Mutagenetix > Incidental Mutation

Incidental Mutation 'R4942:Psd2'

383232

Institutional Source

Beutler Lab

Gene Symbol

Psd2

Ensembl Gene

ENSMUSG00000024347

Gene Name

pleckstrin and Sec7 domain containing 2

Synonyms

EFA6C, 6330404E20Rik

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4942 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

36097883-36147768 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 36111717 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 114 (D114V)

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: D114V

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: D114V

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: D114V

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: D114V

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: D114V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: D114V

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: D114V

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: D114V

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: D114V

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: D114V

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: 99.0%
3x: 98.2%
10x: 96.0%
20x: 91.6%

Validation Efficiency

Allele List at MGI

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

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730522E02Rik	A	G	11: 25,720,472 (GRCm39)		probably null	Het
Adamts7	T	C	9: 90,045,364 (GRCm39)	S23P	probably benign	Het
Adamtsl1	T	A	4: 86,259,451 (GRCm39)	C824*	probably null	Het
Adgre1	A	G	17: 57,713,903 (GRCm39)	Y196C	probably damaging	Het
Arap1	A	G	7: 101,051,009 (GRCm39)	D542G	possibly damaging	Het
B3gat1	A	G	9: 26,666,894 (GRCm39)	D42G	probably benign	Het
Birc6	G	A	17: 74,930,045 (GRCm39)	A2412T	probably damaging	Het
Bnip5	T	C	17: 29,122,232 (GRCm39)	R420G	probably benign	Het
Bsn	A	G	9: 107,983,678 (GRCm39)	Y3459H	unknown	Het
Cacnb1	T	C	11: 97,893,809 (GRCm39)	Y571C	probably damaging	Het
Cdk2ap2	G	A	19: 4,147,508 (GRCm39)		probably null	Het
Cep57	A	G	9: 13,724,723 (GRCm39)	S265P	probably damaging	Het
Clca3a1	A	G	3: 144,710,524 (GRCm39)	I893T	probably benign	Het
Clca3a2	T	A	3: 144,512,263 (GRCm39)	E491V	probably damaging	Het
Cldn10	G	A	14: 119,025,725 (GRCm39)	G53S	possibly damaging	Het
Cobl	A	T	11: 12,204,185 (GRCm39)	I832N	probably damaging	Het
Col9a2	T	C	4: 120,910,316 (GRCm39)	V487A	possibly damaging	Het
Cse1l	C	T	2: 166,771,714 (GRCm39)	T325I	probably damaging	Het
Dlx6	A	G	6: 6,863,468 (GRCm39)	Q30R	probably benign	Het
Dnah8	T	C	17: 30,948,116 (GRCm39)	V1902A	probably benign	Het
Dusp8	A	G	7: 141,635,965 (GRCm39)	F542L	possibly damaging	Het
Emid1	T	G	11: 5,079,430 (GRCm39)	M323L	probably benign	Het
Ercc5	A	G	1: 44,215,125 (GRCm39)	D886G	probably benign	Het
Fam184b	T	C	5: 45,730,649 (GRCm39)	E461G	probably damaging	Het
Fbn1	C	A	2: 125,225,536 (GRCm39)	C572F	possibly damaging	Het
Gigyf1	G	T	5: 137,523,952 (GRCm39)	V1041L	possibly damaging	Het
Grin3b	A	G	10: 79,811,556 (GRCm39)	H714R	probably damaging	Het
Heatr1	A	G	13: 12,428,391 (GRCm39)		probably null	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Llgl1	C	T	11: 60,600,394 (GRCm39)	P581L	probably benign	Het
Lypd6b	C	A	2: 49,836,132 (GRCm39)	H104Q	probably benign	Het
Man1a	A	T	10: 53,809,586 (GRCm39)		probably null	Het
Megf6	A	T	4: 154,338,277 (GRCm39)	D449V	probably damaging	Het
Mtor	T	C	4: 148,556,599 (GRCm39)	V1003A	probably benign	Het
Ncan	C	A	8: 70,552,944 (GRCm39)	W1096L	probably damaging	Het
Ndor1	C	T	2: 25,138,133 (GRCm39)		probably null	Het
Ndufaf1	T	C	2: 119,490,547 (GRCm39)	E171G	possibly damaging	Het
Nell1	T	C	7: 49,770,397 (GRCm39)	V152A	possibly damaging	Het
Nherf4	C	A	9: 44,159,915 (GRCm39)	G402*	probably null	Het
Nt5dc1	A	T	10: 34,198,673 (GRCm39)	V255E	probably damaging	Het
Or2a20	T	A	6: 43,193,928 (GRCm39)	F27Y	probably damaging	Het
Or2y1b	A	T	11: 49,208,375 (GRCm39)	M1L	probably null	Het
Or52h7	A	G	7: 104,214,212 (GRCm39)	I261M	probably benign	Het
Or52z14	G	A	7: 103,253,401 (GRCm39)	R180H	probably benign	Het
Otud7a	T	C	7: 63,407,171 (GRCm39)	I50T	probably damaging	Het
P2ry13	G	A	3: 59,116,983 (GRCm39)	T265I	probably benign	Het
Pde4d	A	G	13: 108,996,733 (GRCm39)	S12G	probably benign	Het
Pigk	C	A	3: 152,450,154 (GRCm39)	N219K	probably damaging	Het
Plcg1	T	A	2: 160,595,509 (GRCm39)		probably null	Het
Ptch1	A	T	13: 63,672,884 (GRCm39)	I770N	probably benign	Het
Ptprq	A	T	10: 107,524,290 (GRCm39)	M481K	probably benign	Het
Rnf216	A	C	5: 143,078,814 (GRCm39)	M45R	probably damaging	Het
Rpsa	T	A	9: 119,960,129 (GRCm39)	W231R	probably benign	Het
Ryr1	G	T	7: 28,768,998 (GRCm39)	T2797N	probably damaging	Het
Ryr3	A	T	2: 112,666,602 (GRCm39)	M1468K	probably damaging	Het
Slc6a7	A	G	18: 61,137,589 (GRCm39)	Y244H	probably damaging	Het
Slco6c1	T	A	1: 97,009,049 (GRCm39)	D462V	probably damaging	Het
Spata31d1b	A	T	13: 59,864,917 (GRCm39)	E688D	possibly damaging	Het
Srpra	G	A	9: 35,126,766 (GRCm39)	R508H	probably benign	Het
Tnrc18	A	T	5: 142,773,737 (GRCm39)	I181N	unknown	Het
Tnrc6a	T	C	7: 122,791,836 (GRCm39)	F1785L	probably damaging	Het
Trio	A	T	15: 27,752,811 (GRCm39)	D2174E	probably benign	Het
Ttn	C	T	2: 76,623,600 (GRCm39)	V15326I	probably damaging	Het
Ubap2	T	A	4: 41,245,461 (GRCm39)		probably benign	Het
Vmn2r113	C	T	17: 23,177,321 (GRCm39)	P702S	probably damaging	Het
Vmn2r66	A	T	7: 84,656,980 (GRCm39)	W142R	probably damaging	Het
Vmn2r73	A	G	7: 85,519,582 (GRCm39)	Y459H	probably damaging	Het
Wsb2	C	T	5: 117,515,550 (GRCm39)	T385M	probably 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
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
R6925:Psd2	UTSW	18	36,112,764 (GRCm39)	missense	probably damaging	1.00
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'- TACCATGGAGCCTGTGAGAG -3'
(R):5'- CTGGTAGAGACAGACTACAGCC -3'

Sequencing Primer
(F):5'- CTGTGAGAGGCCCAGATGTG -3'
(R):5'- AGTACAGCAAGCCTGGTTGC -3'

Posted On

2016-04-27