Mutagenetix > Incidental Mutations

Incidental Mutation 'R7116:Psd3'

551777

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

Is this an essential gene?

Probably non essential (E-score: 0.098) question?

Stock #

R7116 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

67689082-68212027 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 67713738 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 915 (V915A)

Ref Sequence

ENSEMBL: ENSMUSP00000096293 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038959] [ENSMUST00000059374] [ENSMUST00000093468] [ENSMUST00000093469] [ENSMUST00000098696] [ENSMUST00000120071] [ENSMUST00000212505] [ENSMUST00000212960]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000038959
AA Change: V916A

PolyPhen 2 Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: V916A

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

possibly damaging
Transcript: ENSMUST00000059374
AA Change: V287A

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000060306
Gene: ENSMUSG00000030465
AA Change: V287A

Domain	Start	End	E-Value	Type
PH	114	228	3.85e-15	SMART
Blast:Sec7	247	305	1e-8	BLAST

Predicted Effect

possibly damaging
Transcript: ENSMUST00000093468
AA Change: V429A

PolyPhen 2 Score 0.849 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000091178
Gene: ENSMUSG00000030465
AA Change: V429A

Domain	Start	End	E-Value	Type
Sec7	17	206	1.35e-56	SMART
PH	256	370	3.85e-15	SMART
Blast:Sec7	389	451	1e-10	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000093469
AA Change: V915A

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: V915A

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: V915A

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: V915A

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: ENSMUST00000120071
AA Change: V287A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000112545
Gene: ENSMUSG00000030465
AA Change: V287A

Domain	Start	End	E-Value	Type
PH	114	228	3.85e-15	SMART
Blast:Sec7	247	309	3e-11	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000212505
AA Change: V946A

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)

Predicted Effect

probably benign
Transcript: ENSMUST00000212960
AA Change: V1200A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actn1	A	G	12: 80,204,977	S109P	probably damaging	Het
Afg3l1	T	G	8: 123,489,862	L280R	probably damaging	Het
Akap13	T	A	7: 75,720,195	S129T	probably benign	Het
Ankrd11	A	G	8: 122,896,130	S328P	probably damaging	Het
Aox3	A	T	1: 58,153,530	E554D	probably benign	Het
Bcl11a	T	C	11: 24,163,839	V394A	probably damaging	Het
Cass4	A	G	2: 172,427,969	Y657C	unknown	Het
Ccdc88a	C	T	11: 29,504,051	A1738V	probably benign	Het
Cfap74	T	C	4: 155,455,061	F948L	unknown	Het
Chgb	A	T	2: 132,781,317		probably benign	Het
Coro1c	C	T	5: 113,852,206	W138*	probably null	Het
Dgkb	A	G	12: 37,981,990	Q17R	probably benign	Het
Esco2	A	G	14: 65,826,557	Y393H	probably damaging	Het
Eya3	T	A	4: 132,694,799	D228E	probably benign	Het
Fat2	T	C	11: 55,282,336	D2517G	probably damaging	Het
Fry	T	A	5: 150,395,869		probably null	Het
Gal3st2b	A	T	1: 93,940,776	Q243L	possibly damaging	Het
Gimap9	C	T	6: 48,678,055	A192V	probably benign	Het
Glg1	T	A	8: 111,178,957	Q564L	probably benign	Het
H2-Aa	A	T	17: 34,283,627	Y188*	probably null	Het
Hira	T	C	16: 18,912,114	Y188H	probably damaging	Het
Ighv8-8	C	T	12: 115,294,194	D76N	probably benign	Het
Irf6	T	C	1: 193,167,597	F276L	probably damaging	Het
Itpr1	T	C	6: 108,481,268	C2000R	probably damaging	Het
Jakmip3	T	C	7: 139,020,250	V293A	possibly damaging	Het
Kcnh7	A	G	2: 62,877,270	V132A	probably benign	Het
Kcnj1	A	G	9: 32,396,981	T234A	possibly damaging	Het
Kpna3	T	A	14: 61,368,186	N470I	probably benign	Het
Lamb2	T	C	9: 108,487,323	F1121L	probably damaging	Het
Lingo1	T	C	9: 56,620,627	D232G	probably benign	Het
Lpxn	T	A	19: 12,811,258	N70K	probably benign	Het
Ltbp4	T	A	7: 27,305,427	H1657L	probably damaging	Het
Luzp2	C	A	7: 55,265,330	F334L	possibly damaging	Het
Mgat5b	A	T	11: 116,944,959	S142C	possibly damaging	Het
Mroh7	G	A	4: 106,711,320	T396I	probably benign	Het
Muc5b	T	C	7: 141,863,750	S3478P	probably benign	Het
Nfatc2	A	T	2: 168,507,349	M626K	probably benign	Het
Nlrp14	A	G	7: 107,183,048	D484G	possibly damaging	Het
Npc1	T	C	18: 12,211,544	Y423C	probably damaging	Het
Nrsn1	A	G	13: 25,253,405	I180T	probably damaging	Het
Olfr570	T	A	7: 102,900,635	N89K	probably benign	Het
Olfr741	A	T	14: 50,485,568	I37F	probably benign	Het
Osbpl6	A	T	2: 76,595,881	I935F	probably benign	Het
Otog	T	C	7: 46,298,265	F96L	probably damaging	Het
Pde1b	T	C	15: 103,528,318	L534P	possibly damaging	Het
Pdzd8	C	T	19: 59,299,693	E1092K	probably damaging	Het
Pfkl	T	C	10: 78,001,415	H108R	probably benign	Het
Pkhd1l1	G	A	15: 44,557,976	V3047I	probably benign	Het
Plag1	A	T	4: 3,904,812	C126*	probably null	Het
Pphln1	T	A	15: 93,455,525	S229T	probably benign	Het
Pramel5	C	T	4: 144,273,881	D42N	possibly damaging	Het
Ptdss1	T	A	13: 66,945,327	I77N	probably benign	Het
Rsbn1	T	A	3: 103,914,576	C3*	probably null	Het
Shank1	C	T	7: 44,327,161	A561V	unknown	Het
Stip1	C	T	19: 7,021,810	G467S	possibly damaging	Het
Sv2c	A	T	13: 95,976,644	V599E	probably damaging	Het
Vmn2r37	T	C	7: 9,217,899	T322A	probably benign	Het
Vmn2r60	T	A	7: 42,137,063	M430K	probably benign	Het
Wipf3	T	A	6: 54,481,919		probably null	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
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
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
Z1088:Psd3	UTSW	8	67906260	splice site	silent

Predicted Primers

PCR Primer
(F):5'- GGGCTCCTGTCATATTAGGATGTC -3'
(R):5'- TTGGAAGGACTTAGGACCAATG -3'

Sequencing Primer
(F):5'- TGTCCTAAATTGGAGCCAGGAC -3'
(R):5'- GGACTTAGGACCAATGATAAATGTTG -3'

Posted On

2019-05-15