Mutagenetix > Incidental Mutations

Incidental Mutation 'R1449:Psd'

159181

Institutional Source

Beutler Lab

Gene Symbol

Psd

Ensembl Gene

ENSMUSG00000037126

Gene Name

pleckstrin and Sec7 domain containing

Synonyms

Psdl, Efa6a, Efa6, 1110007H17Rik

MMRRC Submission

039504-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1449 (G1)

Quality Score

198

Status

Not validated

Chromosome

Chromosomal Location

46312087-46327156 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 46324811 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 40 (Y40F)

Ref Sequence

ENSEMBL: ENSMUSP00000152942 (fasta)

Gene Model

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

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

probably damaging
Transcript: ENSMUST00000041391
AA Change: Y40F

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: Y40F

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: Y40F

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: Y40F

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: 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

probably benign
Transcript: ENSMUST00000223903

Predicted Effect

probably benign
Transcript: ENSMUST00000223917

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224094

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224444

Predicted Effect

possibly damaging
Transcript: ENSMUST00000224447
AA Change: Y40F

PolyPhen 2 Score 0.659 (Sensitivity: 0.86; Specificity: 0.91)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225072

Predicted Effect

probably damaging
Transcript: ENSMUST00000225323
AA Change: Y40F

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225770

Predicted Effect

unknown
Transcript: ENSMUST00000225781
AA Change: Y40F

Coding Region Coverage

1x: 98.8%
3x: 97.9%
10x: 94.7%
20x: 87.4%

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700013G24Rik	A	G	4: 137,455,355	N274D	possibly damaging	Het
6430571L13Rik	T	A	9: 107,342,490	N47K	probably damaging	Het
Aasdh	C	T	5: 76,886,289	A472T	probably benign	Het
Abca13	A	G	11: 9,298,580	T2776A	probably damaging	Het
Adamts10	T	A	17: 33,545,639	V711D	probably damaging	Het
Adrb3	G	A	8: 27,227,387	R345C	probably damaging	Het
Ak7	T	C	12: 105,742,261	V325A	possibly damaging	Het
Armc6	G	A	8: 70,225,293	L129F	probably benign	Het
Bend6	T	C	1: 33,878,343	N10S	probably benign	Het
Bmpr1b	T	C	3: 141,871,373	E59G	possibly damaging	Het
Brd3	A	G	2: 27,450,251		probably null	Het
Brd3	A	G	2: 27,457,016	Y369H	probably damaging	Het
Cacna1e	C	T	1: 154,485,662		probably null	Het
Camk4	A	G	18: 32,939,475	D27G	probably damaging	Het
Camkk1	T	G	11: 73,033,884	S308A	probably damaging	Het
Catsperb	A	G	12: 101,588,197	T717A	probably benign	Het
Cdh23	A	T	10: 60,376,951	S1563R	probably damaging	Het
Cep44	A	T	8: 56,540,950	S197R	probably benign	Het
Col3a1	T	A	1: 45,321,611	I67N	unknown	Het
Dcaf12l1	T	C	X: 44,789,427	T165A	probably benign	Het
Dicer1	T	C	12: 104,729,243	Y143C	possibly damaging	Het
Dlg5	A	G	14: 24,135,643	I1898T	possibly damaging	Het
Dnah1	T	C	14: 31,263,951	N3762D	probably damaging	Het
Dscaml1	A	T	9: 45,742,223	T1382S	possibly damaging	Het
Entpd3	A	T	9: 120,566,489	R513W	probably damaging	Het
Foxred1	A	G	9: 35,209,442	S132P	probably damaging	Het
Ftsj3	T	C	11: 106,253,000	I273V	probably benign	Het
Hsd17b7	C	T	1: 169,959,682		probably null	Het
Iars	T	A	13: 49,733,710	V1253D	probably damaging	Het
Iqsec1	T	A	6: 90,690,808	K216*	probably null	Het
Itga7	A	G	10: 128,953,501	D971G	probably benign	Het
Kcnk2	G	A	1: 189,340,026	S35L	probably benign	Het
Kif13a	T	C	13: 46,812,736	Y402C	probably damaging	Het
Lamc1	A	G	1: 153,250,495	S484P	probably benign	Het
Lap3	T	C	5: 45,509,519		probably null	Het
Lhx8	G	T	3: 154,328,105	S46*	probably null	Het
Lin7a	T	C	10: 107,323,952	S42P	probably damaging	Het
Lrba	G	A	3: 86,354,278	R1513Q	probably damaging	Het
Maml2	C	A	9: 13,620,684	P398Q	possibly damaging	Het
Mast2	T	C	4: 116,309,013	I1201V	probably damaging	Het
Mmp20	A	T	9: 7,642,768	D201V	probably damaging	Het
Morn5	T	A	2: 36,057,080	C123*	probably null	Het
Mrpl4	A	G	9: 21,007,511	K175E	possibly damaging	Het
Nav3	A	T	10: 109,853,511	S302T	probably benign	Het
Ndrg2	T	C	14: 51,908,134	Y217C	probably damaging	Het
Nfx1	A	G	4: 40,976,803	D159G	probably damaging	Het
Nlrp9b	A	T	7: 20,023,164	T109S	possibly damaging	Het
Npepps	A	G	11: 97,207,154	Y909H	probably benign	Het
Olfr1510	A	G	14: 52,410,567	C102R	probably damaging	Het
Olfr559	A	T	7: 102,724,190	F100Y	probably damaging	Het
Olfr740	A	G	14: 50,453,921	N290D	probably damaging	Het
Olfr801	T	A	10: 129,670,369	D50V	probably damaging	Het
Olfr810	A	C	10: 129,790,854	V245G	probably damaging	Het
Pcdh1	T	C	18: 38,189,876	H968R	probably damaging	Het
Pde1b	T	A	15: 103,525,043	I296N	probably damaging	Het
Phldb1	T	A	9: 44,716,633	T172S	probably benign	Het
Plxdc2	T	C	2: 16,660,781	V215A	possibly damaging	Het
Poln	A	G	5: 34,014,338	I695T	probably damaging	Het
Pou6f2	G	T	13: 18,172,415	Q31K	probably damaging	Het
Rnf126	T	C	10: 79,761,614	N155D	probably benign	Het
Rpl36-ps3	C	A	12: 12,912,031		noncoding transcript	Het
Rrp15	C	A	1: 186,736,268	V184F	possibly damaging	Het
Rslcan18	G	T	13: 67,102,100	L24M	possibly damaging	Het
Sall1	A	G	8: 89,032,483	I331T	probably benign	Het
Slamf7	A	T	1: 171,641,038	N95K	possibly damaging	Het
Slc1a6	T	C	10: 78,800,117	Y339H	probably damaging	Het
Slc39a8	A	G	3: 135,826,685	N72D	probably benign	Het
Slf1	A	G	13: 77,083,449	S604P	probably damaging	Het
Slfn4	C	T	11: 83,188,993	T110M	probably benign	Het
Tnpo1	T	C	13: 98,878,712	T116A	probably damaging	Het
Tor1b	T	C	2: 30,955,881	I190T	probably damaging	Het
Ttn	C	A	2: 76,969,794	E357*	probably null	Het
Tubg2	G	T	11: 101,156,873	E95*	probably null	Het
Ubap2	A	G	4: 41,209,351		probably null	Het
Ube2i	T	C	17: 25,268,564	D67G	possibly damaging	Het
Ubxn11	A	G	4: 134,124,892	E50G	probably damaging	Het
Wnk1	A	G	6: 119,952,818	V1246A	probably damaging	Het
Zcchc7	A	G	4: 44,929,124	T38A	possibly damaging	Het
Zfp236	A	G	18: 82,646,005	S552P	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
R1586:Psd	UTSW	19	46314798	missense	probably damaging	0.98
R2096:Psd	UTSW	19	46324649	splice site	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	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
Z1177:Psd	UTSW	19	46324661	missense	probably benign	0.16

Predicted Primers

PCR Primer
(F):5'- TCCAGAAGCAGGTAGGCCATTCAG -3'
(R):5'- TGGACTTTAGAAGGCCCAACCCAC -3'

Sequencing Primer
(F):5'- TGGCCTTCTCCACAAAACGG -3'
(R):5'- CGCCTGTCTGACTCCAAAG -3'

Posted On

2014-03-14