Mutagenetix > Incidental Mutations

Incidental Mutation 'R7348:Psd2'

570393

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 #

R7348 (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 35980336 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Asparagine at position 287 (S287N)

Ref Sequence

ENSEMBL: ENSMUSP00000135795 (fasta)

Gene Model

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115716
AA Change: S287N

PolyPhen 2 Score 0.759 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: S287N

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

possibly damaging
Transcript: ENSMUST00000175734
AA Change: S287N

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: S287N

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

possibly damaging
Transcript: ENSMUST00000176472
AA Change: S287N

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: S287N

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

possibly damaging
Transcript: ENSMUST00000176873
AA Change: S287N

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: S287N

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

possibly damaging
Transcript: ENSMUST00000177432
AA Change: S287N

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: S287N

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.8%

Validation Efficiency

99% (80/81)

Allele List at MGI

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

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abra	G	A	15: 41,866,159	R282C	probably damaging	Het
Adcy2	T	A	13: 68,734,675	E314D	possibly damaging	Het
Adgrl2	A	T	3: 148,817,766	I274N		Het
Adpgk	A	G	9: 59,313,786	I292V	probably benign	Het
Agtrap	G	T	4: 148,080,597	F124L	probably benign	Het
Ankrd26	A	G	6: 118,508,564	Y1450H	probably damaging	Het
Ap4e1	A	T	2: 127,061,976	S933C	probably damaging	Het
Ap4e1	G	T	2: 127,061,977	S933I	possibly damaging	Het
Ap5s1	A	T	2: 131,212,652	T128S	possibly damaging	Het
Arih1	T	C	9: 59,486,058	Y97C	probably damaging	Het
Atp1a3	A	G	7: 24,978,826	F1034S	unknown	Het
Bmp6	T	C	13: 38,485,903	S388P	probably benign	Het
Ccdc39	A	G	3: 33,832,676	V261A	possibly damaging	Het
Ccdc66	C	T	14: 27,500,336	C150Y	probably damaging	Het
Cep89	G	A	7: 35,429,928	R630H	probably damaging	Het
Cln6	A	G	9: 62,849,176	S201G	probably benign	Het
Cntnap4	T	C	8: 112,665,277	Y125H	probably damaging	Het
Copa	A	G	1: 172,102,223	T286A	possibly damaging	Het
Cul9	A	T	17: 46,510,993	I1852K	possibly damaging	Het
Cyp2j8	C	A	4: 96,444,640	A490S	probably benign	Het
Cyp2t4	A	G	7: 27,157,251	I239V	probably benign	Het
E2f7	C	T	10: 110,780,975	T692I	probably damaging	Het
Fastkd5	A	G	2: 130,615,135	Y512H	probably damaging	Het
Fastkd5	A	C	2: 130,616,439	M77R	probably benign	Het
Fhod3	A	G	18: 25,090,467	R957G	possibly damaging	Het
Gm17018	A	G	19: 45,572,466	Y111C	probably damaging	Het
H6pd	C	A	4: 149,983,902		probably null	Het
Haus5	G	T	7: 30,656,966	P544Q	possibly damaging	Het
Ifi207	CTGTTGATGAAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG	CTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG	1: 173,729,196		probably benign	Het
Igf2r	A	G	17: 12,703,484	Y1248H	probably damaging	Het
Izumo3	T	C	4: 92,147,218	N6S	possibly damaging	Het
Lrp6	G	T	6: 134,450,818	P1604T	probably damaging	Het
Map3k8	T	A	18: 4,340,561	H251L	probably damaging	Het
Mapre3	T	C	5: 30,861,829	Y6H	probably benign	Het
Mlh3	G	T	12: 85,267,441	P657Q	probably damaging	Het
Mrgpra1	T	C	7: 47,335,409	Y174C	probably benign	Het
Ms4a6d	G	A	19: 11,590,073	Q155*	probably null	Het
Myh1	C	A	11: 67,202,539	P152Q	probably damaging	Het
Myh6	A	T	14: 54,952,259	L1110Q	probably damaging	Het
Nf1	T	A	11: 79,536,850	S1778T	probably benign	Het
Nkpd1	G	A	7: 19,524,416	E707K	probably damaging	Het
Nlrp4a	A	G	7: 26,444,273	E21G	probably damaging	Het
Nr4a3	T	G	4: 48,051,290	S15A	possibly damaging	Het
Olfr1354	A	G	10: 78,917,562	T241A	probably damaging	Het
Olfr453	T	C	6: 42,744,856	L273S	possibly damaging	Het
Olfr488	T	C	7: 108,256,123	D5G	probably benign	Het
Olfr491	T	C	7: 108,317,713	V273A	possibly damaging	Het
Parg	G	A	14: 32,250,079	R677Q	possibly damaging	Het
Pcsk5	A	T	19: 17,456,818	C1395*	probably null	Het
Psd3	T	C	8: 67,790,931	N685S	possibly damaging	Het
Pygb	C	T	2: 150,786,983	T39M	probably benign	Het
Rbfox1	C	A	16: 7,408,024	Y351*	probably null	Het
Rftn1	A	G	17: 50,004,323	L396P	probably damaging	Het
S1pr1	A	G	3: 115,712,061	Y295H	probably damaging	Het
Scn5a	T	C	9: 119,535,833	M440V	probably benign	Het
Sel1l2	T	C	2: 140,265,724	N240S	probably benign	Het
Skint1	T	C	4: 112,021,573	L234P	probably damaging	Het
Skint11	T	A	4: 114,244,722	Y311N	probably benign	Het
Slc6a5	A	T	7: 49,910,167		probably benign	Het
Tas2r134	T	C	2: 51,628,402	S298P	possibly damaging	Het
Tbcd	C	A	11: 121,594,311	A773D	probably benign	Het
Tgoln1	G	C	6: 72,616,278	T73R	probably benign	Het
Tmem184a	T	C	5: 139,814,054	E24G	probably null	Het
Tmem207	C	A	16: 26,516,827	W53C	possibly damaging	Het
Tns1	T	A	1: 73,916,917	H549L	possibly damaging	Het
Ttc37	T	C	13: 76,182,884	F1478L	possibly damaging	Het
Ttc41	G	T	10: 86,750,348	E839*	probably null	Het
Ufd1	T	G	16: 18,815,885		probably benign	Het
Usp28	A	G	9: 49,030,877	E713G	probably benign	Het
Utrn	A	G	10: 12,748,018	W159R	probably damaging	Het
Vcl	C	T	14: 21,003,150	A411V	probably benign	Het
Vcl	T	A	14: 21,008,952	C545*	probably null	Het
Vmn1r120	A	T	7: 21,053,452	S111R	probably damaging	Het
Wwox	T	A	8: 114,472,652	C146S	probably benign	Het
Zbtb2	T	C	10: 4,374,574	T57A	possibly damaging	Het
Zfp362	T	C	4: 128,777,217	D336G	possibly damaging	Het
Zfp628	G	A	7: 4,921,818	G1013E	probably damaging	Het
Zfp704	A	G	3: 9,474,598	S231P	probably damaging	Het
Zhx3	G	T	2: 160,782,118	S43*	probably null	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
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
R6925:Psd2	UTSW	18	35979711	missense	probably damaging	1.00
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
R7581:Psd2	UTSW	18	35979997	missense	probably benign	0.01
X0065:Psd2	UTSW	18	36002942	missense	possibly damaging	0.92

Predicted Primers

PCR Primer
(F):5'- GTCAAGGCTGTCTGTCTGTC -3'
(R):5'- TTCCTGCTGAAGAAGGCATAGG -3'

Sequencing Primer
(F):5'- GTCTGGATGCTCCCCTGCTG -3'
(R):5'- AAGGCATAGGATCTGCTTTGCC -3'

Posted On

2019-09-13