Mutagenetix > Incidental Mutation

Incidental Mutation 'R5563:Psd4'

436692

Institutional Source

Beutler Lab

Gene Symbol

Psd4

Ensembl Gene

ENSMUSG00000026979

Gene Name

pleckstrin and Sec7 domain containing 4

Synonyms

SEC7 homolog, EFA6B

MMRRC Submission

043120-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5563 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

24257571-24299882 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 24284897 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 254 (R254G)

Ref Sequence

ENSEMBL: ENSMUSP00000132395 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056641] [ENSMUST00000102942] [ENSMUST00000127242] [ENSMUST00000131930] [ENSMUST00000140547] [ENSMUST00000142522] [ENSMUST00000166388]

AlphaFold

Q8BLR5

Predicted Effect

probably benign
Transcript: ENSMUST00000056641
AA Change: R254G

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

SMART Domains

Protein: ENSMUSP00000062415
Gene: ENSMUSG00000026979
AA Change: R254G

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: ENSMUST00000102942
AA Change: R254G

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

SMART Domains

Protein: ENSMUSP00000100006
Gene: ENSMUSG00000026979
AA Change: R254G

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: ENSMUST00000127242

Predicted Effect

probably benign
Transcript: ENSMUST00000131930

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133730

Predicted Effect

probably benign
Transcript: ENSMUST00000140547

Predicted Effect

probably benign
Transcript: ENSMUST00000142522

Predicted Effect

probably benign
Transcript: ENSMUST00000166388
AA Change: R254G

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

SMART Domains

Protein: ENSMUSP00000132395
Gene: ENSMUSG00000026979
AA Change: R254G

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: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.9%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 29 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abraxas1	C	T	5: 100,960,040 (GRCm39)	R104H	possibly damaging	Het
Actn3	T	C	19: 4,922,344 (GRCm39)	H101R	probably damaging	Het
Akp3	T	C	1: 87,053,646 (GRCm39)	S174P	probably damaging	Het
Aldh5a1	C	A	13: 25,102,609 (GRCm39)	A285S	possibly damaging	Het
Atp7b	G	A	8: 22,518,730 (GRCm39)	P36L	possibly damaging	Het
Cdh20	C	T	1: 104,875,082 (GRCm39)	P288L	probably benign	Het
Fktn	T	A	4: 53,761,327 (GRCm39)	N481K	probably damaging	Het
Fmo5	C	A	3: 97,546,207 (GRCm39)	H173Q	probably damaging	Het
Fnip1	A	G	11: 54,395,688 (GRCm39)	R1021G	probably benign	Het
Gprc5c	G	T	11: 114,755,093 (GRCm39)	V257L	possibly damaging	Het
Grin2a	A	G	16: 9,525,581 (GRCm39)	F337L	probably benign	Het
Ighv3-1	T	A	12: 113,928,206 (GRCm39)	Y51F	probably benign	Het
Jcad	A	G	18: 4,673,944 (GRCm39)	K569E	possibly damaging	Het
Mars1	T	C	10: 127,144,530 (GRCm39)	Q170R	probably benign	Het
Mfsd4b2	C	T	10: 39,798,038 (GRCm39)	E106K	probably benign	Het
Mical2	A	G	7: 111,914,185 (GRCm39)	D285G	probably damaging	Het
Mpp4	A	G	1: 59,163,788 (GRCm39)		probably null	Het
Npat	A	G	9: 53,474,427 (GRCm39)	I740V	probably damaging	Het
Parp6	G	A	9: 59,535,956 (GRCm39)		probably null	Het
Plin2	T	C	4: 86,580,341 (GRCm39)	K140R	probably benign	Het
Prdm2	T	C	4: 142,861,200 (GRCm39)	T697A	probably benign	Het
Prkaa1	A	G	15: 5,199,437 (GRCm39)	E179G	probably damaging	Het
Prtg	G	A	9: 72,764,180 (GRCm39)	R551H	probably damaging	Het
Rhpn2	T	A	7: 35,070,652 (GRCm39)	L194H	probably damaging	Het
Sp7	T	C	15: 102,267,755 (GRCm39)	D17G	possibly damaging	Het
Topbp1	T	C	9: 103,188,712 (GRCm39)	V128A	possibly damaging	Het
Uba5	G	T	9: 103,926,446 (GRCm39)	T372K	probably benign	Het
Vmn2r13	T	A	5: 109,321,846 (GRCm39)	I284L	probably benign	Het
Vmn2r68	T	C	7: 84,871,283 (GRCm39)	T667A	probably 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
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
R7483:Psd4	UTSW	2	24,294,768 (GRCm39)	missense	possibly damaging	0.65
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'- GAAAATTCCAGGCTCCTCCCTAG -3'
(R):5'- CACAGTCCTCAGCTGACTTC -3'

Sequencing Primer
(F):5'- TGCTGAGGAGGACAGTATCTTC -3'
(R):5'- GACTTCCTCAGCTAACTTACCTCAC -3'

Posted On

2016-10-24