Mutagenetix > Incidental Mutations

Incidental Mutation 'R0132:Psd4'

21670

Institutional Source

Beutler Lab

Gene Symbol

Psd4

Ensembl Gene

ENSMUSG00000026979

Gene Name

pleckstrin and Sec7 domain containing 4

Synonyms

SEC7 homolog, EFA6B

MMRRC Submission

038417-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0132 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

24367580-24414954 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 24405351 bp

Zygosity

Heterozygous

Amino Acid Change

Alanine to Glutamic Acid at position 839 (A839E)

Ref Sequence

ENSEMBL: ENSMUSP00000132395 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000056641
AA Change: A839E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000062415
Gene: ENSMUSG00000026979
AA Change: A839E

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 damaging
Transcript: ENSMUST00000102942
AA Change: A839E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000100006
Gene: ENSMUSG00000026979
AA Change: A839E

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

noncoding transcript
Transcript: ENSMUST00000132924

Predicted Effect

probably benign
Transcript: ENSMUST00000140303

Predicted Effect

probably damaging
Transcript: ENSMUST00000166388
AA Change: A839E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000132395
Gene: ENSMUSG00000026979
AA Change: A839E

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

0.6467

Coding Region Coverage

1x: 99.1%
3x: 97.9%
10x: 94.2%
20x: 84.8%

Validation Efficiency

90% (52/58)

Allele List at MGI

Other mutations in this stock

Total: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9530053A07Rik	A	G	7: 28,137,615	R320G	probably damaging	Het
Abcc12	A	G	8: 86,531,568	I773T	probably benign	Het
Adamtsl1	T	A	4: 86,342,723	I1057N	possibly damaging	Het
Anxa5	G	A	3: 36,450,672	A247V	probably damaging	Het
Ascc3	T	G	10: 50,735,329	W1589G	probably damaging	Het
Atp2b2	G	A	6: 113,793,782	P389S	probably damaging	Het
Bpifa6	T	A	2: 153,982,931	S9T	probably benign	Het
Chd8	A	G	14: 52,205,326	V589A	probably benign	Het
Chrnb2	T	C	3: 89,764,406	M1V	probably null	Het
Col16a1	T	A	4: 130,067,096	V449E	unknown	Het
Cttnbp2nl	T	G	3: 105,005,857	K237T	probably damaging	Het
Dazap1	T	G	10: 80,278,226		probably null	Het
Fam187b	T	A	7: 30,989,120	V22E	probably damaging	Het
Gm4788	T	A	1: 139,754,271	T196S	probably damaging	Het
H2-T24	T	A	17: 36,014,986	I238F	probably damaging	Het
Hectd4	A	G	5: 121,333,024	E2658G	probably benign	Het
Herc1	A	C	9: 66,480,910	I3826L	probably benign	Het
Hinfp	A	G	9: 44,299,763	C67R	probably damaging	Het
Hp1bp3	C	T	4: 138,237,209	S348F	probably damaging	Het
Hspg2	T	C	4: 137,551,887	Y3094H	probably damaging	Het
Htr1f	A	G	16: 64,926,728	V67A	probably damaging	Het
Iqcc	T	G	4: 129,616,599	E374D	probably damaging	Het
Kcnj9	T	C	1: 172,326,198	T120A	probably damaging	Het
Kitl	C	T	10: 100,087,364	P208S	probably benign	Het
Lpcat4	A	G	2: 112,246,748	Y479C	probably damaging	Het
Lrrc74b	T	C	16: 17,553,152	N227S	probably damaging	Het
Mdc1	T	A	17: 35,852,581	V1007D	probably damaging	Het
Mocos	T	G	18: 24,679,762	I571S	probably benign	Het
Myh8	A	G	11: 67,292,188	N659D	probably damaging	Het
Naip2	A	G	13: 100,183,788	V240A	probably benign	Het
Nap1l1	T	C	10: 111,485,509	S37P	probably benign	Het
Nin	T	G	12: 70,051,141	K515T	probably damaging	Het
Npl	T	A	1: 153,509,118	K258*	probably null	Het
Ntn4	T	A	10: 93,644,707	S98T	possibly damaging	Het
Olfr177	C	A	16: 58,872,906	M81I	probably benign	Het
Olfr372	C	T	8: 72,058,400	T240M	probably damaging	Het
Olfr417	T	C	1: 174,369,586	V223A	probably damaging	Het
Ppox	C	A	1: 171,279,275	A192S	possibly damaging	Het
Prkdc	T	C	16: 15,713,653	L1380S	probably benign	Het
Ptprn2	T	G	12: 116,722,091	F57V	probably damaging	Het
Ptprt	C	T	2: 162,278,110	V146I	probably benign	Het
R3hdm2	T	A	10: 127,498,453	M915K	probably damaging	Het
Rab26	C	T	17: 24,530,785		probably null	Het
Rnf213	A	G	11: 119,430,361	E1215G	probably benign	Het
Rprd2	T	C	3: 95,774,361	K407E	probably damaging	Het
Siah3	G	A	14: 75,456,134	V27I	possibly damaging	Het
Slc14a2	T	A	18: 78,192,123	N280Y	probably damaging	Het
Slc25a35	A	G	11: 68,971,960	Y247C	probably damaging	Het
Slc29a4	A	G	5: 142,705,530	D55G	probably benign	Het
Slc35d1	C	T	4: 103,208,181	V189I	probably benign	Het
Srrm1	G	A	4: 135,340,573	R322*	probably null	Het
Stac3	A	T	10: 127,503,650	R138S	probably damaging	Het
Tmem260	T	A	14: 48,483,322	C306*	probably null	Het
Tspyl1	A	G	10: 34,283,089	N270S	probably damaging	Het
Ugt2a2	T	A	5: 87,474,861	K293*	probably null	Het
Vmn2r102	A	C	17: 19,678,763	T456P	probably benign	Het
Vmn2r90	T	A	17: 17,712,249	S139R	probably benign	Het
Zmym2	A	G	14: 56,943,258	N876D	probably benign	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
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
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
R4995:Psd4	UTSW	2	24397247	missense	probably benign
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
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'- GAATGCCACCAACGACTGACTTTTG -3'
(R):5'- AGGATGCCTGAATCTACCTCTGCC -3'

Sequencing Primer
(F):5'- CCTCTGTCAGATAAAATTCAGTGCC -3'
(R):5'- GAATCTACCTCTGCCCTCCC -3'

Posted On

2013-04-11