Mutagenetix > Incidental Mutation

Incidental Mutation 'R8221:Psd2'

636733

Institutional Source

Beutler Lab

Gene Symbol

Psd2

Ensembl Gene

ENSMUSG00000024347

Gene Name

pleckstrin and Sec7 domain containing 2

Synonyms

EFA6C, 6330404E20Rik

MMRRC Submission

067639-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8221 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

36097883-36147768 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 36113478 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 317 (R317W)

Ref Sequence

ENSEMBL: ENSMUSP00000135795 (fasta)

Gene Model

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

AlphaFold

Q6P1I6

Predicted Effect

probably damaging
Transcript: ENSMUST00000115716
AA Change: R317W

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

SMART Domains

Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: R317W

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: R317W

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: R317W

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: R317W

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

SMART Domains

Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: R317W

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: R317W

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: R317W

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: R317W

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: R317W

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

0.6329

Coding Region Coverage

1x: 99.9%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

100% (74/74)

Allele List at MGI

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

Other mutations in this stock

Total: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acly	A	G	11: 100,410,576 (GRCm39)	F134S	probably damaging	Het
Acsl5	T	C	19: 55,257,262 (GRCm39)		probably null	Het
Adam29	G	T	8: 56,325,463 (GRCm39)	N330K	probably benign	Het
Adgrv1	A	G	13: 81,677,033 (GRCm39)	S1933P	probably benign	Het
Afap1l2	T	C	19: 56,902,824 (GRCm39)	H785R	probably damaging	Het
Ahnak	T	A	19: 8,987,800 (GRCm39)	L3028*	probably null	Het
Ajuba	T	C	14: 54,807,847 (GRCm39)	T462A	possibly damaging	Het
Ankrd36	A	G	11: 5,534,016 (GRCm39)	N289S	possibly damaging	Het
Ankrd46	A	T	15: 36,486,001 (GRCm39)	L84Q	probably damaging	Het
Ankrd54	T	G	15: 78,940,270 (GRCm39)	D163A	probably damaging	Het
Arhgef28	A	G	13: 98,282,064 (GRCm39)	L10P	probably benign	Het
Atm	A	T	9: 53,367,288 (GRCm39)		probably null	Het
Azin1	G	C	15: 38,492,572 (GRCm39)	F312L	probably damaging	Het
C2cd4c	A	G	10: 79,448,482 (GRCm39)	S222P	probably damaging	Het
Cdyl	A	G	13: 36,000,147 (GRCm39)	T143A	probably benign	Het
Clhc1	G	A	11: 29,503,751 (GRCm39)	V56I	possibly damaging	Het
Cntn4	T	C	6: 106,486,471 (GRCm39)	S300P	probably benign	Het
Col12a1	A	G	9: 79,551,224 (GRCm39)	Y2131H	probably damaging	Het
Cyp3a41b	A	G	5: 145,506,190 (GRCm39)	S287P	probably benign	Het
Dctn4	A	G	18: 60,689,401 (GRCm39)	D424G	probably benign	Het
Dnajb8	C	T	6: 88,199,940 (GRCm39)	R159C	possibly damaging	Het
Dop1b	A	G	16: 93,546,847 (GRCm39)	T284A	probably benign	Het
E330034G19Rik	A	C	14: 24,346,135 (GRCm39)		probably null	Het
Ehhadh	G	A	16: 21,581,373 (GRCm39)	P540S	possibly damaging	Het
Emsy	T	C	7: 98,297,111 (GRCm39)	E24G	probably damaging	Het
F930015N05Rik	A	C	11: 64,326,418 (GRCm39)	L74W	unknown	Het
Fat1	A	G	8: 45,406,390 (GRCm39)	D1047G		Het
Galnt7	A	G	8: 58,005,600 (GRCm39)	V211A	possibly damaging	Het
Gdap2	T	C	3: 100,109,611 (GRCm39)	C543R	unknown	Het
Ghr	A	C	15: 3,362,901 (GRCm39)	D190E	probably benign	Het
Glrx	A	G	13: 75,995,346 (GRCm39)	M89V	probably benign	Het
Gm10323	A	C	13: 67,000,859 (GRCm39)	Y91*	noncoding transcript	Het
Gnb4	A	T	3: 32,644,184 (GRCm39)	D153E	possibly damaging	Het
Gnptab	G	T	10: 88,276,254 (GRCm39)		probably null	Het
Grip2	T	C	6: 91,762,665 (GRCm39)	D193G	possibly damaging	Het
Igsf3	T	C	3: 101,347,038 (GRCm39)	W658R	probably damaging	Het
Ip6k1	T	A	9: 107,923,115 (GRCm39)	F416I	probably benign	Het
Klhl1	T	G	14: 96,517,546 (GRCm39)	T377P	possibly damaging	Het
Lrrc38	G	A	4: 143,077,303 (GRCm39)	G189R	probably damaging	Het
Lrrfip1	T	C	1: 91,042,878 (GRCm39)	S428P	probably benign	Het
Megf10	A	G	18: 57,416,893 (GRCm39)	D754G	probably benign	Het
Mrgprx2	T	A	7: 48,132,527 (GRCm39)	Y97F	probably benign	Het
Msantd2	T	G	9: 37,400,684 (GRCm39)	V22G	probably damaging	Het
Myl6b	T	C	10: 128,333,209 (GRCm39)	K11R	unknown	Het
Nab2	C	A	10: 127,498,645 (GRCm39)	V475L	probably benign	Het
Npas1	T	C	7: 16,189,890 (GRCm39)	E552G	probably damaging	Het
Pknox2	T	C	9: 36,821,040 (GRCm39)	N274S	possibly damaging	Het
Pmepa1	A	T	2: 173,069,700 (GRCm39)	L247Q	probably damaging	Het
Poll	T	C	19: 45,542,047 (GRCm39)	K420E	probably damaging	Het
Polr2a	A	G	11: 69,628,344 (GRCm39)	V1283A	probably benign	Het
Ppil4	A	T	10: 7,671,444 (GRCm39)	Y36F	probably benign	Het
Pramel20	T	G	4: 143,298,530 (GRCm39)	Y158D	probably benign	Het
Pspc1	T	A	14: 57,015,616 (GRCm39)	M1L	probably benign	Het
Qrsl1	A	T	10: 43,758,080 (GRCm39)	F338I	possibly damaging	Het
Rcor3	A	G	1: 191,814,749 (GRCm39)	Y77H	unknown	Het
Sbno2	G	A	10: 79,905,845 (GRCm39)	P157L	probably benign	Het
Scn10a	C	T	9: 119,446,829 (GRCm39)	V1400I	probably damaging	Het
Setd3	C	G	12: 108,073,612 (GRCm39)	G555A	possibly damaging	Het
Slc12a4	A	T	8: 106,678,601 (GRCm39)	M245K	probably benign	Het
Slc1a5	T	A	7: 16,515,902 (GRCm39)	L26Q	probably benign	Het
Slc38a3	T	G	9: 107,534,908 (GRCm39)	M156L	probably damaging	Het
Slc45a2	A	T	15: 11,001,233 (GRCm39)	I111F	probably benign	Het
Slc4a3	T	A	1: 75,528,810 (GRCm39)	M491K	probably benign	Het
Son	A	G	16: 91,453,734 (GRCm39)	D827G	probably damaging	Het
Sppl2c	A	T	11: 104,077,710 (GRCm39)	H170L	probably damaging	Het
St6gal2	T	A	17: 55,797,935 (GRCm39)		probably null	Het
Taf4b	T	A	18: 15,031,106 (GRCm39)	L830H	probably damaging	Het
Tex22	A	G	12: 113,038,696 (GRCm39)		probably null	Het
Tiam2	C	T	17: 3,568,860 (GRCm39)	R1669C	probably damaging	Het
Tmprss15	T	A	16: 78,821,223 (GRCm39)	N506I	probably damaging	Het
Topors	A	T	4: 40,260,686 (GRCm39)	I866K	unknown	Het
Trip12	G	T	1: 84,743,771 (GRCm39)	T512K	possibly damaging	Het
Ubr1	T	A	2: 120,791,585 (GRCm39)	H133L	probably damaging	Het
Wwtr1	T	C	3: 57,366,441 (GRCm39)	D422G	probably damaging	Het
Zfp689	A	C	7: 127,043,758 (GRCm39)	C291G	probably damaging	Het
Zfyve9	A	G	4: 108,576,877 (GRCm39)	L68P	possibly damaging	Het
Zswim5	G	T	4: 116,735,219 (GRCm39)	R188L	probably benign	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
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
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'- CCCACAGTGGATTTTCAGAGAC -3'
(R):5'- TCCTTGAAAGCCTAGTGGGAG -3'

Sequencing Primer
(F):5'- ATTTTCAGAGACCTGGGGCC -3'
(R):5'- AAAGCCTAGTGGGAGCTCCTG -3'

Posted On

2020-07-13