	C	4: 149,744,171 (GRCm39)	N193K	probably benign	Het
Prr36	TACCTCTTC	T	8: 4,265,163 (GRCm39)		probably benign	Het
Prss38	A	T	11: 59,266,384 (GRCm39)	W25R	probably benign	Het
Prss8	T	A	7: 127,526,056 (GRCm39)	Q189L	probably damaging	Het
Rad51ap2	C	T	12: 11,507,692 (GRCm39)	T538I	probably benign	Het
Rarres1	T	C	3: 67,422,517 (GRCm39)	T78A	probably benign	Het
Rbl2	G	T	8: 91,828,922 (GRCm39)	G651*	probably null	Het
Rev3l	A	T	10: 39,699,601 (GRCm39)	Q1366L	probably damaging	Het
Rundc1	T	C	11: 101,320,413 (GRCm39)	S215P	probably benign	Het
Sanbr	A	T	11: 23,572,479 (GRCm39)	C130S	probably benign	Het
Scarf2	G	A	16: 17,620,837 (GRCm39)	W168*	probably null	Het
Sh2d7	A	G	9: 54,448,186 (GRCm39)	D69G	possibly damaging	Het
Slc26a4	A	T	12: 31,579,527 (GRCm39)	Y578*	probably null	Het
Slc2a9	A	T	5: 38,610,538 (GRCm39)	L87Q	probably damaging	Het
Slc39a10	A	T	1: 46,849,230 (GRCm39)	H795Q	probably damaging	Het
Spata13	C	T	14: 60,993,871 (GRCm39)	R1108W	probably damaging	Het
Sqle	T	C	15: 59,187,901 (GRCm39)	S70P	probably benign	Het
Syncrip	A	T	9: 88,346,716 (GRCm39)	F263I	probably damaging	Het
Synj2	T	C	17: 6,088,220 (GRCm39)	S1424P	possibly damaging	Het
Tax1bp3	A	T	11: 73,071,941 (GRCm39)	T89S	possibly damaging	Het
Tcaim	G	A	9: 122,648,092 (GRCm39)		probably null	Het
Tcp10c	T	C	17: 13,582,438 (GRCm39)	I240T	possibly damaging	Het
Ttll8	G	T	15: 88,801,442 (GRCm39)	N415K	probably benign	Het
Tut7	T	C	13: 59,969,463 (GRCm39)	E144G	probably benign	Het
Ugcg	T	C	4: 59,217,111 (GRCm39)	S212P	possibly damaging	Het
Vmn2r32	T	C	7: 7,482,807 (GRCm39)	K56E	probably benign	Het
Vmn2r55	T	C	7: 12,386,000 (GRCm39)	E660G	probably damaging	Het
Vmn2r7	T	C	3: 64,598,301 (GRCm39)	N752S	probably benign	Het
Vps54	T	A	11: 21,225,005 (GRCm39)	M167K	probably benign	Het
Vwa2	A	C	19: 56,897,791 (GRCm39)	M699L	probably benign	Het
Wdr59	A	G	8: 112,192,494 (GRCm39)	V689A		Het
Whamm	T	G	7: 81,235,995 (GRCm39)	N399K	probably damaging	Het
Zfp760	A	G	17: 21,941,760 (GRCm39)	K312E	probably benign	Het
Zkscan3	C	A	13: 21,578,983 (GRCm39)	V171L	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
R6860:Psd	UTSW	19	46,310,858 (GRCm39)	missense	probably damaging	1.00
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'- CACATACTCTTCCTGCAGTCAG -3'
(R):5'- CTGGGTGTGTGCAGAAACAG -3'

Sequencing Primer
(F):5'- GGGTCTGCGTGCACCTTTC -3'
(R):5'- TGTGTGCAGAAACAGAGACAC -3'

Posted On

2019-06-26