Mutagenetix > Incidental Mutations

Incidental Mutation 'R6820:Psd'

537592

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Psdl, Efa6a, Efa6, 1110007H17Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6820 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

46312087-46327156 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 46320844 bp

Zygosity

Heterozygous

Amino Acid Change

Alanine to Glutamic Acid at position 558 (A558E)

Ref Sequence

ENSEMBL: ENSMUSP00000039728 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000041391
AA Change: A558E

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

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: A558E

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: A559E

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: A559E

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: A559E

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

Predicted Effect

probably benign
Transcript: ENSMUST00000225781

Meta Mutation Damage Score

0.5911

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

98% (46/47)

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: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Accs	T	A	2: 93,842,921	N141Y	probably null	Het
Chkb	A	G	15: 89,428,176	L46P	probably damaging	Het
Col9a3	G	A	2: 180,607,134	V260M	probably damaging	Het
Dna2	T	C	10: 62,964,904	I739T	possibly damaging	Het
Dnah17	T	C	11: 118,069,000	H2620R	probably damaging	Het
Dsel	A	G	1: 111,859,817	V996A	probably damaging	Het
Dst	T	C	1: 34,211,256	L1757S	probably damaging	Het
Exoc5	A	T	14: 49,048,930		probably null	Het
Fam120a	A	T	13: 48,880,992	V1048E	possibly damaging	Het
Fam213b	A	T	4: 154,898,166	D50E	probably damaging	Het
Fam50b	G	A	13: 34,747,101	E187K	possibly damaging	Het
Fbxw19	T	A	9: 109,482,011	T377S	probably benign	Het
Fbxw28	A	T	9: 109,338,425	F88Y	probably damaging	Het
Grik5	C	T	7: 25,046,355	R431Q	possibly damaging	Het
Gtsf1	T	C	15: 103,420,527	T92A	probably benign	Het
Hoxc13	A	G	15: 102,921,822	Y212C	probably damaging	Het
Itih2	T	C	2: 10,098,098	I742V	probably benign	Het
Kat7	T	C	11: 95,284,139	T351A	probably damaging	Het
Mlh3	T	C	12: 85,247,723	D1233G	probably damaging	Het
Mroh2b	A	G	15: 4,953,274	D1525G	probably damaging	Het
Nme5	T	C	18: 34,571,573	Y73C	probably damaging	Het
Nr3c2	T	C	8: 77,242,457	V957A	probably damaging	Het
Nup153	A	G	13: 46,709,983	S301P	probably benign	Het
Obscn	T	C	11: 59,051,193	D5013G	probably damaging	Het
Olfr1278	C	T	2: 111,293,110	P281S	probably damaging	Het
Olfr470	A	G	7: 107,845,091	V214A	probably benign	Het
Olfr919	A	G	9: 38,697,475	V297A	possibly damaging	Het
Pak1	A	G	7: 97,886,379	N226D	probably benign	Het
Pak4	A	G	7: 28,563,036	Y384H	probably benign	Het
Pkp3	T	C	7: 141,079,844		probably null	Het
Psmd14	C	A	2: 61,776,724	H172N	probably benign	Het
Pygb	G	T	2: 150,816,754	W366L	possibly damaging	Het
Rbm39	A	T	2: 156,179,226	M1K	probably null	Het
Rnf213	T	C	11: 119,448,838	I3421T	probably damaging	Het
Rsf1	ATGGCG	ATGGCGACGGTGGCG	7: 97,579,904		probably benign	Het
Smg6	T	C	11: 75,041,964	V88A	probably damaging	Het
Tha1	T	C	11: 117,871,678	E80G	probably benign	Het
Tie1	A	G	4: 118,484,386	V243A	probably damaging	Het
Tmem215	T	C	4: 40,473,926	M1T	probably null	Het
Tpm2	A	G	4: 43,518,443	Y221H	probably damaging	Het
Ubap1	C	T	4: 41,379,854	P356L	probably benign	Het
Wbp2nl	G	T	15: 82,313,795	A178S	possibly damaging	Het
Wdr54	A	T	6: 83,154,619	S139T	probably benign	Het
Wipi2	G	C	5: 142,629,800	Q14H	probably benign	Het
Zan	T	C	5: 137,407,844		probably benign	Het
Zfp735	A	G	11: 73,688,957	M1V	probably null	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
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	unclassified	probably null
R2504:Psd	UTSW	19	46324913	missense	possibly damaging	0.90
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	unclassified	probably null
R6496:Psd	UTSW	19	46320314	missense	probably damaging	1.00
R6614:Psd	UTSW	19	46313412	missense	probably benign	0.11
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

Predicted Primers

PCR Primer
(F):5'- TCAGTGGCCTAGACAGTCTC -3'
(R):5'- AGCTTCTGGGTGTAGAGCAAG -3'

Sequencing Primer
(F):5'- TAGACAGTCTCTAGGCATGGC -3'
(R):5'- CAAGGGGAGGGTCTAGATGAC -3'

Posted On

2018-10-18