Mutagenetix > Incidental Mutation

Incidental Mutation 'R4995:Psd4'

385147

Institutional Source

Beutler Lab

Gene Symbol

Psd4

Ensembl Gene

ENSMUSG00000026979

Gene Name

pleckstrin and Sec7 domain containing 4

Synonyms

SEC7 homolog, EFA6B

MMRRC Submission

042589-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4995 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24367580-24414954 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 24397247 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 397 (F397S)

Ref Sequence

ENSEMBL: ENSMUSP00000132395 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056641] [ENSMUST00000102942] [ENSMUST00000127242] [ENSMUST00000131930] [ENSMUST00000140303] [ENSMUST00000140547] [ENSMUST00000142522] [ENSMUST00000166388]

AlphaFold

Q8BLR5

Predicted Effect

probably benign
Transcript: ENSMUST00000056641
AA Change: F397S

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

SMART Domains

Protein: ENSMUSP00000062415
Gene: ENSMUSG00000026979
AA Change: F397S

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: F397S

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

SMART Domains

Protein: ENSMUSP00000100006
Gene: ENSMUSG00000026979
AA Change: F397S

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: ENSMUST00000140303

Predicted Effect

probably benign
Transcript: ENSMUST00000140547

Predicted Effect

probably benign
Transcript: ENSMUST00000142522

Predicted Effect

probably benign
Transcript: ENSMUST00000166388
AA Change: F397S

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

SMART Domains

Protein: ENSMUSP00000132395
Gene: ENSMUSG00000026979
AA Change: F397S

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

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.6%

Validation Efficiency

99% (86/87)

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921504E06Rik	G	A	2: 19,494,184	Q333*	probably null	Het
4930505A04Rik	C	T	11: 30,426,349	V173M	probably damaging	Het
Acvrl1	G	A	15: 101,135,860	R141H	probably benign	Het
Adprm	A	G	11: 67,041,610	F158L	possibly damaging	Het
Aldoart2	C	T	12: 55,566,253	T321M	probably benign	Het
Ap3m2	A	G	8: 22,803,776	V86A	probably benign	Het
Arhgef19	T	A	4: 141,247,515		probably null	Het
Armc4	G	A	18: 7,223,663	T460M	probably damaging	Het
Bcl2l12	T	G	7: 44,994,191		probably null	Het
Bptf	T	C	11: 107,054,565	Q2501R	probably damaging	Het
C230029F24Rik	A	T	1: 49,338,136		noncoding transcript	Het
C7	C	T	15: 5,049,592	G78D	probably damaging	Het
Caly	T	C	7: 140,070,625	T135A	probably benign	Het
Cbl	A	G	9: 44,153,811	M740T	possibly damaging	Het
Cbx4	A	G	11: 119,081,211	V446A	probably benign	Het
Celsr1	C	A	15: 85,937,911	R1735L	probably damaging	Het
Cep250	A	G	2: 155,988,316	D135G	probably damaging	Het
Cgn	T	C	3: 94,779,936	T19A	probably damaging	Het
Chic2	A	T	5: 75,044,204	V32D	probably damaging	Het
Cntln	A	G	4: 85,049,883	K780E	probably benign	Het
Col8a2	A	T	4: 126,310,788	D197V	probably damaging	Het
Crot	A	T	5: 8,974,000	V372E	probably damaging	Het
Cyb561d2	C	T	9: 107,541,548	V26M	probably damaging	Het
Ddx5	G	A	11: 106,785,236	T237I	probably damaging	Het
Dmxl2	G	T	9: 54,501,441		probably benign	Het
Dock8	T	A	19: 25,158,383	S1188R	probably benign	Het
Ehbp1	T	A	11: 22,101,073	H493L	probably damaging	Het
Eif5b	T	A	1: 38,051,711	*1217K	probably null	Het
Eprs	A	G	1: 185,410,139		probably benign	Het
Etfdh	T	C	3: 79,605,788	D376G	probably benign	Het
Fam186a	T	C	15: 99,945,099	Q1088R	probably benign	Het
Fbxw16	G	T	9: 109,441,250	T141N	probably damaging	Het
Fgf11	G	A	11: 69,798,759	H138Y	probably damaging	Het
Gm1673	G	A	5: 33,984,926	R79H	probably damaging	Het
Htra3	T	C	5: 35,671,074	E154G	probably damaging	Het
Hydin	T	A	8: 110,569,642	V3601D	probably damaging	Het
Jup	G	T	11: 100,379,541	S380*	probably null	Het
Klrg1	T	A	6: 122,278,275	D66V	probably benign	Het
Llgl1	C	T	11: 60,709,724	A633V	probably benign	Het
Lmln	T	A	16: 33,074,097	Y203*	probably null	Het
Lrrc58	T	G	16: 37,877,056	C165G	probably benign	Het
Lss	T	C	10: 76,547,537	V557A	probably benign	Het
Mast4	T	C	13: 102,905,754		probably benign	Het
Med13l	C	A	5: 118,730,949	P754Q	possibly damaging	Het
Mga	C	T	2: 119,932,582	R1240*	probably null	Het
Mgat5b	T	A	11: 116,974,199		probably null	Het
Mtor	A	G	4: 148,525,752	D1572G	probably damaging	Het
Muc4	T	A	16: 32,754,214	S1363T	probably benign	Het
Muc4	T	A	16: 32,754,041	S1306T	probably benign	Het
Myo18b	A	G	5: 112,760,392	V2005A	probably damaging	Het
Myo1e	G	A	9: 70,353,272	D571N	probably benign	Het
Mypn	T	C	10: 63,119,968		probably null	Het
Ndufb10	T	C	17: 24,722,757		probably null	Het
Nelfb	G	T	2: 25,206,196	D300E	probably benign	Het
Olfr1389	T	A	11: 49,430,655	Y60N	probably damaging	Het
Olfr1507	A	T	14: 52,490,531	C61*	probably null	Het
Olfr625-ps1	T	A	7: 103,683,367	D206E	probably damaging	Het
Olfr668	T	A	7: 104,925,735	T10S	probably benign	Het
Pcdha11	C	T	18: 37,011,027	T57M	probably benign	Het
Pkp1	A	T	1: 135,880,855	I458N	possibly damaging	Het
Prr12	T	A	7: 45,051,229		probably benign	Het
Prrc2c	A	T	1: 162,705,310		probably benign	Het
Pygm	T	C	19: 6,398,139	I737T	probably damaging	Het
Rfx1	T	A	8: 84,080,114		probably null	Het
Rsl1	A	G	13: 67,182,249	T254A	possibly damaging	Het
Sh3rf3	A	G	10: 59,086,824	Q574R	probably benign	Het
Spire1	T	C	18: 67,552,779		probably null	Het
St6galnac4	G	A	2: 32,594,063	G91D	probably damaging	Het
Sytl2	T	C	7: 90,382,257		probably benign	Het
Tbpl2	T	A	2: 24,093,860	K188N	possibly damaging	Het
Tenm3	A	T	8: 48,229,137	M2486K	possibly damaging	Het
Tgoln1	A	C	6: 72,616,140	V119G	possibly damaging	Het
Tpgs1	A	T	10: 79,669,491	N28Y	probably benign	Het
U2surp	A	C	9: 95,462,794		probably benign	Het
Vmn2r103	A	G	17: 19,773,511	H50R	probably benign	Het
Vmn2r19	A	G	6: 123,329,910	N459S	probably benign	Het
Vmn2r72	T	C	7: 85,738,485	S624G	probably damaging	Het
Vps13c	A	G	9: 67,919,321	T1415A	probably benign	Het
Vwa5b1	G	A	4: 138,608,843	P147S	probably damaging	Het

Other mutations in Psd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00850:Psd4	APN	2	24394286	missense	probably benign	0.25
IGL01302:Psd4	APN	2	24396787	critical splice donor site	probably null
IGL01446:Psd4	APN	2	24405395	missense	probably damaging	1.00
IGL01577:Psd4	APN	2	24403222	missense	probably damaging	0.96
IGL01823:Psd4	APN	2	24394432	missense	probably benign	0.27
IGL02103:Psd4	APN	2	24400528	nonsense	probably null
IGL02212:Psd4	APN	2	24405314	nonsense	probably null
IGL02240:Psd4	APN	2	24396377	missense	probably benign	0.00
IGL02261:Psd4	APN	2	24401744	missense	probably damaging	1.00
IGL02345:Psd4	APN	2	24401823	critical splice donor site	probably null
IGL03272:Psd4	APN	2	24405680	splice site	probably benign
bitcoin	UTSW	2	24401557	missense	probably damaging	1.00
crypto	UTSW	2	24397247	missense	probably benign
Ethereum	UTSW	2	24406984	missense	probably damaging	1.00
underworld	UTSW	2	24405351	missense	probably damaging	1.00
PIT4469001:Psd4	UTSW	2	24394294	missense	probably benign	0.08
R0131:Psd4	UTSW	2	24405351	missense	probably damaging	1.00
R0131:Psd4	UTSW	2	24405351	missense	probably damaging	1.00
R0132:Psd4	UTSW	2	24405351	missense	probably damaging	1.00
R0278:Psd4	UTSW	2	24394438	missense	probably damaging	1.00
R1303:Psd4	UTSW	2	24395018	missense	probably benign	0.00
R1551:Psd4	UTSW	2	24403280	missense	probably benign	0.02
R1715:Psd4	UTSW	2	24405332	missense	probably damaging	1.00
R1854:Psd4	UTSW	2	24397456	missense	probably benign	0.26
R1942:Psd4	UTSW	2	24405793	missense	probably damaging	1.00
R2392:Psd4	UTSW	2	24394667	missense	probably damaging	0.98
R2420:Psd4	UTSW	2	24401241	missense	probably damaging	1.00
R4509:Psd4	UTSW	2	24396335	missense	probably benign
R4512:Psd4	UTSW	2	24402889	missense	probably damaging	1.00
R4558:Psd4	UTSW	2	24404794	missense	probably damaging	1.00
R5120:Psd4	UTSW	2	24405438	missense	probably benign
R5314:Psd4	UTSW	2	24400516	missense	possibly damaging	0.89
R5563:Psd4	UTSW	2	24394885	missense	probably benign
R5638:Psd4	UTSW	2	24397415	missense	probably benign	0.14
R6191:Psd4	UTSW	2	24394487	missense	probably damaging	1.00
R6224:Psd4	UTSW	2	24401557	missense	probably damaging	1.00
R7024:Psd4	UTSW	2	24394543	missense	possibly damaging	0.76
R7046:Psd4	UTSW	2	24394973	missense	probably benign	0.05
R7209:Psd4	UTSW	2	24397345	missense	probably damaging	1.00
R7483:Psd4	UTSW	2	24404756	missense	possibly damaging	0.65
R7498:Psd4	UTSW	2	24406984	missense	probably damaging	1.00
R7571:Psd4	UTSW	2	24407011	missense	probably damaging	1.00
R7741:Psd4	UTSW	2	24401096	critical splice donor site	probably null
R7978:Psd4	UTSW	2	24404855	missense	probably damaging	1.00
R8133:Psd4	UTSW	2	24396689	missense	probably benign
R8254:Psd4	UTSW	2	24403211	missense	probably damaging	0.99
R8786:Psd4	UTSW	2	24405432	missense	probably benign	0.08
R8797:Psd4	UTSW	2	24397428	missense	probably benign	0.02
R9015:Psd4	UTSW	2	24397480	missense
R9413:Psd4	UTSW	2	24397460	missense	probably benign	0.39
X0009:Psd4	UTSW	2	24401525	missense	probably damaging	1.00
X0064:Psd4	UTSW	2	24404738	missense	probably damaging	0.99
Z1177:Psd4	UTSW	2	24394912	missense	possibly damaging	0.95
Z1177:Psd4	UTSW	2	24394931	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TCTGCCACCAGATAGACAGG -3'
(R):5'- CTTCCTTTAGGGAGCTCAACTC -3'

Sequencing Primer
(F):5'- GGGGATATCAGTGTCTATAGCAGTAC -3'
(R):5'- AGGGAGCTCAACTCTGATCTATC -3'

Posted On

2016-05-10