Mutagenetix > Incidental Mutation

Incidental Mutation 'R7082:Psd3'

549609

Institutional Source

Beutler Lab

Gene Symbol

Psd3

Ensembl Gene

ENSMUSG00000030465

Gene Name

pleckstrin and Sec7 domain containing 3

Synonyms

EFA6D, 4931420C21Rik

MMRRC Submission

045176-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.086) question?

Stock #

R7082 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

68141734-68664679 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 68356800 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 640 (M640K)

Ref Sequence

ENSEMBL: ENSMUSP00000096293 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000038959
AA Change: M640K

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: M640K

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: ENSMUST00000093468
AA Change: M155K

PolyPhen 2 Score 0.235 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000091178
Gene: ENSMUSG00000030465
AA Change: M155K

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: M640K

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: M640K

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: M640K

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: M640K

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: M672K

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

Predicted Effect

probably benign
Transcript: ENSMUST00000212960
AA Change: M926K

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

100% (88/88)

Allele List at MGI

Other mutations in this stock

Total: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730596B20Rik	A	T	6: 52,156,260 (GRCm39)	N109Y	unknown	Het
A430005L14Rik	C	T	4: 154,044,221 (GRCm39)	R11W	probably damaging	Het
Aadacl2	T	A	3: 59,932,306 (GRCm39)	S274T	probably damaging	Het
Ahctf1	T	C	1: 179,602,898 (GRCm39)	R887G	probably benign	Het
Aox4	G	T	1: 58,263,352 (GRCm39)	R158L	possibly damaging	Het
Atp10a	T	C	7: 58,308,567 (GRCm39)	I122T	probably damaging	Het
Batf2	G	T	19: 6,221,405 (GRCm39)	A72S	possibly damaging	Het
Bltp3a	G	T	17: 28,109,039 (GRCm39)	R1086L	probably damaging	Het
Bptf	T	C	11: 106,977,573 (GRCm39)	D749G	probably benign	Het
Cacybp	A	G	1: 160,031,229 (GRCm39)	Y200H	probably damaging	Het
Cdc40	A	T	10: 40,743,869 (GRCm39)	V76D	probably benign	Het
Cdc42ep4	T	C	11: 113,619,944 (GRCm39)	D149G	probably benign	Het
Chtop	A	G	3: 90,414,891 (GRCm39)	V9A	probably benign	Het
Cnot9	A	G	1: 74,566,165 (GRCm39)	I185M	probably damaging	Het
Col6a5	A	G	9: 105,808,438 (GRCm39)	I870T	unknown	Het
Cr1l	A	G	1: 194,806,006 (GRCm39)	I159T	probably benign	Het
Cthrc1	T	C	15: 38,940,495 (GRCm39)	S33P	probably benign	Het
Dlg2	T	A	7: 90,381,192 (GRCm39)	W44R	probably benign	Het
Dlgap4	T	C	2: 156,590,342 (GRCm39)		probably null	Het
Dna2	A	G	10: 62,790,096 (GRCm39)	H193R	possibly damaging	Het
Espnl	T	A	1: 91,262,521 (GRCm39)	F322Y	probably benign	Het
Fam171a1	G	A	2: 3,224,512 (GRCm39)	V293I	probably benign	Het
Fam76b	A	G	9: 13,744,308 (GRCm39)	Y135C	probably damaging	Het
Flvcr2	A	T	12: 85,793,728 (GRCm39)	I35F	probably benign	Het
Gm9195	T	A	14: 72,680,152 (GRCm39)	Q2219L	probably benign	Het
Gnptg	T	C	17: 25,453,694 (GRCm39)	T283A	probably benign	Het
Grap2	G	A	15: 80,532,699 (GRCm39)	V289M	probably benign	Het
Hk3	T	C	13: 55,154,710 (GRCm39)	T767A	probably benign	Het
Hs3st5	A	G	10: 36,708,833 (GRCm39)	I123V	probably benign	Het
Il6st	A	G	13: 112,640,566 (GRCm39)	T781A	probably damaging	Het
Inpp5d	T	A	1: 87,623,102 (GRCm39)	H398Q	probably damaging	Het
Kcnk1	A	G	8: 126,722,287 (GRCm39)	Y30C	probably damaging	Het
Klhl6	T	C	16: 19,801,633 (GRCm39)	T41A	probably benign	Het
Krt14	G	A	11: 100,094,167 (GRCm39)	H476Y	possibly damaging	Het
Lingo3	G	C	10: 80,671,625 (GRCm39)	R102G	probably benign	Het
Map3k9	G	A	12: 81,771,476 (GRCm39)	T704M	probably damaging	Het
Mdn1	C	A	4: 32,762,341 (GRCm39)	N5088K	probably benign	Het
Mmp9	T	A	2: 164,790,812 (GRCm39)	S67T	probably benign	Het
Mrps18c	A	G	5: 100,952,270 (GRCm39)	E143G	probably damaging	Het
Msantd5f9	G	T	4: 73,835,808 (GRCm39)	L219M	probably benign	Het
Muc21	A	T	17: 35,932,093 (GRCm39)	S698T	unknown	Het
Nags	C	A	11: 102,038,298 (GRCm39)	R335S	possibly damaging	Het
Nars1	A	G	18: 64,637,425 (GRCm39)	V385A	possibly damaging	Het
Nipal2	A	C	15: 34,584,809 (GRCm39)	V253G	possibly damaging	Het
Nos2	C	A	11: 78,819,405 (GRCm39)	T39K	probably benign	Het
Or10p1	T	A	10: 129,443,416 (GRCm39)	*311Y	probably null	Het
Or10p1	T	A	10: 129,443,417 (GRCm39)	*311L	probably null	Het
Or51t4	T	C	7: 102,598,455 (GRCm39)	V261A	probably damaging	Het
Or52s19	C	A	7: 103,007,495 (GRCm39)	R302L	possibly damaging	Het
Or6c66	C	T	10: 129,461,634 (GRCm39)	V99M	probably benign	Het
Or9s15	G	A	1: 92,524,140 (GRCm39)		probably benign	Het
Panx3	G	A	9: 37,577,913 (GRCm39)	P106S	probably benign	Het
Pappa2	G	A	1: 158,590,689 (GRCm39)	T1655I	possibly damaging	Het
Pcdhb1	A	G	18: 37,400,044 (GRCm39)	D665G	probably damaging	Het
Pde2a	T	C	7: 101,157,303 (GRCm39)	L676P	probably damaging	Het
Pf4	A	G	5: 90,920,851 (GRCm39)	T60A	possibly damaging	Het
Pira12	C	T	7: 3,898,510 (GRCm39)	V313M	probably damaging	Het
Pld5	A	T	1: 175,917,442 (GRCm39)	C164S	probably benign	Het
Ptf1a	A	G	2: 19,450,676 (GRCm39)	D2G	possibly damaging	Het
Ptprq	C	T	10: 107,544,591 (GRCm39)	C313Y	probably benign	Het
Ranbp10	A	G	8: 106,500,578 (GRCm39)	S467P	probably damaging	Het
Rap1gap	C	T	4: 137,446,247 (GRCm39)	T333M	probably damaging	Het
Rfpl4	A	G	7: 5,118,558 (GRCm39)	L4P	probably benign	Het
Rgs12	A	G	5: 35,124,050 (GRCm39)	N611S	probably benign	Het
Sacs	C	A	14: 61,447,966 (GRCm39)	N3337K	possibly damaging	Het
Sbno2	A	T	10: 79,895,924 (GRCm39)		probably null	Het
Scrn2	T	A	11: 96,923,908 (GRCm39)	V264E	possibly damaging	Het
Serpinb9c	T	A	13: 33,338,390 (GRCm39)	I198L	probably benign	Het
Shank2	T	C	7: 143,964,096 (GRCm39)	F568S	probably damaging	Het
Slc47a1	C	T	11: 61,268,767 (GRCm39)	R36Q	probably benign	Het
Slc4a8	A	C	15: 100,688,908 (GRCm39)	E406A	probably damaging	Het
Speg	C	T	1: 75,388,091 (GRCm39)	T1483I	probably damaging	Het
Srbd1	A	G	17: 86,365,160 (GRCm39)	V632A	probably damaging	Het
Srd5a2	A	T	17: 74,328,515 (GRCm39)	Y188N	probably damaging	Het
Sspo	A	T	6: 48,455,543 (GRCm39)		probably null	Het
Ssx2ip	A	T	3: 146,136,703 (GRCm39)	D317V	probably benign	Het
Tmco3	G	T	8: 13,370,847 (GRCm39)	E172*	probably null	Het
Trpc4	G	A	3: 54,206,519 (GRCm39)	W573*	probably null	Het
Ttn	T	C	2: 76,580,340 (GRCm39)	I23518V	probably benign	Het
Tubal3	A	G	13: 3,983,050 (GRCm39)	T277A	possibly damaging	Het
Unc5b	A	T	10: 60,610,867 (GRCm39)	L391H	probably damaging	Het
Vmn2r76	A	G	7: 85,874,440 (GRCm39)	F846L	probably benign	Het
Vps13c	T	A	9: 67,790,735 (GRCm39)	Y338N	probably damaging	Het
Zc3hav1	G	T	6: 38,309,328 (GRCm39)	S498*	probably null	Het
Zfand4	T	A	6: 116,305,337 (GRCm39)		probably null	Het
Zfp451	A	T	1: 33,811,972 (GRCm39)		probably null	Het
Zfp607a	A	T	7: 27,578,183 (GRCm39)	I418F	probably damaging	Het
Zfp612	A	G	8: 110,816,337 (GRCm39)	T515A	probably damaging	Het
Zfp708	G	T	13: 67,219,200 (GRCm39)	L208I	possibly damaging	Het

Other mutations in Psd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00769:Psd3	APN	8	68,361,331 (GRCm39)	splice site	probably benign
IGL01095:Psd3	APN	8	68,361,165 (GRCm39)	missense	probably damaging	1.00
IGL01139:Psd3	APN	8	68,361,187 (GRCm39)	missense	probably damaging	1.00
IGL01330:Psd3	APN	8	68,149,830 (GRCm39)	missense	probably damaging	1.00
IGL01350:Psd3	APN	8	68,173,544 (GRCm39)	missense	probably damaging	1.00
IGL01487:Psd3	APN	8	68,149,766 (GRCm39)	missense	probably benign	0.01
IGL01780:Psd3	APN	8	68,416,521 (GRCm39)	missense	probably benign
IGL02020:Psd3	APN	8	68,426,822 (GRCm39)	intron	probably benign
IGL02232:Psd3	APN	8	68,356,797 (GRCm39)	missense	probably damaging	1.00
IGL02350:Psd3	APN	8	68,416,521 (GRCm39)	missense	probably benign
IGL02357:Psd3	APN	8	68,416,521 (GRCm39)	missense	probably benign
PIT4495001:Psd3	UTSW	8	68,416,565 (GRCm39)	missense	probably benign	0.00
R0052:Psd3	UTSW	8	68,335,631 (GRCm39)	critical splice donor site	probably null
R0052:Psd3	UTSW	8	68,335,631 (GRCm39)	critical splice donor site	probably null
R0242:Psd3	UTSW	8	68,210,738 (GRCm39)	missense	probably damaging	0.99
R0242:Psd3	UTSW	8	68,210,738 (GRCm39)	missense	probably damaging	0.99
R0581:Psd3	UTSW	8	68,173,598 (GRCm39)	missense	probably damaging	1.00
R0655:Psd3	UTSW	8	68,416,341 (GRCm39)	missense	probably benign	0.19
R1740:Psd3	UTSW	8	68,573,491 (GRCm39)	missense	probably damaging	1.00
R1789:Psd3	UTSW	8	68,413,217 (GRCm39)	missense	probably benign	0.26
R1847:Psd3	UTSW	8	68,172,656 (GRCm39)	missense	possibly damaging	0.93
R1951:Psd3	UTSW	8	68,416,139 (GRCm39)	missense	probably benign	0.00
R1954:Psd3	UTSW	8	68,149,727 (GRCm39)	missense	probably damaging	1.00
R2143:Psd3	UTSW	8	68,417,003 (GRCm39)	missense	probably damaging	1.00
R4387:Psd3	UTSW	8	68,453,413 (GRCm39)	missense	probably damaging	1.00
R4801:Psd3	UTSW	8	68,573,800 (GRCm39)	missense	probably benign
R4802:Psd3	UTSW	8	68,573,800 (GRCm39)	missense	probably benign
R4913:Psd3	UTSW	8	68,573,821 (GRCm39)	missense	probably damaging	0.99
R5045:Psd3	UTSW	8	68,166,477 (GRCm39)	missense	probably damaging	0.99
R5173:Psd3	UTSW	8	68,149,641 (GRCm39)	missense	probably damaging	1.00
R5264:Psd3	UTSW	8	68,166,377 (GRCm39)	missense	probably benign	0.23
R5350:Psd3	UTSW	8	68,361,513 (GRCm39)	missense	probably benign	0.00
R5816:Psd3	UTSW	8	68,413,162 (GRCm39)	missense	possibly damaging	0.90
R5994:Psd3	UTSW	8	68,172,620 (GRCm39)	missense	probably damaging	1.00
R6157:Psd3	UTSW	8	68,574,179 (GRCm39)	start codon destroyed	probably benign	0.14
R6241:Psd3	UTSW	8	68,270,791 (GRCm39)	intron	probably benign
R6586:Psd3	UTSW	8	68,416,197 (GRCm39)	missense	probably damaging	0.96
R6735:Psd3	UTSW	8	68,573,398 (GRCm39)	critical splice donor site	probably null
R6908:Psd3	UTSW	8	68,416,829 (GRCm39)	missense	probably benign	0.00
R6984:Psd3	UTSW	8	68,270,697 (GRCm39)	missense	possibly damaging	0.85
R7116:Psd3	UTSW	8	68,166,390 (GRCm39)	missense	probably benign	0.12
R7297:Psd3	UTSW	8	68,573,686 (GRCm39)	missense	probably damaging	0.98
R7334:Psd3	UTSW	8	68,361,357 (GRCm39)	missense	possibly damaging	0.94
R7348:Psd3	UTSW	8	68,243,583 (GRCm39)	missense	possibly damaging	0.65
R7357:Psd3	UTSW	8	68,574,149 (GRCm39)	missense	probably benign	0.01
R7369:Psd3	UTSW	8	68,356,818 (GRCm39)	missense	possibly damaging	0.95
R7385:Psd3	UTSW	8	68,453,408 (GRCm39)	missense	probably damaging	1.00
R7733:Psd3	UTSW	8	68,573,568 (GRCm39)	missense	possibly damaging	0.75
R7873:Psd3	UTSW	8	68,335,634 (GRCm39)	missense	possibly damaging	0.95
R8110:Psd3	UTSW	8	68,573,708 (GRCm39)	missense	probably damaging	1.00
R8765:Psd3	UTSW	8	68,416,093 (GRCm39)	missense	possibly damaging	0.69
R8768:Psd3	UTSW	8	68,417,003 (GRCm39)	missense	probably damaging	1.00
R8817:Psd3	UTSW	8	68,413,135 (GRCm39)	missense	possibly damaging	0.95
R8837:Psd3	UTSW	8	68,172,596 (GRCm39)	missense	probably damaging	0.99
R8878:Psd3	UTSW	8	68,210,750 (GRCm39)	missense	probably benign	0.28
R8903:Psd3	UTSW	8	68,165,945 (GRCm39)	missense	unknown
R8955:Psd3	UTSW	8	68,416,461 (GRCm39)	missense	probably benign	0.08
R9216:Psd3	UTSW	8	68,573,539 (GRCm39)	missense	probably benign	0.00
R9241:Psd3	UTSW	8	68,415,967 (GRCm39)	missense	probably benign	0.00
R9351:Psd3	UTSW	8	68,413,301 (GRCm39)	missense	probably benign	0.18
R9449:Psd3	UTSW	8	68,165,833 (GRCm39)	missense	unknown
R9451:Psd3	UTSW	8	68,363,487 (GRCm39)	missense	unknown
R9709:Psd3	UTSW	8	68,194,414 (GRCm39)	missense	probably null	0.99
R9797:Psd3	UTSW	8	68,210,778 (GRCm39)	missense	probably damaging	0.99
Z1088:Psd3	UTSW	8	68,358,912 (GRCm39)	splice site	silent

Predicted Primers

PCR Primer
(F):5'- GGGTGTTCCTCTTGAGACAATG -3'
(R):5'- TGTCCCATAATGAGCAATGTTTGTC -3'

Sequencing Primer
(F):5'- CCTCTTGAGACAATGTATTACATCG -3'
(R):5'- CTCATCAGAGAGCTGGTACTG -3'

Posted On

2019-05-15