Mutagenetix > Incidental Mutation

Incidental Mutation 'R0685:Psd2'

61151

Institutional Source

Beutler Lab

Gene Symbol

Psd2

Ensembl Gene

ENSMUSG00000024347

Gene Name

pleckstrin and Sec7 domain containing 2

Synonyms

EFA6C, 6330404E20Rik

MMRRC Submission

038870-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0685 (G1)

Quality Score

127

Status

Validated

Chromosome

Chromosomal Location

36097883-36147768 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 36136044 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 443 (D443G)

Ref Sequence

ENSEMBL: ENSMUSP00000135285 (fasta)

Gene Model

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

AlphaFold

Q6P1I6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115716
AA Change: D443G

PolyPhen 2 Score 0.828 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: D443G

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

noncoding transcript
Transcript: ENSMUST00000175720

Predicted Effect

possibly damaging
Transcript: ENSMUST00000175734
AA Change: D444G

PolyPhen 2 Score 0.627 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: D444G

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: D443G

PolyPhen 2 Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: D443G

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: D444G

PolyPhen 2 Score 0.627 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: D444G

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: D443G

PolyPhen 2 Score 0.828 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: D443G

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

0.5224

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.6%
20x: 95.6%

Validation Efficiency

98% (89/91)

Allele List at MGI

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

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020N01Rik	A	G	10: 21,469,337 (GRCm39)	D17G	probably damaging	Het
Abi3bp	A	G	16: 56,353,316 (GRCm39)	T82A	possibly damaging	Het
Adgre4	A	C	17: 56,099,035 (GRCm39)	E180D	probably benign	Het
Ankrd28	G	A	14: 31,465,407 (GRCm39)		probably benign	Het
Aoc3	A	G	11: 101,227,273 (GRCm39)	D382G	possibly damaging	Het
Apob	C	A	12: 8,060,742 (GRCm39)	R3075S	probably benign	Het
Aqr	A	G	2: 113,971,458 (GRCm39)	F459S	probably damaging	Het
Bcr	T	C	10: 74,967,475 (GRCm39)	W570R	probably damaging	Het
Bloc1s5	C	T	13: 38,787,895 (GRCm39)	R163K	probably benign	Het
Bod1	A	T	11: 31,619,267 (GRCm39)	N101K	possibly damaging	Het
Bysl	A	T	17: 47,913,396 (GRCm39)	S296T	probably benign	Het
Chl1	G	A	6: 103,685,503 (GRCm39)		probably null	Het
Clstn1	G	A	4: 149,731,312 (GRCm39)	A885T	probably benign	Het
Cyp3a25	G	T	5: 145,935,356 (GRCm39)	P87T	probably damaging	Het
Dync1h1	T	C	12: 110,623,626 (GRCm39)	V3633A	probably damaging	Het
Dynlt5	T	C	4: 102,859,735 (GRCm39)	Y96H	probably damaging	Het
Elp4	C	A	2: 105,622,622 (GRCm39)	C241F	possibly damaging	Het
Fat4	T	A	3: 39,055,327 (GRCm39)	F4182Y	probably benign	Het
Gabbr2	G	A	4: 46,787,521 (GRCm39)	H381Y	possibly damaging	Het
Gm10577	G	T	4: 100,877,515 (GRCm39)		probably benign	Het
Gm9955	G	T	18: 24,842,314 (GRCm39)		probably benign	Het
Gstm5	T	A	3: 107,804,635 (GRCm39)	I73N	probably damaging	Het
Gypa	T	A	8: 81,223,331 (GRCm39)		probably benign	Het
Hectd2	T	A	19: 36,546,831 (GRCm39)	V64D	probably damaging	Het
Igkv10-95	T	A	6: 68,657,543 (GRCm39)	Y20N	probably benign	Het
Il15	T	C	8: 83,064,188 (GRCm39)		probably benign	Het
Iqca1	C	A	1: 90,070,453 (GRCm39)	G133V	probably null	Het
Kiz	C	A	2: 146,697,978 (GRCm39)		probably benign	Het
Lcmt2	C	A	2: 120,969,721 (GRCm39)	S234I	probably benign	Het
Lilra5	A	G	7: 4,244,956 (GRCm39)		probably benign	Het
Lin37	T	C	7: 30,255,299 (GRCm39)	E187G	probably damaging	Het
Lrrc37	T	C	11: 103,507,714 (GRCm39)		probably benign	Het
Mcmdc2	T	A	1: 9,982,039 (GRCm39)		probably null	Het
Mctp1	T	C	13: 76,973,918 (GRCm39)		probably null	Het
Mdp1	C	A	14: 55,896,726 (GRCm39)	G112*	probably null	Het
Mmp15	T	C	8: 96,098,762 (GRCm39)	Y530H	possibly damaging	Het
Mtss2	T	C	8: 111,454,029 (GRCm39)		probably null	Het
Muc5ac	T	C	7: 141,361,446 (GRCm39)	S1586P	probably benign	Het
Nap1l5	A	T	6: 58,883,757 (GRCm39)	C66S	possibly damaging	Het
Ninl	G	T	2: 150,781,775 (GRCm39)	Q1237K	possibly damaging	Het
Or5p70	A	T	7: 107,994,470 (GRCm39)	T48S	possibly damaging	Het
Or9m1b	T	C	2: 87,836,762 (GRCm39)	E111G	probably damaging	Het
Orc6	T	G	8: 86,027,783 (GRCm39)	S37R	possibly damaging	Het
Papss1	A	C	3: 131,288,854 (GRCm39)	N119H	possibly damaging	Het
Phf13	A	T	4: 152,076,069 (GRCm39)	F278I	probably damaging	Het
Pole2	C	A	12: 69,258,187 (GRCm39)	A239S	probably damaging	Het
Ppt2	T	C	17: 34,845,546 (GRCm39)	D75G	probably damaging	Het
Psen1	C	A	12: 83,761,594 (GRCm39)	S132*	probably null	Het
Psme4	A	G	11: 30,828,415 (GRCm39)	T1812A	probably damaging	Het
Rasgrf1	T	C	9: 89,797,535 (GRCm39)		probably benign	Het
Reep3	A	G	10: 66,857,518 (GRCm39)		probably benign	Het
Rexo4	A	T	2: 26,848,586 (GRCm39)		probably benign	Het
Rnf6	A	C	5: 146,148,468 (GRCm39)	S183R	probably damaging	Het
Scai	A	T	2: 38,993,749 (GRCm39)	M297K	probably damaging	Het
Scn9a	A	T	2: 66,313,843 (GRCm39)	S1947R	probably benign	Het
Sema6c	T	C	3: 95,080,021 (GRCm39)	C772R	possibly damaging	Het
Skint7	T	C	4: 111,837,542 (GRCm39)	S107P	possibly damaging	Het
Slc24a3	A	G	2: 145,448,715 (GRCm39)	N420D	probably benign	Het
Smc1b	T	C	15: 84,955,021 (GRCm39)	D1077G	possibly damaging	Het
Smg7	G	A	1: 152,742,399 (GRCm39)	P82L	probably damaging	Het
Sp3	A	C	2: 72,801,342 (GRCm39)	F268V	probably damaging	Het
Srms	T	C	2: 180,854,426 (GRCm39)	D47G	probably benign	Het
Ss18	A	C	18: 14,784,238 (GRCm39)	M150R	probably damaging	Het
Taf5	G	A	19: 47,063,293 (GRCm39)	R281Q	probably benign	Het
Tars1	T	C	15: 11,385,259 (GRCm39)	K644R	probably benign	Het
Tinag	C	A	9: 76,859,285 (GRCm39)	W441L	probably damaging	Het
Tmtc1	T	C	6: 148,312,738 (GRCm39)	S244G	probably benign	Het
Tpr	T	C	1: 150,309,476 (GRCm39)	V1670A	possibly damaging	Het
Trpv3	A	G	11: 73,187,640 (GRCm39)		probably benign	Het
Uhrf1	G	T	17: 56,617,742 (GRCm39)	V155L	probably damaging	Het
Ush2a	G	A	1: 188,132,475 (GRCm39)	C899Y	probably damaging	Het
Vmn2r115	G	A	17: 23,578,249 (GRCm39)	R574H	probably benign	Het
Vmn2r63	T	C	7: 42,577,434 (GRCm39)	D368G	probably benign	Het
Vps13a	A	G	19: 16,758,105 (GRCm39)	V10A	probably damaging	Het
Wbp11	A	G	6: 136,791,636 (GRCm39)		probably benign	Het
Zcwpw1	A	G	5: 137,797,854 (GRCm39)	D145G	probably benign	Het
Zfp607a	G	A	7: 27,577,901 (GRCm39)	V324I	probably damaging	Het
Zfp618	A	G	4: 63,052,011 (GRCm39)	I931V	probably benign	Het
Zfp821	T	C	8: 110,451,174 (GRCm39)	V389A	possibly damaging	Het
Zfp976	T	A	7: 42,263,141 (GRCm39)	H232L	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
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
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'- GACTCAGCTACCACGATGCTTCAC -3'
(R):5'- ACTAGGCAGTCTCCAACTCTGTCC -3'

Sequencing Primer
(F):5'- TCTGCACTGAGTTTGAAGAGAGC -3'
(R):5'- CAACTCTGTCCCAAAGTTATGG -3'

Posted On

2013-07-30