Mutagenetix > Incidental Mutation

Incidental Mutation 'R6925:Psd2'

541131

Institutional Source

Beutler Lab

Gene Symbol

Psd2

Ensembl Gene

ENSMUSG00000024347

Gene Name

pleckstrin and Sec7 domain containing 2

Synonyms

EFA6C, 6330404E20Rik

MMRRC Submission

045043-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6925 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

36097883-36147768 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 36112764 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Asparagine at position 153 (S153N)

Ref Sequence

ENSEMBL: ENSMUSP00000135431 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000115716] [ENSMUST00000175734] [ENSMUST00000176472] [ENSMUST00000176873] [ENSMUST00000177432]

AlphaFold

Q6P1I6

Predicted Effect

probably damaging
Transcript: ENSMUST00000115716
AA Change: S153N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: S153N

Domain	Start	End	E-Value	Type
low complexity region	153	169	N/A	INTRINSIC
low complexity region	216	234	N/A	INTRINSIC
low complexity region	247	264	N/A	INTRINSIC
Sec7	270	461	4.69e-56	SMART
PH	510	624	4.35e-14	SMART
Blast:Sec7	653	705	4e-24	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000175734
AA Change: S153N

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

SMART Domains

Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: S153N

Domain	Start	End	E-Value	Type
low complexity region	153	169	N/A	INTRINSIC
low complexity region	216	234	N/A	INTRINSIC
low complexity region	247	264	N/A	INTRINSIC
Sec7	270	462	4.1e-55	SMART
PH	511	625	1.9e-16	SMART
Blast:Sec7	654	706	4e-24	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000176472
AA Change: S153N

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

SMART Domains

Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: S153N

Domain	Start	End	E-Value	Type
low complexity region	153	169	N/A	INTRINSIC
low complexity region	216	234	N/A	INTRINSIC
low complexity region	247	264	N/A	INTRINSIC
Sec7	270	461	4.69e-56	SMART
Pfam:PH_9	511	553	4.5e-12	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000176873
AA Change: S153N

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

SMART Domains

Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: S153N

Domain	Start	End	E-Value	Type
low complexity region	153	169	N/A	INTRINSIC
low complexity region	216	234	N/A	INTRINSIC
low complexity region	247	264	N/A	INTRINSIC
Sec7	270	462	4.2e-55	SMART
PH	511	625	1.9e-16	SMART
Blast:Sec7	654	706	4e-24	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000177432
AA Change: S153N

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

SMART Domains

Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: S153N

Domain	Start	End	E-Value	Type
low complexity region	153	169	N/A	INTRINSIC
low complexity region	216	234	N/A	INTRINSIC
low complexity region	247	264	N/A	INTRINSIC
Sec7	270	461	4.69e-56	SMART
PH	510	621	5.36e-14	SMART
Blast:Sec7	650	702	4e-24	BLAST

Meta Mutation Damage Score

0.0877

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.0%

Validation Efficiency

100% (91/91)

Allele List at MGI

All alleles(2) : Targeted, other(2)

Other mutations in this stock

Total: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acat1	A	T	9: 53,503,329 (GRCm39)	V170E	probably benign	Het
Atp2b2	T	A	6: 113,737,681 (GRCm39)	I902F	probably damaging	Het
Cacna1d	A	G	14: 29,773,594 (GRCm39)	V1697A	probably benign	Het
Ccdc14	T	A	16: 34,511,119 (GRCm39)	F31Y	probably benign	Het
Ccdc17	T	A	4: 116,455,407 (GRCm39)	V250E	probably damaging	Het
Cct7	A	G	6: 85,436,164 (GRCm39)	N25S	probably damaging	Het
Cdcp3	A	G	7: 130,824,436 (GRCm39)	Q177R	possibly damaging	Het
Cep19	G	C	16: 31,922,760 (GRCm39)	G9R	probably damaging	Het
Ces5a	A	T	8: 94,249,685 (GRCm39)		probably null	Het
Chd1l	T	G	3: 97,490,142 (GRCm39)	E471A	probably damaging	Het
Chd6	A	G	2: 160,855,047 (GRCm39)	I787T	probably damaging	Het
Cntnap5c	A	C	17: 58,702,261 (GRCm39)	T1194P	probably benign	Het
Col6a3	T	A	1: 90,743,724 (GRCm39)	M208L	probably benign	Het
Coro7	A	T	16: 4,446,538 (GRCm39)		probably null	Het
Csrnp2	T	C	15: 100,379,839 (GRCm39)	K484R	probably benign	Het
Cyp2c39	T	A	19: 39,501,639 (GRCm39)	V64E	probably damaging	Het
Ddr2	T	C	1: 169,825,701 (GRCm39)	K300E	probably benign	Het
Ddx56	T	C	11: 6,213,980 (GRCm39)	E393G	probably damaging	Het
Diaph1	A	C	18: 37,986,732 (GRCm39)	Y1084*	probably null	Het
Disp1	A	T	1: 182,868,042 (GRCm39)	F1459L	probably benign	Het
Dnajc8	G	A	4: 132,271,424 (GRCm39)	A80T	probably damaging	Het
Elfn1	T	A	5: 139,957,440 (GRCm39)	M148K	probably benign	Het
Emcn	T	A	3: 137,124,763 (GRCm39)	I154N	probably damaging	Het
Enah	T	A	1: 181,733,464 (GRCm39)		probably null	Het
Enah	C	G	1: 181,733,463 (GRCm39)		probably null	Het
Ep300	C	A	15: 81,534,182 (GRCm39)	Q2080K	probably benign	Het
Epha2	T	A	4: 141,036,068 (GRCm39)	M168K	probably benign	Het
Ercc6	T	A	14: 32,284,565 (GRCm39)	I776N	probably damaging	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Fat4	G	T	3: 39,050,353 (GRCm39)		probably null	Het
G3bp1	A	G	11: 55,388,786 (GRCm39)	R333G	possibly damaging	Het
Gm3604	A	G	13: 62,517,204 (GRCm39)	F385L	probably benign	Het
Gm5800	T	C	14: 51,951,157 (GRCm39)	I147M	possibly damaging	Het
Hipk1	A	G	3: 103,685,561 (GRCm39)	F18S	unknown	Het
Ighv3-8	A	T	12: 114,285,950 (GRCm39)	C131S	probably benign	Het
Il23r	T	G	6: 67,400,477 (GRCm39)	T618P	probably damaging	Het
Il31ra	G	A	13: 112,664,063 (GRCm39)	T538I	possibly damaging	Het
Kcns2	A	G	15: 34,840,059 (GRCm39)	D474G	unknown	Het
Klc4	T	C	17: 46,947,155 (GRCm39)	T407A	possibly damaging	Het
Klra5	C	T	6: 129,888,420 (GRCm39)	S2N	probably benign	Het
Krt10	T	C	11: 99,279,677 (GRCm39)	Y161C	probably damaging	Het
Kxd1	A	T	8: 70,975,928 (GRCm39)	M1K	probably null	Het
Lgals1	A	C	15: 78,812,240 (GRCm39)	D27A	possibly damaging	Het
Lgr5	T	C	10: 115,302,251 (GRCm39)	S308G	probably benign	Het
Lrp1	G	A	10: 127,392,857 (GRCm39)	S2736L	probably benign	Het
Lrpap1	G	T	5: 35,259,880 (GRCm39)	H73N	probably benign	Het
Mcpt1	C	A	14: 56,256,522 (GRCm39)	T86K	probably damaging	Het
Megf6	A	T	4: 154,339,044 (GRCm39)	D527V	probably damaging	Het
Mical3	A	T	6: 120,936,351 (GRCm39)	S1392T	probably benign	Het
Mmp2	A	T	8: 93,566,010 (GRCm39)	D437V	probably damaging	Het
Mob4	T	A	1: 55,191,881 (GRCm39)	Y166*	probably null	Het
Mrap2	G	A	9: 87,064,527 (GRCm39)	M89I	possibly damaging	Het
Mug1	G	A	6: 121,858,746 (GRCm39)	A1155T	probably damaging	Het
Myh2	G	T	11: 67,084,044 (GRCm39)	A1556S	probably benign	Het
Nfatc3	A	G	8: 106,845,954 (GRCm39)	D1028G	probably benign	Het
Ngef	T	G	1: 87,430,985 (GRCm39)		probably null	Het
Nlrp1a	A	T	11: 70,983,339 (GRCm39)	L1209Q	probably null	Het
Npr2	C	T	4: 43,647,553 (GRCm39)	R819C	probably damaging	Het
Nsd2	A	T	5: 34,036,454 (GRCm39)	D646V	probably damaging	Het
Nsun7	A	G	5: 66,434,415 (GRCm39)	H252R	probably damaging	Het
Or2a25	T	A	6: 42,888,791 (GRCm39)	C111*	probably null	Het
Or2k2	A	T	4: 58,785,647 (GRCm39)	I25N	possibly damaging	Het
Or51a10	C	T	7: 103,698,947 (GRCm39)	V205I	probably benign	Het
Or8g32	A	T	9: 39,305,156 (GRCm39)	Q20L	probably benign	Het
Or8g32	G	T	9: 39,305,157 (GRCm39)	Q20H	probably benign	Het
Pcdhga2	A	T	18: 37,803,638 (GRCm39)	D494V	probably damaging	Het
Pcsk2	A	G	2: 143,655,667 (GRCm39)	E617G	probably damaging	Het
Pdc	T	C	1: 150,208,931 (GRCm39)	I138T	probably damaging	Het
Phc2	T	A	4: 128,641,927 (GRCm39)	S750T	probably damaging	Het
Pkd2l1	T	A	19: 44,179,947 (GRCm39)	N88Y	possibly damaging	Het
Plcl1	C	T	1: 55,445,757 (GRCm39)	R71*	probably null	Het
Prag1	C	A	8: 36,571,048 (GRCm39)	L544M	probably damaging	Het
Prkg2	A	G	5: 99,114,369 (GRCm39)		probably null	Het
Rab11fip1	A	T	8: 27,643,000 (GRCm39)	S600T	probably damaging	Het
Rbms1	T	G	2: 60,592,648 (GRCm39)	T222P	probably benign	Het
Slfn8	A	T	11: 82,904,243 (GRCm39)	Y382*	probably null	Het
Socs4	T	A	14: 47,527,195 (GRCm39)	C43*	probably null	Het
Sorl1	T	A	9: 41,944,922 (GRCm39)	T868S	probably damaging	Het
St6gal1	A	G	16: 23,174,963 (GRCm39)	Y267C	probably damaging	Het
Syne1	A	G	10: 5,076,682 (GRCm39)	V6879A	probably benign	Het
Syne2	C	A	12: 75,900,906 (GRCm39)	H22N	possibly damaging	Het
Tmeff2	T	A	1: 50,967,180 (GRCm39)	L25Q	probably damaging	Het
Tmprss11g	G	T	5: 86,635,285 (GRCm39)	D396E	probably benign	Het
Tmprss11g	T	A	5: 86,635,295 (GRCm39)	H393L	probably benign	Het
Vmn2r23	A	G	6: 123,681,512 (GRCm39)	E140G	probably damaging	Het
Wapl	T	C	14: 34,399,320 (GRCm39)	S130P	probably benign	Het
Zeb2	T	A	2: 44,884,541 (GRCm39)	K982M	probably damaging	Het
Zfhx3	C	G	8: 109,683,453 (GRCm39)	H3631D	unknown	Het
Zfp719	T	C	7: 43,240,130 (GRCm39)	S573P	probably damaging	Het
Zfp979	A	T	4: 147,697,999 (GRCm39)	C237S	possibly damaging	Het

Other mutations in Psd2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01486:Psd2	APN	18	36,113,388 (GRCm39)	missense	probably benign	0.00
IGL01578:Psd2	APN	18	36,112,838 (GRCm39)	missense	probably damaging	1.00
IGL02086:Psd2	APN	18	36,138,959 (GRCm39)	missense	probably damaging	1.00
IGL02132:Psd2	APN	18	36,137,809 (GRCm39)	splice site	probably benign
IGL02480:Psd2	APN	18	36,139,136 (GRCm39)	missense	probably damaging	1.00
IGL02726:Psd2	APN	18	36,120,355 (GRCm39)	critical splice donor site	probably null
recluse	UTSW	18	36,112,764 (GRCm39)	missense	probably damaging	1.00
widow	UTSW	18	36,113,478 (GRCm39)	missense	probably damaging	0.99
3-1:Psd2	UTSW	18	36,117,454 (GRCm39)	missense	probably damaging	1.00
R0103:Psd2	UTSW	18	36,137,770 (GRCm39)	missense	probably damaging	1.00
R0103:Psd2	UTSW	18	36,137,770 (GRCm39)	missense	probably damaging	1.00
R0320:Psd2	UTSW	18	36,112,697 (GRCm39)	missense	probably damaging	1.00
R0573:Psd2	UTSW	18	36,113,546 (GRCm39)	splice site	probably benign
R0685:Psd2	UTSW	18	36,136,044 (GRCm39)	missense	possibly damaging	0.90
R0698:Psd2	UTSW	18	36,145,764 (GRCm39)	missense	probably benign	0.22
R0730:Psd2	UTSW	18	36,111,627 (GRCm39)	missense	possibly damaging	0.85
R0971:Psd2	UTSW	18	36,112,839 (GRCm39)	missense	probably damaging	1.00
R1085:Psd2	UTSW	18	36,145,830 (GRCm39)	missense	probably benign	0.10
R1535:Psd2	UTSW	18	36,138,843 (GRCm39)	missense	probably benign	0.31
R2056:Psd2	UTSW	18	36,139,744 (GRCm39)	missense	possibly damaging	0.60
R4011:Psd2	UTSW	18	36,120,300 (GRCm39)	missense	probably benign	0.01
R4246:Psd2	UTSW	18	36,139,172 (GRCm39)	missense	probably damaging	1.00
R4335:Psd2	UTSW	18	36,140,583 (GRCm39)	missense	probably damaging	0.96
R4584:Psd2	UTSW	18	36,145,881 (GRCm39)	missense	probably benign
R4942:Psd2	UTSW	18	36,111,717 (GRCm39)	missense	probably damaging	1.00
R5120:Psd2	UTSW	18	36,112,863 (GRCm39)	missense	possibly damaging	0.92
R5373:Psd2	UTSW	18	36,140,556 (GRCm39)	missense	probably damaging	1.00
R5374:Psd2	UTSW	18	36,140,556 (GRCm39)	missense	probably damaging	1.00
R5839:Psd2	UTSW	18	36,140,577 (GRCm39)	missense	probably damaging	0.97
R6200:Psd2	UTSW	18	36,139,776 (GRCm39)	splice site	probably null
R6967:Psd2	UTSW	18	36,113,385 (GRCm39)	missense	probably damaging	0.97
R7074:Psd2	UTSW	18	36,143,737 (GRCm39)	missense	probably benign	0.03
R7142:Psd2	UTSW	18	36,113,097 (GRCm39)	missense	possibly damaging	0.85
R7239:Psd2	UTSW	18	36,113,472 (GRCm39)	missense	probably damaging	1.00
R7348:Psd2	UTSW	18	36,113,389 (GRCm39)	missense	possibly damaging	0.85
R7581:Psd2	UTSW	18	36,113,050 (GRCm39)	missense	probably benign	0.01
R7793:Psd2	UTSW	18	36,136,032 (GRCm39)	missense	probably benign	0.37
R8221:Psd2	UTSW	18	36,113,478 (GRCm39)	missense	probably damaging	0.99
R8310:Psd2	UTSW	18	36,112,766 (GRCm39)	missense	probably damaging	1.00
R8939:Psd2	UTSW	18	36,121,292 (GRCm39)	missense	probably damaging	0.98
R9463:Psd2	UTSW	18	36,143,798 (GRCm39)	missense	probably damaging	0.98
X0065:Psd2	UTSW	18	36,135,995 (GRCm39)	missense	possibly damaging	0.92
Z1177:Psd2	UTSW	18	36,111,333 (GRCm39)	critical splice acceptor site	probably null

Predicted Primers

PCR Primer
(F):5'- TCCTAGCTAGAGACTGGTGG -3'
(R):5'- CAAGACATTCTCTGAGCGGC -3'

Sequencing Primer
(F):5'- GTGTGGTAGCTAGCCTTAGTGTC -3'
(R):5'- TAGAGATGGACCGCCTCAG -3'

Posted On

2018-11-28