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

Accession Numbers

Genbank: NM_028707

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6925 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35964830-36014715 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 35979711 bp (GRCm38)

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
5430419D17Rik	A	G	7: 131,222,707	Q177R	possibly damaging	Het
Acat1	A	T	9: 53,592,029	V170E	probably benign	Het
Atp2b2	T	A	6: 113,760,720	I902F	probably damaging	Het
Cacna1d	A	G	14: 30,051,637	V1697A	probably benign	Het
Ccdc14	T	A	16: 34,690,749	F31Y	probably benign	Het
Ccdc17	T	A	4: 116,598,210	V250E	probably damaging	Het
Cct7	A	G	6: 85,459,182	N25S	probably damaging	Het
Cep19	G	C	16: 32,103,942	G9R	probably damaging	Het
Ces5a	A	T	8: 93,523,057		probably null	Het
Chd1l	T	G	3: 97,582,826	E471A	probably damaging	Het
Chd6	A	G	2: 161,013,127	I787T	probably damaging	Het
Cntnap5c	A	C	17: 58,395,266	T1194P	probably benign	Het
Col6a3	T	A	1: 90,816,002	M208L	probably benign	Het
Coro7	A	T	16: 4,628,674		probably null	Het
Csrnp2	T	C	15: 100,481,958	K484R	probably benign	Het
Cyp2c39	T	A	19: 39,513,195	V64E	probably damaging	Het
Ddr2	T	C	1: 169,998,132	K300E	probably benign	Het
Ddx56	T	C	11: 6,263,980	E393G	probably damaging	Het
Diaph1	A	C	18: 37,853,679	Y1084*	probably null	Het
Disp1	A	T	1: 183,086,478	F1459L	probably benign	Het
Dnajc8	G	A	4: 132,544,113	A80T	probably damaging	Het
Elfn1	T	A	5: 139,971,685	M148K	probably benign	Het
Emcn	T	A	3: 137,419,002	I154N	probably damaging	Het
Enah	C	G	1: 181,905,898		probably null	Het
Enah	T	A	1: 181,905,899		probably null	Het
Ep300	C	A	15: 81,649,981	Q2080K	probably benign	Het
Epha2	T	A	4: 141,308,757	M168K	probably benign	Het
Ercc6	T	A	14: 32,562,608	I776N	probably damaging	Het
Fan1	T	A	7: 64,372,486	N340Y	probably damaging	Het
Fat4	G	T	3: 38,996,204		probably null	Het
G3bp1	A	G	11: 55,497,960	R333G	possibly damaging	Het
Gm3604	A	G	13: 62,369,390	F385L	probably benign	Het
Gm5800	T	C	14: 51,713,700	I147M	possibly damaging	Het
Hipk1	A	G	3: 103,778,245	F18S	unknown	Het
Ighv3-8	A	T	12: 114,322,330	C131S	probably benign	Het
Il23r	T	G	6: 67,423,493	T618P	probably damaging	Het
Il31ra	G	A	13: 112,527,529	T538I	possibly damaging	Het
Kcns2	A	G	15: 34,839,913	D474G	unknown	Het
Klc4	T	C	17: 46,636,229	T407A	possibly damaging	Het
Klra5	C	T	6: 129,911,457	S2N	probably benign	Het
Krt10	T	C	11: 99,388,851	Y161C	probably damaging	Het
Kxd1	A	T	8: 70,523,278	M1K	probably null	Het
Lgals1	A	C	15: 78,928,040	D27A	possibly damaging	Het
Lgr5	T	C	10: 115,466,346	S308G	probably benign	Het
Lrp1	G	A	10: 127,556,988	S2736L	probably benign	Het
Lrpap1	G	T	5: 35,102,536	H73N	probably benign	Het
Mcpt1	C	A	14: 56,019,065	T86K	probably damaging	Het
Megf6	A	T	4: 154,254,587	D527V	probably damaging	Het
Mical3	A	T	6: 120,959,390	S1392T	probably benign	Het
Mmp2	A	T	8: 92,839,382	D437V	probably damaging	Het
Mob4	T	A	1: 55,152,722	Y166*	probably null	Het
Mrap2	G	A	9: 87,182,474	M89I	possibly damaging	Het
Mug1	G	A	6: 121,881,787	A1155T	probably damaging	Het
Myh2	G	T	11: 67,193,218	A1556S	probably benign	Het
Nfatc3	A	G	8: 106,119,322	D1028G	probably benign	Het
Ngef	T	G	1: 87,503,263		probably null	Het
Nlrp1a	A	T	11: 71,092,513	L1209Q	probably null	Het
Npr2	C	T	4: 43,647,553	R819C	probably damaging	Het
Nsd2	A	T	5: 33,879,110	D646V	probably damaging	Het
Nsun7	A	G	5: 66,277,072	H252R	probably damaging	Het
Olfr267	A	T	4: 58,785,647	I25N	possibly damaging	Het
Olfr447	T	A	6: 42,911,857	C111*	probably null	Het
Olfr642	C	T	7: 104,049,740	V205I	probably benign	Het
Olfr951	A	T	9: 39,393,860	Q20L	probably benign	Het
Olfr951	G	T	9: 39,393,861	Q20H	probably benign	Het
Pcdhga2	A	T	18: 37,670,585	D494V	probably damaging	Het
Pcsk2	A	G	2: 143,813,747	E617G	probably damaging	Het
Pdc	T	C	1: 150,333,180	I138T	probably damaging	Het
Phc2	T	A	4: 128,748,134	S750T	probably damaging	Het
Pkd2l1	T	A	19: 44,191,508	N88Y	possibly damaging	Het
Plcl1	C	T	1: 55,406,598	R71*	probably null	Het
Prag1	C	A	8: 36,103,894	L544M	probably damaging	Het
Prkg2	A	G	5: 98,966,510		probably null	Het
Rab11fip1	A	T	8: 27,152,972	S600T	probably damaging	Het
Rbms1	T	G	2: 60,762,304	T222P	probably benign	Het
Slfn8	A	T	11: 83,013,417	Y382*	probably null	Het
Socs4	T	A	14: 47,289,738	C43*	probably null	Het
Sorl1	T	A	9: 42,033,626	T868S	probably damaging	Het
St6gal1	A	G	16: 23,356,213	Y267C	probably damaging	Het
Syne1	A	G	10: 5,126,682	V6879A	probably benign	Het
Syne2	C	A	12: 75,854,132	H22N	possibly damaging	Het
Tmeff2	T	A	1: 50,928,021	L25Q	probably damaging	Het
Tmprss11g	G	T	5: 86,487,426	D396E	probably benign	Het
Tmprss11g	T	A	5: 86,487,436	H393L	probably benign	Het
Vmn2r23	A	G	6: 123,704,553	E140G	probably damaging	Het
Wapl	T	C	14: 34,677,363	S130P	probably benign	Het
Zeb2	T	A	2: 44,994,529	K982M	probably damaging	Het
Zfhx3	C	G	8: 108,956,821	H3631D	unknown	Het
Zfp719	T	C	7: 43,590,706	S573P	probably damaging	Het
Zfp979	A	T	4: 147,613,542	C237S	possibly damaging	Het

Other mutations in Psd2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01486:Psd2	APN	18	35980335	missense	probably benign	0.00
IGL01578:Psd2	APN	18	35979785	missense	probably damaging	1.00
IGL02086:Psd2	APN	18	36005906	missense	probably damaging	1.00
IGL02132:Psd2	APN	18	36004756	splice site	probably benign
IGL02480:Psd2	APN	18	36006083	missense	probably damaging	1.00
IGL02726:Psd2	APN	18	35987302	critical splice donor site	probably null
Arachnida	UTSW	18	36006723	splice site	probably null
recluse	UTSW	18	35979711	missense	probably damaging	1.00
widow	UTSW	18	35980425	missense	probably damaging	0.99
3-1:Psd2	UTSW	18	35984401	missense	probably damaging	1.00
R0103:Psd2	UTSW	18	36004717	missense	probably damaging	1.00
R0103:Psd2	UTSW	18	36004717	missense	probably damaging	1.00
R0320:Psd2	UTSW	18	35979644	missense	probably damaging	1.00
R0573:Psd2	UTSW	18	35980493	splice site	probably benign
R0685:Psd2	UTSW	18	36002991	missense	possibly damaging	0.90
R0698:Psd2	UTSW	18	36012711	missense	probably benign	0.22
R0730:Psd2	UTSW	18	35978574	missense	possibly damaging	0.85
R0971:Psd2	UTSW	18	35979786	missense	probably damaging	1.00
R1085:Psd2	UTSW	18	36012777	missense	probably benign	0.10
R1535:Psd2	UTSW	18	36005790	missense	probably benign	0.31
R2056:Psd2	UTSW	18	36006691	missense	possibly damaging	0.60
R4011:Psd2	UTSW	18	35987247	missense	probably benign	0.01
R4246:Psd2	UTSW	18	36006119	missense	probably damaging	1.00
R4335:Psd2	UTSW	18	36007530	missense	probably damaging	0.96
R4584:Psd2	UTSW	18	36012828	missense	probably benign
R4942:Psd2	UTSW	18	35978664	missense	probably damaging	1.00
R5120:Psd2	UTSW	18	35979810	missense	possibly damaging	0.92
R5373:Psd2	UTSW	18	36007503	missense	probably damaging	1.00
R5374:Psd2	UTSW	18	36007503	missense	probably damaging	1.00
R5839:Psd2	UTSW	18	36007524	missense	probably damaging	0.97
R6200:Psd2	UTSW	18	36006723	splice site	probably null
R6967:Psd2	UTSW	18	35980332	missense	probably damaging	0.97
R7074:Psd2	UTSW	18	36010684	missense	probably benign	0.03
R7142:Psd2	UTSW	18	35980044	missense	possibly damaging	0.85
R7239:Psd2	UTSW	18	35980419	missense	probably damaging	1.00
R7348:Psd2	UTSW	18	35980336	missense	possibly damaging	0.85
R7581:Psd2	UTSW	18	35979997	missense	probably benign	0.01
R7793:Psd2	UTSW	18	36002979	missense	probably benign	0.37
R8221:Psd2	UTSW	18	35980425	missense	probably damaging	0.99
R8310:Psd2	UTSW	18	35979713	missense	probably damaging	1.00
R8939:Psd2	UTSW	18	35988239	missense	probably damaging	0.98
R9463:Psd2	UTSW	18	36010745	missense	probably damaging	0.98
X0065:Psd2	UTSW	18	36002942	missense	possibly damaging	0.92
Z1177:Psd2	UTSW	18	35978280	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