Mutagenetix > Incidental Mutation

Incidental Mutation 'R2504:Psd'

252294

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Psdl, Efa6a, Efa6, 1110007H17Rik

MMRRC Submission

040412-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2504 (G1)

Quality Score

155

Status

Not validated

Chromosome

Chromosomal Location

46312087-46327156 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 46324913 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 6 (M6K)

Ref Sequence

ENSEMBL: ENSMUSP00000152942 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026256] [ENSMUST00000041391] [ENSMUST00000051234] [ENSMUST00000096029] [ENSMUST00000167861] [ENSMUST00000177667] [ENSMUST00000223903] [ENSMUST00000223917] [ENSMUST00000224447] [ENSMUST00000225781] [ENSMUST00000225323]

AlphaFold

Q5DTT2

Predicted Effect

probably benign
Transcript: ENSMUST00000026256

SMART Domains

Protein: ENSMUSP00000026256
Gene: ENSMUSG00000025226

Domain	Start	End	E-Value	Type
Pfam:F-box	18	63	1.9e-6	PFAM
low complexity region	76	84	N/A	INTRINSIC
LRR	113	138	1.01e1	SMART
LRR	139	164	1.89e-1	SMART
LRR	165	190	2.27e-4	SMART
LRR	192	217	3.47e0	SMART
LRR	218	243	2.57e-3	SMART
LRR	244	269	2.05e1	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000041391
AA Change: M6K

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: M6K

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: ENSMUST00000051234

SMART Domains

Protein: ENSMUSP00000053469
Gene: ENSMUSG00000036748

Domain	Start	End	E-Value	Type
Pfam:CUE	144	183	4.6e-7	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000096029
AA Change: M6K

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: M6K

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: ENSMUST00000167861

SMART Domains

Protein: ENSMUSP00000129589
Gene: ENSMUSG00000036748

Domain	Start	End	E-Value	Type
Pfam:CUE	144	183	5.7e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000177667

SMART Domains

Protein: ENSMUSP00000137489
Gene: ENSMUSG00000025226

Domain	Start	End	E-Value	Type
Pfam:F-box	18	63	2.1e-6	PFAM
low complexity region	76	84	N/A	INTRINSIC
LRR	113	138	1.01e1	SMART
LRR	139	164	1.89e-1	SMART
LRR	165	190	2.27e-4	SMART
LRR	192	217	3.47e0	SMART
LRR	218	243	2.57e-3	SMART
LRR	244	269	2.05e1	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000223903
AA Change: M6K

Predicted Effect

unknown
Transcript: ENSMUST00000223917
AA Change: M6K

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224094

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224444

Predicted Effect

probably benign
Transcript: ENSMUST00000224447
AA Change: M6K

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)

Predicted Effect

unknown
Transcript: ENSMUST00000225781
AA Change: M6K

Predicted Effect

possibly damaging
Transcript: ENSMUST00000225323
AA Change: M6K

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225072

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225770

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.4%

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410089E03Rik	G	A	15: 8,219,216	E1750K	probably damaging	Het
4933425L06Rik	A	G	13: 105,109,742	I270M	probably benign	Het
Aatk	T	C	11: 120,018,855	D28G	probably benign	Het
Abcg1	T	A	17: 31,092,395	S125T	probably damaging	Het
Actbl2	T	C	13: 111,256,183	S351P	possibly damaging	Het
Ankrd34b	A	G	13: 92,439,061		probably null	Het
BC030867	T	C	11: 102,255,296	Y133H	possibly damaging	Het
BC051665	C	T	13: 60,782,654	V295I	probably benign	Het
C1qtnf2	A	G	11: 43,491,156	N265S	probably damaging	Het
Ccdc14	C	T	16: 34,721,850	R573*	probably null	Het
Cd55b	A	T	1: 130,409,875	Y247N	probably damaging	Het
Celsr2	A	T	3: 108,413,591	V635E	probably benign	Het
Clec16a	T	C	16: 10,559,687		probably benign	Het
Clec4b1	A	G	6: 123,065,945	Y41C	probably damaging	Het
Cntn5	A	T	9: 10,172,121	D19E	probably benign	Het
Cop1	A	G	1: 159,232,805	N53S	probably damaging	Het
Csad	A	T	15: 102,188,667	M1K	probably null	Het
Cyb5rl	A	G	4: 107,080,945	I200V	probably benign	Het
Cyp26a1	A	G	19: 37,698,342	T81A	probably damaging	Het
Cyp2d12	A	T	15: 82,559,036	H433L	probably benign	Het
D7Ertd443e	T	A	7: 134,349,479		probably null	Het
Dennd1b	A	G	1: 139,170,170		probably benign	Het
Dmap1	G	T	4: 117,675,298	T357K	probably damaging	Het
Dzip1	G	T	14: 118,881,044	T759K	probably benign	Het
Elmo2	A	G	2: 165,298,687	V300A	probably damaging	Het
Eml5	T	C	12: 98,844,105	D864G	possibly damaging	Het
Ep400	A	G	5: 110,668,645	V2670A	probably damaging	Het
Epha3	T	A	16: 63,603,625	I534F	probably damaging	Het
Epha4	A	C	1: 77,382,991	Y742D	probably damaging	Het
Ergic2	A	G	6: 148,204,774		probably null	Het
Ero1l	A	T	14: 45,299,088		probably null	Het
Fam229a	A	G	4: 129,491,486	D70G	probably damaging	Het
Fbn2	C	T	18: 58,093,359	R781Q	probably damaging	Het
Fbxo16	A	T	14: 65,270,714		probably benign	Het
Fbxo39	T	A	11: 72,317,285	S154R	probably benign	Het
Fer	T	A	17: 63,991,580		probably null	Het
Filip1l	A	G	16: 57,570,662	I538V	possibly damaging	Het
Filip1l	A	T	16: 57,571,047	D428V	probably damaging	Het
Fsip2	T	C	2: 82,979,610	I2091T	possibly damaging	Het
Glyat	A	C	19: 12,651,398	T186P	possibly damaging	Het
Gm10604	A	G	4: 11,980,083	S74P	unknown	Het
Gm4787	T	G	12: 81,379,137	K82N	possibly damaging	Het
Hectd4	T	C	5: 121,220,620	I50T	unknown	Het
Hectd4	T	C	5: 121,263,967	S373P	possibly damaging	Het
Hmcn1	A	T	1: 150,686,867	C2313*	probably null	Het
Igfn1	A	T	1: 135,969,316	S1171T	probably benign	Het
Ints8	T	C	4: 11,241,642	D267G	probably benign	Het
Itln1	A	G	1: 171,529,159	C251R	probably damaging	Het
Jcad	C	T	18: 4,674,026	T596M	probably damaging	Het
Kcnj16	C	T	11: 111,025,583	T357M	probably benign	Het
Kif13a	G	A	13: 46,814,200	T346M	probably damaging	Het
Klhl24	G	A	16: 20,120,167	A491T	probably benign	Het
Kntc1	C	T	5: 123,778,347	Q748*	probably null	Het
Krt25	T	A	11: 99,317,296	K369*	probably null	Het
Krt75	C	T	15: 101,568,031	R433Q	probably benign	Het
Krt76	A	G	15: 101,884,858	F582L	unknown	Het
Lysmd1	G	A	3: 95,138,397	V182I	probably benign	Het
Mab21l2	T	A	3: 86,547,555	E46V	probably damaging	Het
Magi2	A	T	5: 20,358,936	K355N	probably damaging	Het
March10	T	C	11: 105,385,572	D630G	probably damaging	Het
Mast4	A	T	13: 102,738,639	I1215N	probably damaging	Het
Nckap1	G	A	2: 80,530,218	T523I	probably benign	Het
Nexmif	T	A	X: 104,084,393	D1306V	probably damaging	Het
Nfkb1	A	C	3: 135,589,329	I918R	possibly damaging	Het
Nup50	A	T	15: 84,933,658	T93S	probably benign	Het
Nwd2	T	C	5: 63,804,374	Y434H	probably benign	Het
Olfr61	T	C	7: 140,638,484	V261A	probably benign	Het
Osbpl1a	C	A	18: 12,905,031	V288L	probably benign	Het
Pan3	A	G	5: 147,527,036	E562G	possibly damaging	Het
Pappa	T	A	4: 65,180,889	Y548*	probably null	Het
Phf3	A	T	1: 30,810,789	L1181Q	probably damaging	Het
Phip	T	C	9: 82,915,339	H537R	possibly damaging	Het
Pkhd1l1	T	C	15: 44,485,428	I240T	probably damaging	Het
Pole	G	A	5: 110,290,502		probably null	Het
Polq	T	A	16: 37,011,942	S15T	unknown	Het
Prrt2	T	C	7: 127,020,224	E23G	possibly damaging	Het
Prss37	A	T	6: 40,517,826		probably null	Het
Prune2	T	C	19: 17,000,036	L45P	probably damaging	Het
Psmd1	A	G	1: 86,089,997	E510G	possibly damaging	Het
Ptch1	T	G	13: 63,524,959	E944A	probably benign	Het
Pxdn	T	A	12: 30,003,406	I1194N	probably damaging	Het
Rbp3	C	T	14: 33,956,018	T641M	probably damaging	Het
Rgmb	C	A	17: 15,807,647	R270L	probably benign	Het
Rpgrip1l	A	G	8: 91,280,716		probably null	Het
Rps2	G	A	17: 24,720,379		probably benign	Het
Rsbn1l	G	T	5: 20,902,366	A550E	probably damaging	Het
S1pr4	C	T	10: 81,499,304	R112H	probably benign	Het
Scfd2	T	C	5: 74,531,177	N148S	probably damaging	Het
Scin	C	T	12: 40,081,706	M276I	probably benign	Het
Sec24d	T	C	3: 123,353,606	I708T	possibly damaging	Het
Skint11	T	A	4: 114,228,812	F41I	possibly damaging	Het
Slc15a4	A	T	5: 127,617,239	F44Y	possibly damaging	Het
Slc6a18	A	G	13: 73,675,806	Y72H	probably benign	Het
Slc7a11	A	T	3: 50,377,746		probably null	Het
Slc7a14	G	T	3: 31,237,501	N209K	possibly damaging	Het
Sstr2	T	C	11: 113,624,431	C59R	probably damaging	Het
Stab1	A	G	14: 31,163,040		probably null	Het
Stag1	G	T	9: 100,866,210	S475I	probably damaging	Het
Stxbp5l	A	G	16: 37,115,667	Y1183H	probably damaging	Het
Svep1	A	T	4: 58,135,628		probably null	Het
Tm9sf2	A	G	14: 122,158,684	T653A	probably benign	Het
Tmeff1	T	C	4: 48,662,059	S366P	possibly damaging	Het
Tnnt2	G	T	1: 135,852,065	W300L	probably damaging	Het
Traj32	A	G	14: 54,186,103		probably benign	Het
Trp53bp2	A	T	1: 182,441,639	M223L	probably benign	Het
Tsga10	G	A	1: 37,815,677	T246M	probably damaging	Het
Txn2	A	T	15: 77,926,670		probably benign	Het
Ubr3	T	A	2: 69,938,198	F450I	probably damaging	Het
Usp47	T	C	7: 112,104,470		probably null	Het
Vars2	C	T	17: 35,664,793	R244Q	probably damaging	Het
Xrra1	T	A	7: 99,897,596	F251L	probably damaging	Het
Zfp804a	G	A	2: 82,257,519	R564Q	probably benign	Het
Zfp983	T	C	17: 21,658,967	C29R	probably damaging	Het

Other mutations in Psd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01291:Psd	APN	19	46314747	missense	possibly damaging	0.77
IGL01307:Psd	APN	19	46314658	missense	probably damaging	1.00
IGL02329:Psd	APN	19	46319659	missense	possibly damaging	0.66
IGL02423:Psd	APN	19	46314504	missense	possibly damaging	0.95
IGL02644:Psd	APN	19	46323395	missense	probably damaging	1.00
IGL02724:Psd	APN	19	46319545	missense	probably benign	0.04
IGL03117:Psd	APN	19	46323122	unclassified	probably benign
ANU05:Psd	UTSW	19	46314747	missense	possibly damaging	0.77
G1Funyon:Psd	UTSW	19	46321102	intron	probably benign
P0035:Psd	UTSW	19	46320961	missense	possibly damaging	0.56
R0054:Psd	UTSW	19	46323342	missense	probably damaging	1.00
R0054:Psd	UTSW	19	46323342	missense	probably damaging	1.00
R0403:Psd	UTSW	19	46320972	unclassified	probably benign
R0499:Psd	UTSW	19	46322161	missense	probably damaging	0.98
R0542:Psd	UTSW	19	46314210	missense	probably damaging	1.00
R0543:Psd	UTSW	19	46319517	missense	possibly damaging	0.62
R0894:Psd	UTSW	19	46313441	missense	probably damaging	1.00
R1449:Psd	UTSW	19	46324811	missense	probably damaging	0.99
R1586:Psd	UTSW	19	46314798	missense	probably damaging	0.98
R2096:Psd	UTSW	19	46324649	splice site	probably null
R2857:Psd	UTSW	19	46324420	missense	probably benign	0.00
R2863:Psd	UTSW	19	46314762	missense	probably damaging	0.97
R3897:Psd	UTSW	19	46324585	missense	possibly damaging	0.93
R3967:Psd	UTSW	19	46324406	missense	probably benign
R3970:Psd	UTSW	19	46324406	missense	probably benign
R4435:Psd	UTSW	19	46314494	missense	probably damaging	1.00
R4612:Psd	UTSW	19	46313339	missense	probably benign	0.15
R4940:Psd	UTSW	19	46322417	missense	probably damaging	1.00
R5055:Psd	UTSW	19	46322468	missense	probably benign	0.00
R5485:Psd	UTSW	19	46316089	splice site	probably null
R5768:Psd	UTSW	19	46312739	missense	possibly damaging	0.84
R5775:Psd	UTSW	19	46314772	nonsense	probably null
R6057:Psd	UTSW	19	46323314	missense	possibly damaging	0.77
R6349:Psd	UTSW	19	46313387	splice site	probably null
R6496:Psd	UTSW	19	46320314	missense	probably damaging	1.00
R6614:Psd	UTSW	19	46313412	missense	probably benign	0.11
R6820:Psd	UTSW	19	46320844	missense	probably damaging	1.00
R6849:Psd	UTSW	19	46317746	missense	probably damaging	0.97
R6860:Psd	UTSW	19	46322419	missense	probably damaging	1.00
R7286:Psd	UTSW	19	46314801	missense	probably damaging	0.98
R7326:Psd	UTSW	19	46324454	missense	probably benign	0.01
R7351:Psd	UTSW	19	46322430	missense	probably benign	0.27
R7593:Psd	UTSW	19	46312913	missense	possibly damaging	0.47
R7614:Psd	UTSW	19	46313438	missense	probably damaging	1.00
R7943:Psd	UTSW	19	46324730	missense	possibly damaging	0.54
R8301:Psd	UTSW	19	46321102	intron	probably benign
R8498:Psd	UTSW	19	46324349	missense	probably damaging	1.00
R8712:Psd	UTSW	19	46313336	missense	probably damaging	1.00
R8952:Psd	UTSW	19	46322461	missense	probably damaging	1.00
R8980:Psd	UTSW	19	46322218	missense	possibly damaging	0.95
R9168:Psd	UTSW	19	46320794	missense	probably damaging	1.00
R9322:Psd	UTSW	19	46313441	missense	probably damaging	1.00
R9512:Psd	UTSW	19	46317715	missense	possibly damaging	0.79
R9569:Psd	UTSW	19	46320278	missense	possibly damaging	0.94
R9638:Psd	UTSW	19	46313402	frame shift	probably null
R9645:Psd	UTSW	19	46313402	frame shift	probably null
R9721:Psd	UTSW	19	46323189	missense	probably benign	0.00
Z1177:Psd	UTSW	19	46324661	missense	probably benign	0.16

Predicted Primers

PCR Primer
(F):5'- GTACAAGGTGCTGTCACACG -3'
(R):5'- CAGGATAGGTCTCTGGACTTTAG -3'

Sequencing Primer
(F):5'- GCTGTCACACGTCCCAGATC -3'
(R):5'- ATAGGTCTCTGGACTTTAGAAGGC -3'

Posted On

2014-12-04