Mutagenetix > Incidental Mutation

Incidental Mutation 'R1789:Psd3'

201624

Institutional Source

Beutler Lab

Gene Symbol

Psd3

Ensembl Gene

ENSMUSG00000030465

Gene Name

pleckstrin and Sec7 domain containing 3

Synonyms

EFA6D, 4931420C21Rik

MMRRC Submission

039820-MU

Accession Numbers

Ncbi RefSeq: NM_030263.5, NM_027626.1; MGI:1918215

Essential gene?

Probably non essential (E-score: 0.099) question?

Stock #

R1789 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

67689082-68212027 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 67960565 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 724 (I724V)

Ref Sequence

ENSEMBL: ENSMUSP00000148783 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038959] [ENSMUST00000093469] [ENSMUST00000098696] [ENSMUST00000212505] [ENSMUST00000212960]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000038959
AA Change: I438V

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: I438V

Domain	Start	End	E-Value	Type
low complexity region	204	218	N/A	INTRINSIC
Blast:Sec7	431	496	5e-28	BLAST
Sec7	502	693	3.9e-53	SMART
PH	743	857	3.85e-15	SMART
Blast:Sec7	876	938	2e-10	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000093469
AA Change: I438V

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: I438V

Domain	Start	End	E-Value	Type
low complexity region	204	218	N/A	INTRINSIC
Blast:Sec7	431	496	5e-28	BLAST
Sec7	502	692	2.4e-53	SMART
PH	742	856	3.85e-15	SMART
Blast:Sec7	875	937	2e-10	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000098696
AA Change: I438V

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: I438V

Domain	Start	End	E-Value	Type
low complexity region	204	218	N/A	INTRINSIC
Blast:Sec7	431	496	5e-28	BLAST
Sec7	502	692	2.4e-53	SMART
PH	742	856	3.85e-15	SMART
Blast:Sec7	875	937	2e-10	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127631

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150169

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000212123

Predicted Effect

probably benign
Transcript: ENSMUST00000212505
AA Change: I471V

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)

Predicted Effect

probably benign
Transcript: ENSMUST00000212960
AA Change: I724V

PolyPhen 2 Score 0.257 (Sensitivity: 0.91; Specificity: 0.88)

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.2%
20x: 92.1%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	G	A	16: 20,365,951	P986L	probably damaging	Het
Acad10	A	T	5: 121,631,393	Y667N	possibly damaging	Het
Ahi1	G	A	10: 20,963,115	G121D	probably benign	Het
Ampd1	T	A	3: 103,099,126	I690N	possibly damaging	Het
Amy1	C	A	3: 113,558,165	W425L	possibly damaging	Het
Arhgap27	A	T	11: 103,333,005	V823E	probably damaging	Het
Arhgef17	A	G	7: 100,929,870	S624P	probably damaging	Het
Arid5b	T	C	10: 68,186,067	H231R	probably damaging	Het
Aspscr1	C	A	11: 120,688,560	T78N	probably damaging	Het
Auts2	T	A	5: 131,472,450	T42S	probably damaging	Het
Ccdc171	A	G	4: 83,554,808	D158G	probably damaging	Het
Ces4a	G	A	8: 105,138,097	G69S	probably damaging	Het
Cfap61	T	C	2: 145,939,993		probably null	Het
Chrna5	T	C	9: 55,004,651	V245A	possibly damaging	Het
Cntnap5c	G	A	17: 58,013,921	G163R	probably damaging	Het
Col5a2	A	G	1: 45,378,305		probably null	Het
Col5a2	T	C	1: 45,394,776	Q759R	probably damaging	Het
Comp	A	G	8: 70,377,146	D340G	probably benign	Het
Cyfip1	T	A	7: 55,926,395	D1104E	probably damaging	Het
Dnah11	A	T	12: 118,038,780	S308T	probably damaging	Het
Dnah5	A	G	15: 28,270,426	H958R	probably benign	Het
Elp3	A	G	14: 65,547,919	Y478H	probably damaging	Het
Fat3	T	C	9: 16,376,985	Y414C	probably benign	Het
Fbxo10	C	A	4: 45,046,389	A574S	probably damaging	Het
Fsip2	G	T	2: 82,977,562	L1408F	probably benign	Het
Fubp3	T	C	2: 31,611,735	V425A	possibly damaging	Het
Gm7168	A	T	17: 13,949,584	R404S	probably benign	Het
Gm8773	A	T	5: 5,575,652	Q116L	possibly damaging	Het
Gpd1	T	G	15: 99,723,202	F299C	probably damaging	Het
Gpr137	C	T	19: 6,942,057		probably benign	Het
Grin3b	T	C	10: 79,973,408	S331P	probably benign	Het
Grk3	T	A	5: 112,941,718	I281F	probably damaging	Het
Hoxb7	T	A	11: 96,286,781	S18R	probably damaging	Het
Igf1r	C	T	7: 68,214,933	R1160*	probably null	Het
Itfg1	A	G	8: 85,725,512		probably null	Het
Itgb8	T	C	12: 119,202,455	I114V	probably benign	Het
Kcnk1	A	G	8: 126,025,384	E243G	possibly damaging	Het
Kif27	A	G	13: 58,344,008	L439P	probably damaging	Het
Kif2c	T	A	4: 117,167,361	Q279L	probably benign	Het
Kmt2d	A	T	15: 98,852,074		probably benign	Het
L3mbtl1	A	G	2: 162,974,502	T821A	probably benign	Het
Lrrc24	A	T	15: 76,722,578	M206K	probably benign	Het
Mamdc4	T	G	2: 25,567,622	K460Q	possibly damaging	Het
Maml2	C	G	9: 13,697,345	L30V	probably damaging	Het
Mc5r	C	G	18: 68,338,670		probably null	Het
Myo10	T	G	15: 25,726,525		probably null	Het
Myo1e	T	A	9: 70,338,784	L419Q	probably damaging	Het
Myo6	C	A	9: 80,300,572	H1115Q	probably damaging	Het
Myo7a	A	G	7: 98,107,095	V10A	probably damaging	Het
Myoz2	C	T	3: 123,026,127	R61H	probably damaging	Het
Ncdn	G	A	4: 126,752,003	R38C	probably damaging	Het
Nckap1	T	A	2: 80,520,556	T736S	probably benign	Het
Ncor2	G	A	5: 125,019,890	A2325V	probably damaging	Het
Nid2	T	A	14: 19,752,431	V140E	possibly damaging	Het
Nlrp9c	C	A	7: 26,380,490	D704Y	probably benign	Het
Notch3	T	A	17: 32,158,725	S126C	probably damaging	Het
Olfr1128	A	T	2: 87,544,983	L187H	probably damaging	Het
Olfr130	T	C	17: 38,067,948	I259T	probably damaging	Het
Olfr215	A	C	6: 116,582,697	F83C	probably damaging	Het
Olfr484	A	G	7: 108,124,915	F116S	probably benign	Het
Olfr804	T	C	10: 129,705,607	M243T	possibly damaging	Het
Olfr818	A	T	10: 129,945,582	L160*	probably null	Het
Pdzd7	A	G	19: 45,039,228	I269T	probably damaging	Het
Phf3	A	T	1: 30,806,206	D1299E	probably damaging	Het
Pitx2	T	A	3: 129,218,754	Y271N	probably damaging	Het
Polk	T	C	13: 96,496,632	E301G	probably damaging	Het
Prkdc	C	A	16: 15,739,524	N2230K	probably damaging	Het
Prlr	A	G	15: 10,322,536	E170G	probably benign	Het
Prss55	A	G	14: 64,075,730	I235T	probably damaging	Het
Rabep2	A	G	7: 126,438,799	T248A	possibly damaging	Het
Rbm26	T	A	14: 105,117,073	K949N	probably benign	Het
Rnf213	T	A	11: 119,440,221	D2085E	probably damaging	Het
Serpinb7	A	T	1: 107,450,273	H232L	possibly damaging	Het
Slu7	A	G	11: 43,445,242	Q484R	probably benign	Het
Smg1	A	G	7: 118,145,798	S3044P	possibly damaging	Het
Snrnp48	A	G	13: 38,221,360	D248G	possibly damaging	Het
Snrpc	C	A	17: 27,845,219	P66Q	unknown	Het
Snrpn	T	A	7: 59,983,459		probably benign	Het
Spag17	T	A	3: 99,939,356	S65R	possibly damaging	Het
Srsf6	C	A	2: 162,934,488		probably benign	Het
Stil	T	A	4: 115,041,782	M1203K	probably benign	Het
Syt17	T	C	7: 118,436,838	T106A	probably benign	Het
Tbx15	C	T	3: 99,352,246	Q478*	probably null	Het
Tg	A	T	15: 66,737,548	Q319L	probably benign	Het
Thada	A	G	17: 84,448,033	L243P	probably damaging	Het
Thada	G	T	17: 84,448,034	L243I	probably damaging	Het
Tnnt3	A	G	7: 142,512,364	R211G	probably damaging	Het
Togaram1	A	T	12: 65,002,635	Q1282L	possibly damaging	Het
Tpm3-rs7	T	G	14: 113,314,947	M91R	probably damaging	Het
Trappc9	G	A	15: 73,025,967	R377W	probably damaging	Het
Ttll7	T	G	3: 146,915,780	L378R	probably damaging	Het
Tyw1	T	G	5: 130,258,993	I22R	probably damaging	Het
Ubr3	T	C	2: 70,016,367	S1645P	possibly damaging	Het
Ubr4	T	C	4: 139,393,053	L263P	probably damaging	Het
Unc13c	T	C	9: 73,756,339	E1071G	possibly damaging	Het
Vmn2r44	G	T	7: 8,380,123	D157E	possibly damaging	Het
Vps16	C	T	2: 130,443,600	T821I	probably benign	Het
Washc4	T	C	10: 83,579,525	V793A	possibly damaging	Het
Wdr35	G	T	12: 8,977,435		probably null	Het
Zfp277	A	G	12: 40,364,085	F254L	probably benign	Het

Other mutations in Psd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00769:Psd3	APN	8	67908679	splice site	probably benign
IGL01095:Psd3	APN	8	67908513	missense	probably damaging	1.00
IGL01139:Psd3	APN	8	67908535	missense	probably damaging	1.00
IGL01330:Psd3	APN	8	67697178	missense	probably damaging	1.00
IGL01350:Psd3	APN	8	67720892	missense	probably damaging	1.00
IGL01487:Psd3	APN	8	67697114	missense	probably benign	0.01
IGL01780:Psd3	APN	8	67963869	missense	probably benign
IGL02020:Psd3	APN	8	67974170	intron	probably benign
IGL02232:Psd3	APN	8	67904145	missense	probably damaging	1.00
IGL02350:Psd3	APN	8	67963869	missense	probably benign
IGL02357:Psd3	APN	8	67963869	missense	probably benign
PIT4495001:Psd3	UTSW	8	67963913	missense	probably benign	0.00
R0052:Psd3	UTSW	8	67882979	critical splice donor site	probably null
R0052:Psd3	UTSW	8	67882979	critical splice donor site	probably null
R0242:Psd3	UTSW	8	67758086	missense	probably damaging	0.99
R0242:Psd3	UTSW	8	67758086	missense	probably damaging	0.99
R0581:Psd3	UTSW	8	67720946	missense	probably damaging	1.00
R0655:Psd3	UTSW	8	67963689	missense	probably benign	0.19
R1740:Psd3	UTSW	8	68120839	missense	probably damaging	1.00
R1847:Psd3	UTSW	8	67720004	missense	possibly damaging	0.93
R1951:Psd3	UTSW	8	67963487	missense	probably benign	0.00
R1954:Psd3	UTSW	8	67697075	missense	probably damaging	1.00
R2143:Psd3	UTSW	8	67964351	missense	probably damaging	1.00
R4387:Psd3	UTSW	8	68000761	missense	probably damaging	1.00
R4801:Psd3	UTSW	8	68121148	missense	probably benign
R4802:Psd3	UTSW	8	68121148	missense	probably benign
R4913:Psd3	UTSW	8	68121169	missense	probably damaging	0.99
R5045:Psd3	UTSW	8	67713825	missense	probably damaging	0.99
R5173:Psd3	UTSW	8	67696989	missense	probably damaging	1.00
R5264:Psd3	UTSW	8	67713725	missense	probably benign	0.23
R5350:Psd3	UTSW	8	67908861	missense	probably benign	0.00
R5816:Psd3	UTSW	8	67960510	missense	possibly damaging	0.90
R5994:Psd3	UTSW	8	67719968	missense	probably damaging	1.00
R6157:Psd3	UTSW	8	68121527	start codon destroyed	probably benign	0.14
R6241:Psd3	UTSW	8	67818139	intron	probably benign
R6586:Psd3	UTSW	8	67963545	missense	probably damaging	0.96
R6735:Psd3	UTSW	8	68120746	critical splice donor site	probably null
R6908:Psd3	UTSW	8	67964177	missense	probably benign	0.00
R6984:Psd3	UTSW	8	67818045	missense	possibly damaging	0.85
R7082:Psd3	UTSW	8	67904148	missense	probably benign	0.03
R7116:Psd3	UTSW	8	67713738	missense	probably benign	0.12
R7297:Psd3	UTSW	8	68121034	missense	probably damaging	0.98
R7334:Psd3	UTSW	8	67908705	missense	possibly damaging	0.94
R7348:Psd3	UTSW	8	67790931	missense	possibly damaging	0.65
R7357:Psd3	UTSW	8	68121497	missense	probably benign	0.01
R7369:Psd3	UTSW	8	67904166	missense	possibly damaging	0.95
R7385:Psd3	UTSW	8	68000756	missense	probably damaging	1.00
R7733:Psd3	UTSW	8	68120916	missense	possibly damaging	0.75
R7873:Psd3	UTSW	8	67882982	missense	possibly damaging	0.95
R8110:Psd3	UTSW	8	68121056	missense	probably damaging	1.00
R8765:Psd3	UTSW	8	67963441	missense	possibly damaging	0.69
R8768:Psd3	UTSW	8	67964351	missense	probably damaging	1.00
R8817:Psd3	UTSW	8	67960483	missense	possibly damaging	0.95
R8837:Psd3	UTSW	8	67719944	missense	probably damaging	0.99
R8878:Psd3	UTSW	8	67758098	missense	probably benign	0.28
R8903:Psd3	UTSW	8	67713293	missense	unknown
R8955:Psd3	UTSW	8	67963809	missense	probably benign	0.08
R9216:Psd3	UTSW	8	68120887	missense	probably benign	0.00
R9241:Psd3	UTSW	8	67963315	missense	probably benign	0.00
R9351:Psd3	UTSW	8	67960649	missense	probably benign	0.18
R9449:Psd3	UTSW	8	67713181	missense	unknown
R9451:Psd3	UTSW	8	67910835	missense	unknown
R9709:Psd3	UTSW	8	67741762	missense	probably null	0.99
R9797:Psd3	UTSW	8	67758126	missense	probably damaging	0.99
Z1088:Psd3	UTSW	8	67906260	splice site	silent

Predicted Primers

PCR Primer
(F):5'- AATGGCACTGCTACCTTCC -3'
(R):5'- GATTCTCGATCAAGAGGAGCAC -3'

Sequencing Primer
(F):5'- TTCCCCAGAAGGCAATCTCTTGAG -3'
(R):5'- CACCTTAGGGGAGATGATGATATTC -3'

Posted On

2014-06-23