Mutagenetix > Incidental Mutations

Incidental Mutation 'R7239:Psd2'

563113

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 #

R7239 (G1)

Quality Score

193.009

Status

Validated

Chromosome

Chromosomal Location

35964830-36014715 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 35980419 bp

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 315 (A315T)

Ref Sequence

ENSEMBL: ENSMUSP00000135795 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000115716
AA Change: A315T

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

SMART Domains

Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: A315T

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: A315T

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

SMART Domains

Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: A315T

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: A315T

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

SMART Domains

Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: A315T

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: A315T

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

SMART Domains

Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: A315T

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: A315T

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

SMART Domains

Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: A315T

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: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

99% (76/77)

Allele List at MGI

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

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	A	G	16: 21,653,518	V144A	probably damaging	Het
4930402H24Rik	C	A	2: 130,806,788	R258L	unknown	Het
Abca5	A	T	11: 110,326,704	Y109N	possibly damaging	Het
Abcb5	T	C	12: 118,928,725	Q433R	probably benign	Het
Adamts7	G	A	9: 90,186,557		probably null	Het
Adgrv1	T	C	13: 81,476,612	D3746G	possibly damaging	Het
Arhgap29	C	T	3: 121,988,950	S159L	probably benign	Het
Arhgap5	T	A	12: 52,517,376	C377S	probably benign	Het
Atp1a3	G	A	7: 25,000,704	P77L	probably damaging	Het
B4galt1	T	C	4: 40,812,754	D257G	probably damaging	Het
Bin1	T	A	18: 32,406,171	N52K	probably damaging	Het
Catsperg2	A	G	7: 29,710,082	M562T	probably benign	Het
Ccdc33	G	A	9: 58,032,909	Q713*	probably null	Het
Cd96	A	T	16: 46,109,114	L156Q	probably damaging	Het
Clpb	A	G	7: 101,711,455	T231A	probably damaging	Het
Dnmt3a	A	T	12: 3,872,850	Q151L	probably benign	Het
Dock2	C	T	11: 34,231,677	V1629M	probably benign	Het
Edem1	G	A	6: 108,854,380	D601N	probably benign	Het
Eno2	C	T	6: 124,768,265	V20M	probably damaging	Het
Eny2	A	C	15: 44,433,854	D52A	probably benign	Het
Esp36	T	C	17: 38,417,241	R93G	possibly damaging	Het
Fam227a	A	G	15: 79,634,062		probably null	Het
Fat4	C	A	3: 38,983,840	H3880Q	possibly damaging	Het
Fbxw24	A	T	9: 109,605,530	V334E	possibly damaging	Het
Flrt1	T	C	19: 7,095,964	Q406R	probably benign	Het
Frmpd2	A	G	14: 33,552,077	N1092S	probably benign	Het
Gm904	C	A	13: 50,645,251	T82K	probably benign	Het
Gnas	G	C	2: 174,298,615	G252R	unknown	Het
Gpatch2l	A	G	12: 86,260,575		probably null	Het
Hist1h2ac	A	T	13: 23,683,610	I103N	probably damaging	Het
Ift74	T	C	4: 94,652,950	V204A	probably benign	Het
Ikzf4	A	G	10: 128,641,244	L119P	probably damaging	Het
Ing3	G	A	6: 21,952,194	E56K	probably damaging	Het
Klhl25	T	C	7: 75,866,768	I474T	probably benign	Het
Klhl5	T	C	5: 65,161,186	V556A	probably damaging	Het
Krt14	A	T	11: 100,204,255	M382K	probably benign	Het
Lmcd1	T	C	6: 112,315,784	V199A	possibly damaging	Het
Lpcat4	T	A	2: 112,242,707	F200I	possibly damaging	Het
Lrp1b	T	C	2: 41,004,713	T2282A		Het
Lrrk1	T	C	7: 66,262,155	T1886A	probably benign	Het
Meis2	T	C	2: 116,059,003		probably null	Het
Mki67	C	T	7: 135,700,176	R1043K	possibly damaging	Het
Myct1	G	T	10: 5,604,601	R156L	possibly damaging	Het
Nckap5l	G	T	15: 99,426,209	H804Q	probably damaging	Het
Ndst3	T	G	3: 123,606,906	E450D	probably damaging	Het
Nipbl	A	T	15: 8,292,135		probably null	Het
Npy	A	G	6: 49,823,607	N4D	probably benign	Het
Olfr855	A	T	9: 19,585,191	Y218F	probably damaging	Het
Osgin2	T	C	4: 16,008,748	S18G	probably benign	Het
Pcdha9	T	G	18: 36,998,498	F207V	probably benign	Het
Pcdhb13	A	T	18: 37,444,644	I692F	probably damaging	Het
Pde3b	T	A	7: 114,416,149	V200E	probably damaging	Het
Ppp6r3	A	T	19: 3,493,981	L345I	probably benign	Het
Rnf111	G	A	9: 70,469,373	T328I	probably damaging	Het
Rnf213	T	C	11: 119,458,788	L3825P		Het
Rtl1	C	T	12: 109,592,475	V977I	probably benign	Het
Scn1a	G	A	2: 66,277,656		probably null	Het
Slc25a2	G	T	18: 37,637,695	N260K	probably benign	Het
Sprtn	T	C	8: 124,900,244	V121A	probably damaging	Het
Ssx2ip	T	G	3: 146,428,016	L260W	probably damaging	Het
Syde1	G	A	10: 78,588,781	R406C	probably damaging	Het
Tab1	A	G	15: 80,133,171	R6G	probably benign	Het
Tenm4	G	A	7: 96,553,496	R106H	probably benign	Het
Tenm4	G	A	7: 96,735,813	V526I	possibly damaging	Het
Tfap2b	T	C	1: 19,234,180	F405L	probably damaging	Het
Trbv13-1	C	A	6: 41,116,391	T87K	probably benign	Het
Trmt44	G	T	5: 35,574,786	A87E	probably benign	Het
Ttll3	CAAAGTAA	CAAAGTAAAGTAA	6: 113,399,157		probably null	Het
Ttn	T	C	2: 76,787,290	D16279G	probably damaging	Het
Ttn	G	A	2: 76,881,328	R8290C	unknown	Het
Ugt2b37	T	A	5: 87,254,731	I14L	probably benign	Het
Vmn1r13	A	T	6: 57,210,626	M257L	probably benign	Het
Vmn1r184	C	T	7: 26,267,177	P116L	possibly damaging	Het
Zfp426	T	C	9: 20,470,591	T367A	probably benign	Het
Zfp647	A	T	15: 76,911,756	C235S	probably 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
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
R7348:Psd2	UTSW	18	35980336	missense	possibly damaging	0.85
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'- GCCCCACAGTGGATTTTCAGAG -3'
(R):5'- CCTTGAAAGCCTAGTGGGAG -3'

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

Posted On

2019-06-26