Mutagenetix > Incidental Mutation

Incidental Mutation 'R7483:Psd4'

579885

Institutional Source

Beutler Lab

Gene Symbol

Psd4

Ensembl Gene

ENSMUSG00000026979

Gene Name

pleckstrin and Sec7 domain containing 4

Synonyms

SEC7 homolog, EFA6B

MMRRC Submission

045557-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7483 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

24257571-24299882 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 24294768 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 776 (D776V)

Ref Sequence

ENSEMBL: ENSMUSP00000062415 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056641] [ENSMUST00000102942] [ENSMUST00000140303] [ENSMUST00000166388]

AlphaFold

Q8BLR5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000056641
AA Change: D776V

PolyPhen 2 Score 0.650 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000062415
Gene: ENSMUSG00000026979
AA Change: D776V

Domain	Start	End	E-Value	Type
low complexity region	156	176	N/A	INTRINSIC
low complexity region	350	361	N/A	INTRINSIC
low complexity region	420	438	N/A	INTRINSIC
low complexity region	458	474	N/A	INTRINSIC
Sec7	497	688	9.39e-47	SMART
PH	727	843	1.1e-10	SMART
low complexity region	883	893	N/A	INTRINSIC
low complexity region	897	920	N/A	INTRINSIC
low complexity region	961	973	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102942
AA Change: D776V

PolyPhen 2 Score 0.650 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000100006
Gene: ENSMUSG00000026979
AA Change: D776V

Domain	Start	End	E-Value	Type
low complexity region	156	176	N/A	INTRINSIC
low complexity region	350	361	N/A	INTRINSIC
low complexity region	420	438	N/A	INTRINSIC
low complexity region	458	474	N/A	INTRINSIC
Sec7	497	688	9.39e-47	SMART
PH	727	843	1.1e-10	SMART
low complexity region	883	893	N/A	INTRINSIC
low complexity region	897	920	N/A	INTRINSIC
low complexity region	961	973	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000140303

Predicted Effect

possibly damaging
Transcript: ENSMUST00000166388
AA Change: D776V

PolyPhen 2 Score 0.650 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000132395
Gene: ENSMUSG00000026979
AA Change: D776V

Domain	Start	End	E-Value	Type
low complexity region	156	176	N/A	INTRINSIC
low complexity region	350	361	N/A	INTRINSIC
low complexity region	420	438	N/A	INTRINSIC
low complexity region	458	474	N/A	INTRINSIC
Sec7	497	688	9.39e-47	SMART
PH	727	843	1.1e-10	SMART
low complexity region	883	893	N/A	INTRINSIC
low complexity region	897	920	N/A	INTRINSIC
low complexity region	961	973	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad10	A	T	5: 121,794,075 (GRCm39)		probably null	Het
Ahnak	T	C	19: 8,982,186 (GRCm39)	S1157P	probably damaging	Het
Akap12	T	G	10: 4,303,967 (GRCm39)	V364G	probably benign	Het
Ankrd17	A	G	5: 90,447,855 (GRCm39)	S229P	probably benign	Het
Apof	A	T	10: 128,104,636 (GRCm39)	Y5F	probably benign	Het
Arhgap24	T	A	5: 102,989,174 (GRCm39)	M94K	probably benign	Het
Ash2l	G	T	8: 26,312,798 (GRCm39)	D479E	probably damaging	Het
Atp8a2	A	T	14: 60,245,824 (GRCm39)	C623S	probably benign	Het
Bmper	T	A	9: 23,395,238 (GRCm39)	N656K	probably benign	Het
Braf	T	C	6: 39,604,772 (GRCm39)	I619V	possibly damaging	Het
Brwd1	T	C	16: 95,857,373 (GRCm39)	R396G	probably damaging	Het
Car7	A	T	8: 105,276,216 (GRCm39)	T234S	probably benign	Het
Catsper4	A	T	4: 133,945,552 (GRCm39)	V169E	probably damaging	Het
Cemip	T	G	7: 83,647,784 (GRCm39)	I99L	probably damaging	Het
Chrna7	C	A	7: 62,754,738 (GRCm39)	V290L	probably damaging	Het
Clip1	A	T	5: 123,755,447 (GRCm39)	D944E	probably benign	Het
Cplane2	A	G	4: 140,947,153 (GRCm39)	D178G	probably damaging	Het
Cyp2c68	T	C	19: 39,677,581 (GRCm39)	T470A	probably benign	Het
Dmbx1	G	T	4: 115,780,908 (GRCm39)	A31D	probably damaging	Het
Dnah7b	T	C	1: 46,214,579 (GRCm39)	F1115L	probably damaging	Het
Dock10	T	C	1: 80,493,283 (GRCm39)	I1897V	probably benign	Het
Efcab3	A	G	11: 105,000,112 (GRCm39)	I234V	probably benign	Het
Eid2b	T	G	7: 27,977,243 (GRCm39)	L13R	probably damaging	Het
Enam	A	G	5: 88,649,679 (GRCm39)	Y396C	probably damaging	Het
Fam161a	A	T	11: 22,971,006 (GRCm39)	T395S	probably damaging	Het
Fat1	A	G	8: 45,476,197 (GRCm39)	R1748G	probably benign	Het
Fdxacb1	C	A	9: 50,681,451 (GRCm39)	T124K	possibly damaging	Het
Fer1l6	A	T	15: 58,513,794 (GRCm39)	D1563V	possibly damaging	Het
Gm20834	T	C	Y: 10,323,226 (GRCm39)	H70R	probably damaging	Het
Gucy2d	T	A	7: 98,098,964 (GRCm39)	M261K	probably damaging	Het
Hcar2	T	A	5: 124,002,861 (GRCm39)	Q214L	probably benign	Het
Hdac11	C	T	6: 91,136,214 (GRCm39)	H75Y	probably damaging	Het
Hoxa2	C	A	6: 52,141,279 (GRCm39)	A116S	probably benign	Het
Ints2	A	G	11: 86,106,444 (GRCm39)	C989R	probably damaging	Het
Jpt1	T	C	11: 115,393,950 (GRCm39)	E36G	probably damaging	Het
Kdm5d	G	A	Y: 914,044 (GRCm39)	R327Q	possibly damaging	Het
Klhl1	T	C	14: 96,584,304 (GRCm39)	M309V	probably benign	Het
Larp4	A	G	15: 99,889,659 (GRCm39)	K193E	probably benign	Het
Lmo3	C	T	6: 138,393,500 (GRCm39)	C40Y	probably damaging	Het
Mcm4	A	G	16: 15,448,306 (GRCm39)	V417A	probably benign	Het
Med8	A	G	4: 118,268,176 (GRCm39)	E34G	probably damaging	Het
Mex3b	G	T	7: 82,517,114 (GRCm39)	A86S	possibly damaging	Het
Muc6	T	C	7: 141,224,245 (GRCm39)	T1646A	unknown	Het
Myo15b	A	T	11: 115,749,570 (GRCm39)	E113D		Het
Myo7a	T	A	7: 97,712,881 (GRCm39)	H1698L	probably benign	Het
Myocos	T	A	1: 162,484,678 (GRCm39)	M44L	unknown	Het
Nalcn	A	G	14: 123,551,499 (GRCm39)	V1036A	probably damaging	Het
Nfrkb	C	T	9: 31,325,328 (GRCm39)	Q924*	probably null	Het
Nol6	A	G	4: 41,117,424 (GRCm39)	L923P	possibly damaging	Het
Nrxn3	T	C	12: 89,477,232 (GRCm39)	Y472H	probably damaging	Het
Nudcd1	A	G	15: 44,269,253 (GRCm39)	Y136H	possibly damaging	Het
Obox2	T	C	7: 15,131,241 (GRCm39)	C116R	probably damaging	Het
Onecut3	A	T	10: 80,331,310 (GRCm39)	S157C	unknown	Het
Or10ak11	A	G	4: 118,687,517 (GRCm39)	V39A	probably damaging	Het
Or11g27	T	A	14: 50,771,472 (GRCm39)	V201D	probably benign	Het
Or2d2b	T	A	7: 106,705,982 (GRCm39)	I29F	probably benign	Het
Or4f15	T	C	2: 111,814,124 (GRCm39)	I98M	probably damaging	Het
Oscp1	C	T	4: 125,967,726 (GRCm39)	R91*	probably null	Het
Pclo	A	T	5: 14,762,606 (GRCm39)	D408V		Het
Pde8a	T	C	7: 80,932,581 (GRCm39)	V81A	probably benign	Het
Pde8b	T	A	13: 95,164,251 (GRCm39)	D653V	probably damaging	Het
Peg10	T	TCCG	6: 4,756,451 (GRCm39)		probably benign	Het
Pik3cg	T	C	12: 32,245,647 (GRCm39)	Y867C	probably damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Ptprb	A	G	10: 116,119,334 (GRCm39)	E156G	probably benign	Het
Rad54b	A	G	4: 11,610,372 (GRCm39)	Y663C	probably damaging	Het
Ranbp3l	T	A	15: 9,030,955 (GRCm39)	V78D	possibly damaging	Het
Rbm12	T	C	2: 155,940,138 (GRCm39)	I45V	unknown	Het
Scn9a	A	G	2: 66,363,692 (GRCm39)	V862A	probably damaging	Het
Sdcbp	T	C	4: 6,393,089 (GRCm39)	I242T	possibly damaging	Het
Slc25a24	A	G	3: 109,066,751 (GRCm39)	T302A	probably damaging	Het
Slc45a3	G	T	1: 131,904,549 (GRCm39)		probably benign	Het
Srpk1	T	C	17: 28,813,192 (GRCm39)	I517M	probably benign	Het
Tmx4	A	G	2: 134,481,581 (GRCm39)	M114T	probably benign	Het
Trhr	T	A	15: 44,092,627 (GRCm39)	V288D	probably damaging	Het
Tspoap1	A	T	11: 87,652,351 (GRCm39)	I42F	probably benign	Het
Ttn	A	T	2: 76,781,856 (GRCm39)	D1063E	unknown	Het
Tusc3	A	G	8: 39,538,635 (GRCm39)	I225V	probably benign	Het
Ugt2b38	A	G	5: 87,571,973 (GRCm39)	S20P	probably damaging	Het
Upf2	A	G	2: 6,032,219 (GRCm39)	T922A	unknown	Het
Usp38	C	T	8: 81,741,190 (GRCm39)		probably benign	Het
Vmn1r216	A	G	13: 23,283,738 (GRCm39)	I140M	probably damaging	Het
Vmn2r115	T	A	17: 23,565,371 (GRCm39)	N419K	possibly damaging	Het
Vmn2r55	C	T	7: 12,404,755 (GRCm39)	G216D	probably benign	Het
Vwa8	A	C	14: 79,219,674 (GRCm39)		probably null	Het
Wnt7b	C	A	15: 85,421,615 (GRCm39)	R349L	possibly damaging	Het
Xbp1	T	C	11: 5,471,098 (GRCm39)	V35A	probably benign	Het
Zan	A	T	5: 137,445,057 (GRCm39)	M1734K	unknown	Het
Zfhx4	A	G	3: 5,477,237 (GRCm39)	E3284G	probably damaging	Het
Zfp458	A	G	13: 67,404,978 (GRCm39)	L487S	possibly damaging	Het
Zfp687	C	T	3: 94,914,841 (GRCm39)	R1220H	probably damaging	Het
Zp1	A	G	19: 10,895,280 (GRCm39)	L324P	possibly damaging	Het

Other mutations in Psd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00850:Psd4	APN	2	24,284,298 (GRCm39)	missense	probably benign	0.25
IGL01302:Psd4	APN	2	24,286,799 (GRCm39)	critical splice donor site	probably null
IGL01446:Psd4	APN	2	24,295,407 (GRCm39)	missense	probably damaging	1.00
IGL01577:Psd4	APN	2	24,293,234 (GRCm39)	missense	probably damaging	0.96
IGL01823:Psd4	APN	2	24,284,444 (GRCm39)	missense	probably benign	0.27
IGL02103:Psd4	APN	2	24,290,540 (GRCm39)	nonsense	probably null
IGL02212:Psd4	APN	2	24,295,326 (GRCm39)	nonsense	probably null
IGL02240:Psd4	APN	2	24,286,389 (GRCm39)	missense	probably benign	0.00
IGL02261:Psd4	APN	2	24,291,756 (GRCm39)	missense	probably damaging	1.00
IGL02345:Psd4	APN	2	24,291,835 (GRCm39)	critical splice donor site	probably null
IGL03272:Psd4	APN	2	24,295,692 (GRCm39)	splice site	probably benign
bitcoin	UTSW	2	24,291,569 (GRCm39)	missense	probably damaging	1.00
crypto	UTSW	2	24,287,259 (GRCm39)	missense	probably benign
Ethereum	UTSW	2	24,296,996 (GRCm39)	missense	probably damaging	1.00
underworld	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
PIT4469001:Psd4	UTSW	2	24,284,306 (GRCm39)	missense	probably benign	0.08
R0131:Psd4	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
R0131:Psd4	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
R0132:Psd4	UTSW	2	24,295,363 (GRCm39)	missense	probably damaging	1.00
R0278:Psd4	UTSW	2	24,284,450 (GRCm39)	missense	probably damaging	1.00
R1303:Psd4	UTSW	2	24,285,030 (GRCm39)	missense	probably benign	0.00
R1551:Psd4	UTSW	2	24,293,292 (GRCm39)	missense	probably benign	0.02
R1715:Psd4	UTSW	2	24,295,344 (GRCm39)	missense	probably damaging	1.00
R1854:Psd4	UTSW	2	24,287,468 (GRCm39)	missense	probably benign	0.26
R1942:Psd4	UTSW	2	24,295,805 (GRCm39)	missense	probably damaging	1.00
R2392:Psd4	UTSW	2	24,284,679 (GRCm39)	missense	probably damaging	0.98
R2420:Psd4	UTSW	2	24,291,253 (GRCm39)	missense	probably damaging	1.00
R4509:Psd4	UTSW	2	24,286,347 (GRCm39)	missense	probably benign
R4512:Psd4	UTSW	2	24,292,901 (GRCm39)	missense	probably damaging	1.00
R4558:Psd4	UTSW	2	24,294,806 (GRCm39)	missense	probably damaging	1.00
R4995:Psd4	UTSW	2	24,287,259 (GRCm39)	missense	probably benign
R5120:Psd4	UTSW	2	24,295,450 (GRCm39)	missense	probably benign
R5314:Psd4	UTSW	2	24,290,528 (GRCm39)	missense	possibly damaging	0.89
R5563:Psd4	UTSW	2	24,284,897 (GRCm39)	missense	probably benign
R5638:Psd4	UTSW	2	24,287,427 (GRCm39)	missense	probably benign	0.14
R6191:Psd4	UTSW	2	24,284,499 (GRCm39)	missense	probably damaging	1.00
R6224:Psd4	UTSW	2	24,291,569 (GRCm39)	missense	probably damaging	1.00
R7024:Psd4	UTSW	2	24,284,555 (GRCm39)	missense	possibly damaging	0.76
R7046:Psd4	UTSW	2	24,284,985 (GRCm39)	missense	probably benign	0.05
R7209:Psd4	UTSW	2	24,287,357 (GRCm39)	missense	probably damaging	1.00
R7498:Psd4	UTSW	2	24,296,996 (GRCm39)	missense	probably damaging	1.00
R7571:Psd4	UTSW	2	24,297,023 (GRCm39)	missense	probably damaging	1.00
R7741:Psd4	UTSW	2	24,291,108 (GRCm39)	critical splice donor site	probably null
R7978:Psd4	UTSW	2	24,294,867 (GRCm39)	missense	probably damaging	1.00
R8133:Psd4	UTSW	2	24,286,701 (GRCm39)	missense	probably benign
R8254:Psd4	UTSW	2	24,293,223 (GRCm39)	missense	probably damaging	0.99
R8786:Psd4	UTSW	2	24,295,444 (GRCm39)	missense	probably benign	0.08
R8797:Psd4	UTSW	2	24,287,440 (GRCm39)	missense	probably benign	0.02
R9015:Psd4	UTSW	2	24,287,492 (GRCm39)	missense
R9413:Psd4	UTSW	2	24,287,472 (GRCm39)	missense	probably benign	0.39
X0009:Psd4	UTSW	2	24,291,537 (GRCm39)	missense	probably damaging	1.00
X0064:Psd4	UTSW	2	24,294,750 (GRCm39)	missense	probably damaging	0.99
Z1177:Psd4	UTSW	2	24,284,943 (GRCm39)	frame shift	probably null
Z1177:Psd4	UTSW	2	24,284,924 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- CGTGTAAAGCTGACGGGAAC -3'
(R):5'- CCTAGTCAAGATAGTAGCTCCCATC -3'

Sequencing Primer
(F):5'- GAACAGTGTCATTCTGGAACCATGC -3'
(R):5'- ACCACAGACGTTGAGTGGC -3'

Posted On

2019-10-07