Mutagenetix > Incidental Mutation

Incidental Mutation 'R0242:Psd3'

59564

Institutional Source

Beutler Lab

Gene Symbol

Psd3

Ensembl Gene

ENSMUSG00000030465

Gene Name

pleckstrin and Sec7 domain containing 3

Synonyms

EFA6D, 4931420C21Rik

MMRRC Submission

038480-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.093) question?

Stock #

R0242 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

68141734-68664679 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 68210738 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 270 (M270T)

Ref Sequence

ENSEMBL: ENSMUSP00000091178 (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: M757T

PolyPhen 2 Score 0.171 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: M757T

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: M128T

PolyPhen 2 Score 0.781 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000060306
Gene: ENSMUSG00000030465
AA Change: M128T

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000093468
AA Change: M270T

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000091178
Gene: ENSMUSG00000030465
AA Change: M270T

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: M756T

PolyPhen 2 Score 0.142 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: M756T

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: M756T

PolyPhen 2 Score 0.142 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: M756T

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: M128T

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000112545
Gene: ENSMUSG00000030465
AA Change: M128T

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: M787T

PolyPhen 2 Score 0.142 (Sensitivity: 0.92; Specificity: 0.86)

Predicted Effect

probably benign
Transcript: ENSMUST00000212960
AA Change: M1041T

PolyPhen 2 Score 0.025 (Sensitivity: 0.95; Specificity: 0.81)

Meta Mutation Damage Score

0.1195

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.3%
20x: 94.5%

Validation Efficiency

97% (110/113)

Allele List at MGI

Other mutations in this stock

Total: 110 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029H14Rik	T	C	8: 13,601,676 (GRCm39)	D230G	probably benign	Het
Abhd13	A	G	8: 10,037,561 (GRCm39)	I53V	probably benign	Het
Adgrl2	A	C	3: 148,544,821 (GRCm39)		probably null	Het
Aldh16a1	G	A	7: 44,794,088 (GRCm39)	A596V	probably damaging	Het
Aldh3b2	T	A	19: 4,029,414 (GRCm39)	Y262*	probably null	Het
Ambn	A	G	5: 88,615,831 (GRCm39)	Q420R	possibly damaging	Het
Ankib1	A	C	5: 3,750,344 (GRCm39)		probably benign	Het
Arhgap9	C	A	10: 127,165,407 (GRCm39)	H430Q	probably benign	Het
Arhgef25	C	T	10: 127,019,933 (GRCm39)	G435E	probably damaging	Het
Armc12	A	T	17: 28,751,366 (GRCm39)	D120V	possibly damaging	Het
Asxl3	G	A	18: 22,649,738 (GRCm39)	E576K	possibly damaging	Het
Bcdin3d	T	C	15: 99,368,776 (GRCm39)	E141G	probably benign	Het
Bmpr1b	G	A	3: 141,546,437 (GRCm39)	T483M	probably damaging	Het
Caprin2	C	T	6: 148,744,452 (GRCm39)	S991N	probably damaging	Het
Cd96	T	C	16: 45,892,129 (GRCm39)	I286M	possibly damaging	Het
Cdcp1	G	T	9: 123,009,237 (GRCm39)	F480L	probably benign	Het
Celf5	T	C	10: 81,300,243 (GRCm39)	T258A	probably benign	Het
Cgnl1	A	G	9: 71,628,939 (GRCm39)	V577A	probably damaging	Het
Clca3b	A	G	3: 144,547,226 (GRCm39)	S304P	probably benign	Het
Cmya5	A	T	13: 93,232,108 (GRCm39)	H993Q	probably benign	Het
Cnbp	A	T	6: 87,822,746 (GRCm39)	C6S	probably damaging	Het
Col14a1	C	T	15: 55,360,907 (GRCm39)	R1605W	probably damaging	Het
Cops7a	T	C	6: 124,941,817 (GRCm39)	N11S	probably benign	Het
Coro7	T	C	16: 4,448,042 (GRCm39)		probably benign	Het
Cpvl	T	C	6: 53,909,485 (GRCm39)	H217R	possibly damaging	Het
Cuedc1	T	C	11: 88,075,447 (GRCm39)		probably benign	Het
Cyp2c66	A	G	19: 39,130,369 (GRCm39)	Y68C	probably damaging	Het
Dicer1	G	A	12: 104,668,710 (GRCm39)	T1324M	probably benign	Het
Dlgap2	A	G	8: 14,777,562 (GRCm39)	D268G	probably benign	Het
Dnm1	T	A	2: 32,207,001 (GRCm39)	M535L	possibly damaging	Het
Dock7	A	T	4: 98,850,517 (GRCm39)	F1575Y	probably benign	Het
Dpp10	T	A	1: 123,326,275 (GRCm39)	H403L	possibly damaging	Het
Dync1h1	A	G	12: 110,616,285 (GRCm39)	D3112G	possibly damaging	Het
Eno3	A	G	11: 70,548,761 (GRCm39)	E21G	probably null	Het
Fam120b	T	A	17: 15,643,186 (GRCm39)	V655D	probably damaging	Het
Fkbp5	A	T	17: 28,647,426 (GRCm39)	D136E	probably benign	Het
Gdap1l1	T	A	2: 163,289,573 (GRCm39)	Y179*	probably null	Het
Gfer	A	G	17: 24,913,277 (GRCm39)	W192R	probably damaging	Het
Gm4782	A	G	6: 50,586,838 (GRCm39)	T408A	probably benign	Het
Golgb1	C	T	16: 36,695,992 (GRCm39)	Q164*	probably null	Het
Gpnmb	A	G	6: 49,024,276 (GRCm39)	N197S	probably damaging	Het
Gtf2f1	G	A	17: 57,310,802 (GRCm39)	T414M	probably benign	Het
Hc	A	G	2: 34,926,166 (GRCm39)		probably benign	Het
Hcfc1	A	T	X: 72,992,035 (GRCm39)		probably benign	Het
Helz2	C	T	2: 180,872,223 (GRCm39)	R2539Q	probably damaging	Het
Hsd17b12	T	A	2: 93,988,160 (GRCm39)	I19F	probably benign	Het
Incenp	T	C	19: 9,871,114 (GRCm39)	T172A	unknown	Het
Jmy	A	G	13: 93,578,126 (GRCm39)	Y681H	probably benign	Het
Kbtbd11	A	G	8: 15,077,508 (GRCm39)	T36A	probably benign	Het
Kcnh4	T	C	11: 100,646,525 (GRCm39)	D267G	probably damaging	Het
Krt34	C	T	11: 99,932,157 (GRCm39)	E56K	probably damaging	Het
Krt40	T	A	11: 99,429,568 (GRCm39)	E335D	probably damaging	Het
Krt86	T	A	15: 101,374,454 (GRCm39)	Y282*	probably null	Het
Lgi3	C	T	14: 70,772,255 (GRCm39)	R267*	probably null	Het
Lnpk	A	G	2: 74,367,633 (GRCm39)		probably benign	Het
Lrp1b	T	A	2: 40,888,195 (GRCm39)	H2355L	probably benign	Het
Lrrc8e	G	A	8: 4,285,401 (GRCm39)	R542H	probably benign	Het
Mia2	T	C	12: 59,155,642 (GRCm39)	Y452H	probably damaging	Het
Mmachc	C	T	4: 116,561,738 (GRCm39)	R132Q	probably damaging	Het
Mtbp	T	A	15: 55,440,882 (GRCm39)	N356K	possibly damaging	Het
Myo5b	A	G	18: 74,794,787 (GRCm39)	H552R	possibly damaging	Het
Niban1	A	G	1: 151,593,967 (GRCm39)	D884G	probably benign	Het
Noxred1	A	G	12: 87,273,753 (GRCm39)	V96A	probably benign	Het
Nr1d2	T	A	14: 18,211,933 (GRCm38)	D390V	possibly damaging	Het
Oas1e	A	T	5: 120,929,839 (GRCm39)		probably benign	Het
Odad2	A	T	18: 7,211,516 (GRCm39)	V786D	probably damaging	Het
Or1r1	T	C	11: 73,874,538 (GRCm39)	S299G	probably benign	Het
Or6c1b	T	A	10: 129,273,217 (GRCm39)	Y179N	probably damaging	Het
Otog	G	T	7: 45,916,805 (GRCm39)	C914F	probably damaging	Het
Pank2	G	T	2: 131,122,117 (GRCm39)	C214F	probably damaging	Het
Pcdhb1	T	A	18: 37,399,788 (GRCm39)	S580T	probably benign	Het
Pdia3	T	C	2: 121,244,592 (GRCm39)	S2P	probably damaging	Het
Peli1	G	T	11: 21,092,602 (GRCm39)	R83L	probably damaging	Het
Pla2g3	T	A	11: 3,441,935 (GRCm39)	C366*	probably null	Het
Pon3	T	A	6: 5,240,860 (GRCm39)	D107V	probably benign	Het
Ppip5k2	A	G	1: 97,668,816 (GRCm39)	C532R	probably damaging	Het
Prph	A	T	15: 98,953,608 (GRCm39)	D174V	probably damaging	Het
Pum3	A	G	19: 27,400,155 (GRCm39)		probably benign	Het
Pus1	A	T	5: 110,927,664 (GRCm39)	H30Q	probably benign	Het
Pwwp3a	T	C	10: 80,070,092 (GRCm39)	S354P	probably benign	Het
Rab7	A	T	6: 87,982,114 (GRCm39)	V87E	probably damaging	Het
Rbm5	A	T	9: 107,628,907 (GRCm39)		probably benign	Het
Reln	A	G	5: 22,147,595 (GRCm39)		probably null	Het
S1pr3	A	G	13: 51,572,938 (GRCm39)	T40A	probably benign	Het
Sdk1	T	A	5: 142,129,677 (GRCm39)		probably benign	Het
Senp7	T	A	16: 55,999,884 (GRCm39)	I853N	probably damaging	Het
Serpinb6c	T	A	13: 34,083,230 (GRCm39)		probably benign	Het
Shroom1	T	G	11: 53,356,312 (GRCm39)		probably null	Het
Slc24a3	T	C	2: 145,448,584 (GRCm39)	I376T	probably benign	Het
Slc46a1	T	C	11: 78,359,493 (GRCm39)	I375T	possibly damaging	Het
Slc4a9	T	C	18: 36,666,733 (GRCm39)	F527S	probably damaging	Het
Slc4a9	T	A	18: 36,674,286 (GRCm39)	I924N	probably damaging	Het
Slx4	T	A	16: 3,804,816 (GRCm39)	E666V	probably damaging	Het
Snrnp27	G	A	6: 86,652,575 (GRCm39)		probably benign	Het
Sorcs1	C	T	19: 50,216,659 (GRCm39)	G640E	probably damaging	Het
Spmap2l	G	T	5: 77,164,152 (GRCm39)	E52*	probably null	Het
Sptan1	A	T	2: 29,908,413 (GRCm39)	M1725L	probably benign	Het
Sync	G	A	4: 129,187,514 (GRCm39)	R182K	probably damaging	Het
Syne2	G	A	12: 76,144,808 (GRCm39)	G1586S	probably damaging	Het
Sytl1	G	T	4: 132,980,768 (GRCm39)	T522K	probably damaging	Het
Tex2	T	A	11: 106,410,781 (GRCm39)	K414*	probably null	Het
Tex55	C	T	16: 38,644,929 (GRCm39)		probably benign	Het
Thsd7a	G	A	6: 12,503,915 (GRCm39)	T413I	probably benign	Het
Tm9sf1	C	T	14: 55,875,392 (GRCm39)	A451T	possibly damaging	Het
Ttn	A	T	2: 76,656,496 (GRCm39)		probably benign	Het
Uba2	T	C	7: 33,854,054 (GRCm39)	I140V	possibly damaging	Het
Ushbp1	C	A	8: 71,842,762 (GRCm39)	G361*	probably null	Het
Wbp2nl	C	T	15: 82,197,988 (GRCm39)	A175V	probably benign	Het
Zc3h12d	A	G	10: 7,738,330 (GRCm39)	E212G	probably damaging	Het
Zc3h7b	T	C	15: 81,653,031 (GRCm39)		probably benign	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
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
R7082:Psd3	UTSW	8	68,356,800 (GRCm39)	missense	probably benign	0.03
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'- TGAAGACAGGTTCTGTGCCCATCC -3'
(R):5'- CCCCTCAGAAGGTACTGATGAGAAGG -3'

Sequencing Primer
(F):5'- AGACACAAACGTGAGTCTCTG -3'
(R):5'- AGGCTAATGGAACGCACC -3'

Posted On

2013-07-11