Mutagenetix > Incidental Mutation

Incidental Mutation 'R6908:Psd3'

538867

Institutional Source

Beutler Lab

Gene Symbol

Psd3

Ensembl Gene

ENSMUSG00000030465

Gene Name

pleckstrin and Sec7 domain containing 3

Synonyms

EFA6D, 4931420C21Rik

MMRRC Submission

Accession Numbers

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

Essential gene?

Probably non essential (E-score: 0.115) question?

Stock #

R6908 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

67689082-68212027 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 67964177 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Lysine at position 356 (I356K)

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: I70K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: I70K

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: I70K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: I70K

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: I70K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: I70K

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: ENSMUST00000212505
AA Change: I103K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Predicted Effect

probably benign
Transcript: ENSMUST00000212960
AA Change: I356K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.2%

Validation Efficiency

95% (52/55)

Allele List at MGI

Other mutations in this stock

Total: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abi3bp	T	C	16: 56,657,305	I1197T	probably benign	Het
Atp2a1	A	G	7: 126,448,535		probably null	Het
B3glct	T	C	5: 149,696,476		probably null	Het
Bbs9	T	G	9: 22,567,723	I154S	probably damaging	Het
Brip1	T	C	11: 86,077,884	Y825C	probably damaging	Het
Ccdc186	A	T	19: 56,791,939		probably null	Het
Celf6	T	C	9: 59,603,823	V349A	probably benign	Het
Chd9	A	G	8: 90,956,416	T495A	probably benign	Het
Cxxc1	G	A	18: 74,220,559	C546Y	probably damaging	Het
Cxxc5	T	C	18: 35,859,215	V223A	probably damaging	Het
Dlc1	A	G	8: 36,937,687	F316S	probably benign	Het
Dnajc12	C	A	10: 63,397,325	Q82K	probably benign	Het
Dock8	G	A	19: 25,188,382	E1877K	probably damaging	Het
Epha3	T	G	16: 63,598,249	H611P	probably damaging	Het
Fpr-rs6	C	A	17: 20,182,439	C220F	probably damaging	Het
Fryl	A	G	5: 73,022,211	L2951P	probably damaging	Het
Gbp10	T	G	5: 105,221,032	T314P	probably damaging	Het
Hbb-bs	T	C	7: 103,827,534	N77D	probably benign	Het
Ints13	A	T	6: 146,555,033	D438E	probably damaging	Het
Itgb6	C	T	2: 60,650,021	V324M	probably benign	Het
Kdm7a	G	T	6: 39,144,439	L861M	possibly damaging	Het
Kirrel3	A	G	9: 35,013,401	T302A	possibly damaging	Het
Lama2	A	T	10: 27,031,196		probably null	Het
Lrp2	A	T	2: 69,472,365	C3007S	probably damaging	Het
Lypd3	G	C	7: 24,638,433	G75R	probably damaging	Het
Mastl	T	C	2: 23,155,976		probably benign	Het
Mcf2l	T	C	8: 13,018,919	V1087A	probably benign	Het
Mcmdc2	C	A	1: 9,930,778		probably null	Het
Ms4a3	A	G	19: 11,638,295	I39T	probably damaging	Het
Mylk	T	G	16: 34,880,273	C495G	probably benign	Het
Myo10	A	G	15: 25,804,383	D1588G	probably damaging	Het
Myo15	A	T	11: 60,506,006	T2634S	probably damaging	Het
Nlrp1b	T	C	11: 71,217,296	I460V	probably benign	Het
Nmt1	T	G	11: 103,058,254	S312A	possibly damaging	Het
Nynrin	T	G	14: 55,863,878	S335A	probably benign	Het
Olfr710	T	C	7: 106,944,632	Y123C	possibly damaging	Het
Paxip1	T	C	5: 27,791,224	Y19C	possibly damaging	Het
Pcdhb2	G	T	18: 37,296,524	A517S	probably damaging	Het
Pkd2l1	A	G	19: 44,152,446	I559T	probably damaging	Het
Plec	G	A	15: 76,185,881	Q806*	probably null	Het
Prss51	C	T	14: 64,096,152	A70V	probably benign	Het
Ptprn2	A	T	12: 116,888,888	I522F	probably benign	Het
Rab39	T	C	9: 53,706,069	D16G	probably damaging	Het
Ralgps1	T	C	2: 33,143,100	Q439R	probably benign	Het
Rapgef2	A	T	3: 79,104,063	D238E	probably benign	Het
Ripor2	G	A	13: 24,706,232	G697S	probably damaging	Het
Scn11a	A	T	9: 119,792,426	F642I	probably damaging	Het
Serinc4	G	A	2: 121,453,605	T310I	probably benign	Het
Sfpq	GCCGCCGCAGCAGCCTCCGCCGCAGCAGCC	GCCGCCGCAGCAGCC	4: 127,021,626		probably benign	Het
Slc36a3	T	C	11: 55,149,886		probably benign	Het
Smc1b	A	G	15: 85,107,010	S656P	probably damaging	Het
Sorbs1	A	G	19: 40,352,332	S455P	probably damaging	Het
Ttn	C	A	2: 76,889,858		probably benign	Het
Tyw5	T	C	1: 57,401,523	R27G	probably damaging	Het
Vmn1r209	T	C	13: 22,806,230	T97A	possibly damaging	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
R1789:Psd3	UTSW	8	67960565	missense	probably benign	0.26
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
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'- GGCTCTCTGTGGCTTATGAC -3'
(R):5'- GTGATCATGGAGGAAGCACTTTAC -3'

Sequencing Primer
(F):5'- ATGACTGGCAGTACTCAGTTC -3'
(R):5'- TGGAGGAAGCACTTTACTCCCAC -3'

Posted On

2018-11-06