Incidental Mutation 'R7348:Psd3'
ID 570359
Institutional Source Beutler Lab
Gene Symbol Psd3
Ensembl Gene ENSMUSG00000030465
Gene Name pleckstrin and Sec7 domain containing 3
Synonyms EFA6D, 4931420C21Rik
MMRRC Submission 045380-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.093) question?
Stock # R7348 (G1)
Quality Score 225.009
Status Validated
Chromosome 8
Chromosomal Location 68141734-68664679 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 68243583 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 685 (N685S)
Ref Sequence ENSEMBL: ENSMUSP00000096293 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038959] [ENSMUST00000059374] [ENSMUST00000093468] [ENSMUST00000093469] [ENSMUST00000098696] [ENSMUST00000120071] [ENSMUST00000212505] [ENSMUST00000212960]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000038959
AA Change: N686S

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: N686S

DomainStartEndE-ValueType
low complexity region 204 218 N/A INTRINSIC
Blast:Sec7 431 496 5e-28 BLAST
Sec7 502 693 3.9e-53 SMART
PH 743 857 3.85e-15 SMART
Blast:Sec7 876 938 2e-10 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000059374
AA Change: N57S

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000060306
Gene: ENSMUSG00000030465
AA Change: N57S

DomainStartEndE-ValueType
PH 114 228 3.85e-15 SMART
Blast:Sec7 247 305 1e-8 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000093468
AA Change: N199S

PolyPhen 2 Score 0.865 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000091178
Gene: ENSMUSG00000030465
AA Change: N199S

DomainStartEndE-ValueType
Sec7 17 206 1.35e-56 SMART
PH 256 370 3.85e-15 SMART
Blast:Sec7 389 451 1e-10 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000093469
AA Change: N685S

PolyPhen 2 Score 0.651 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: N685S

DomainStartEndE-ValueType
low complexity region 204 218 N/A INTRINSIC
Blast:Sec7 431 496 5e-28 BLAST
Sec7 502 692 2.4e-53 SMART
PH 742 856 3.85e-15 SMART
Blast:Sec7 875 937 2e-10 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000098696
AA Change: N685S

PolyPhen 2 Score 0.651 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: N685S

DomainStartEndE-ValueType
low complexity region 204 218 N/A INTRINSIC
Blast:Sec7 431 496 5e-28 BLAST
Sec7 502 692 2.4e-53 SMART
PH 742 856 3.85e-15 SMART
Blast:Sec7 875 937 2e-10 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000120071
AA Change: N57S

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000112545
Gene: ENSMUSG00000030465
AA Change: N57S

DomainStartEndE-ValueType
PH 114 228 3.85e-15 SMART
Blast:Sec7 247 309 3e-11 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000212505
AA Change: N716S

PolyPhen 2 Score 0.651 (Sensitivity: 0.87; Specificity: 0.91)
Predicted Effect probably benign
Transcript: ENSMUST00000212960
AA Change: N970S

PolyPhen 2 Score 0.401 (Sensitivity: 0.89; Specificity: 0.89)
Meta Mutation Damage Score 0.0657 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 98.8%
Validation Efficiency 99% (80/81)
Allele List at MGI
Other mutations in this stock
Total: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abra G A 15: 41,729,555 (GRCm39) R282C probably damaging Het
Adcy2 T A 13: 68,882,794 (GRCm39) E314D possibly damaging Het
Adgrl2 A T 3: 148,523,402 (GRCm39) I274N Het
Adpgk A G 9: 59,221,069 (GRCm39) I292V probably benign Het
Agtrap G T 4: 148,165,054 (GRCm39) F124L probably benign Het
Ankrd26 A G 6: 118,485,525 (GRCm39) Y1450H probably damaging Het
Ap4e1 A T 2: 126,903,896 (GRCm39) S933C probably damaging Het
Ap4e1 G T 2: 126,903,897 (GRCm39) S933I possibly damaging Het
Ap5s1 A T 2: 131,054,572 (GRCm39) T128S possibly damaging Het
Arih1 T C 9: 59,393,341 (GRCm39) Y97C probably damaging Het
Atp1a3 A G 7: 24,678,251 (GRCm39) F1034S unknown Het
Bmp6 T C 13: 38,669,879 (GRCm39) S388P probably benign Het
Ccdc39 A G 3: 33,886,825 (GRCm39) V261A possibly damaging Het
Ccdc66 C T 14: 27,222,293 (GRCm39) C150Y probably damaging Het
Cep89 G A 7: 35,129,353 (GRCm39) R630H probably damaging Het
Cln6 A G 9: 62,756,458 (GRCm39) S201G probably benign Het
Cntnap4 T C 8: 113,391,909 (GRCm39) Y125H probably damaging Het
Copa A G 1: 171,929,790 (GRCm39) T286A possibly damaging Het
Cul9 A T 17: 46,821,919 (GRCm39) I1852K possibly damaging Het
Cyp2j8 C A 4: 96,332,877 (GRCm39) A490S probably benign Het
Cyp2t4 A G 7: 26,856,676 (GRCm39) I239V probably benign Het
Dpcd A G 19: 45,560,905 (GRCm39) Y111C probably damaging Het
E2f7 C T 10: 110,616,836 (GRCm39) T692I probably damaging Het
Fastkd5 A G 2: 130,457,055 (GRCm39) Y512H probably damaging Het
Fastkd5 A C 2: 130,458,359 (GRCm39) M77R probably benign Het
Fhod3 A G 18: 25,223,524 (GRCm39) R957G possibly damaging Het
H6pd C A 4: 150,068,359 (GRCm39) probably null Het
Haus5 G T 7: 30,356,391 (GRCm39) P544Q possibly damaging Het
Ifi207 CTGTTGATGAAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG CTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG 1: 173,556,762 (GRCm39) probably benign Het
Igf2r A G 17: 12,922,371 (GRCm39) Y1248H probably damaging Het
Izumo3 T C 4: 92,035,455 (GRCm39) N6S possibly damaging Het
Lrp6 G T 6: 134,427,781 (GRCm39) P1604T probably damaging Het
Map3k8 T A 18: 4,340,561 (GRCm39) H251L probably damaging Het
Mapre3 T C 5: 31,019,173 (GRCm39) Y6H probably benign Het
Mlh3 G T 12: 85,314,215 (GRCm39) P657Q probably damaging Het
Mrgpra1 T C 7: 46,985,157 (GRCm39) Y174C probably benign Het
Ms4a6d G A 19: 11,567,437 (GRCm39) Q155* probably null Het
Myh1 C A 11: 67,093,365 (GRCm39) P152Q probably damaging Het
Myh6 A T 14: 55,189,716 (GRCm39) L1110Q probably damaging Het
Nf1 T A 11: 79,427,676 (GRCm39) S1778T probably benign Het
Nkpd1 G A 7: 19,258,341 (GRCm39) E707K probably damaging Het
Nlrp4a A G 7: 26,143,698 (GRCm39) E21G probably damaging Het
Nr4a3 T G 4: 48,051,290 (GRCm39) S15A possibly damaging Het
Or2f1 T C 6: 42,721,790 (GRCm39) L273S possibly damaging Het
Or5p1 T C 7: 107,916,920 (GRCm39) V273A possibly damaging Het
Or5p64 T C 7: 107,855,330 (GRCm39) D5G probably benign Het
Or7a38 A G 10: 78,753,396 (GRCm39) T241A probably damaging Het
Parg G A 14: 31,972,036 (GRCm39) R677Q possibly damaging Het
Pcsk5 A T 19: 17,434,182 (GRCm39) C1395* probably null Het
Psd2 G A 18: 36,113,389 (GRCm39) S287N possibly damaging Het
Pygb C T 2: 150,628,903 (GRCm39) T39M probably benign Het
Rbfox1 C A 16: 7,225,888 (GRCm39) Y351* probably null Het
Rftn1 A G 17: 50,311,351 (GRCm39) L396P probably damaging Het
S1pr1 A G 3: 115,505,710 (GRCm39) Y295H probably damaging Het
Scn5a T C 9: 119,364,899 (GRCm39) M440V probably benign Het
Sel1l2 T C 2: 140,107,644 (GRCm39) N240S probably benign Het
Skic3 T C 13: 76,331,003 (GRCm39) F1478L possibly damaging Het
Skint1 T C 4: 111,878,770 (GRCm39) L234P probably damaging Het
Skint11 T A 4: 114,101,919 (GRCm39) Y311N probably benign Het
Slc6a5 A T 7: 49,559,915 (GRCm39) probably benign Het
Tas2r134 T C 2: 51,518,414 (GRCm39) S298P possibly damaging Het
Tbcd C A 11: 121,485,137 (GRCm39) A773D probably benign Het
Tgoln1 G C 6: 72,593,261 (GRCm39) T73R probably benign Het
Tmem184a T C 5: 139,799,809 (GRCm39) E24G probably null Het
Tmem207 C A 16: 26,335,577 (GRCm39) W53C possibly damaging Het
Tns1 T A 1: 73,956,076 (GRCm39) H549L possibly damaging Het
Ttc41 G T 10: 86,586,212 (GRCm39) E839* probably null Het
Ufd1 T G 16: 18,634,635 (GRCm39) probably benign Het
Usp28 A G 9: 48,942,177 (GRCm39) E713G probably benign Het
Utrn A G 10: 12,623,762 (GRCm39) W159R probably damaging Het
Vcl C T 14: 21,053,218 (GRCm39) A411V probably benign Het
Vcl T A 14: 21,059,020 (GRCm39) C545* probably null Het
Vmn1r120 A T 7: 20,787,377 (GRCm39) S111R probably damaging Het
Wwox T A 8: 115,199,392 (GRCm39) C146S probably benign Het
Zbtb2 T C 10: 4,324,574 (GRCm39) T57A possibly damaging Het
Zfp362 T C 4: 128,671,010 (GRCm39) D336G possibly damaging Het
Zfp628 G A 7: 4,924,817 (GRCm39) G1013E probably damaging Het
Zfp704 A G 3: 9,539,658 (GRCm39) S231P probably damaging Het
Zhx3 G T 2: 160,624,038 (GRCm39) S43* probably null Het
Other mutations in Psd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00769:Psd3 APN 8 68,361,331 (GRCm39) splice site probably benign
IGL01095:Psd3 APN 8 68,361,165 (GRCm39) missense probably damaging 1.00
IGL01139:Psd3 APN 8 68,361,187 (GRCm39) missense probably damaging 1.00
IGL01330:Psd3 APN 8 68,149,830 (GRCm39) missense probably damaging 1.00
IGL01350:Psd3 APN 8 68,173,544 (GRCm39) missense probably damaging 1.00
IGL01487:Psd3 APN 8 68,149,766 (GRCm39) missense probably benign 0.01
IGL01780:Psd3 APN 8 68,416,521 (GRCm39) missense probably benign
IGL02020:Psd3 APN 8 68,426,822 (GRCm39) intron probably benign
IGL02232:Psd3 APN 8 68,356,797 (GRCm39) missense probably damaging 1.00
IGL02350:Psd3 APN 8 68,416,521 (GRCm39) missense probably benign
IGL02357:Psd3 APN 8 68,416,521 (GRCm39) missense probably benign
PIT4495001:Psd3 UTSW 8 68,416,565 (GRCm39) missense probably benign 0.00
R0052:Psd3 UTSW 8 68,335,631 (GRCm39) critical splice donor site probably null
R0052:Psd3 UTSW 8 68,335,631 (GRCm39) critical splice donor site probably null
R0242:Psd3 UTSW 8 68,210,738 (GRCm39) missense probably damaging 0.99
R0242:Psd3 UTSW 8 68,210,738 (GRCm39) missense probably damaging 0.99
R0581:Psd3 UTSW 8 68,173,598 (GRCm39) missense probably damaging 1.00
R0655:Psd3 UTSW 8 68,416,341 (GRCm39) missense probably benign 0.19
R1740:Psd3 UTSW 8 68,573,491 (GRCm39) missense probably damaging 1.00
R1789:Psd3 UTSW 8 68,413,217 (GRCm39) missense probably benign 0.26
R1847:Psd3 UTSW 8 68,172,656 (GRCm39) missense possibly damaging 0.93
R1951:Psd3 UTSW 8 68,416,139 (GRCm39) missense probably benign 0.00
R1954:Psd3 UTSW 8 68,149,727 (GRCm39) missense probably damaging 1.00
R2143:Psd3 UTSW 8 68,417,003 (GRCm39) missense probably damaging 1.00
R4387:Psd3 UTSW 8 68,453,413 (GRCm39) missense probably damaging 1.00
R4801:Psd3 UTSW 8 68,573,800 (GRCm39) missense probably benign
R4802:Psd3 UTSW 8 68,573,800 (GRCm39) missense probably benign
R4913:Psd3 UTSW 8 68,573,821 (GRCm39) missense probably damaging 0.99
R5045:Psd3 UTSW 8 68,166,477 (GRCm39) missense probably damaging 0.99
R5173:Psd3 UTSW 8 68,149,641 (GRCm39) missense probably damaging 1.00
R5264:Psd3 UTSW 8 68,166,377 (GRCm39) missense probably benign 0.23
R5350:Psd3 UTSW 8 68,361,513 (GRCm39) missense probably benign 0.00
R5816:Psd3 UTSW 8 68,413,162 (GRCm39) missense possibly damaging 0.90
R5994:Psd3 UTSW 8 68,172,620 (GRCm39) missense probably damaging 1.00
R6157:Psd3 UTSW 8 68,574,179 (GRCm39) start codon destroyed probably benign 0.14
R6241:Psd3 UTSW 8 68,270,791 (GRCm39) intron probably benign
R6586:Psd3 UTSW 8 68,416,197 (GRCm39) missense probably damaging 0.96
R6735:Psd3 UTSW 8 68,573,398 (GRCm39) critical splice donor site probably null
R6908:Psd3 UTSW 8 68,416,829 (GRCm39) missense probably benign 0.00
R6984:Psd3 UTSW 8 68,270,697 (GRCm39) missense possibly damaging 0.85
R7082:Psd3 UTSW 8 68,356,800 (GRCm39) missense probably benign 0.03
R7116:Psd3 UTSW 8 68,166,390 (GRCm39) missense probably benign 0.12
R7297:Psd3 UTSW 8 68,573,686 (GRCm39) missense probably damaging 0.98
R7334:Psd3 UTSW 8 68,361,357 (GRCm39) missense possibly damaging 0.94
R7357:Psd3 UTSW 8 68,574,149 (GRCm39) missense probably benign 0.01
R7369:Psd3 UTSW 8 68,356,818 (GRCm39) missense possibly damaging 0.95
R7385:Psd3 UTSW 8 68,453,408 (GRCm39) missense probably damaging 1.00
R7733:Psd3 UTSW 8 68,573,568 (GRCm39) missense possibly damaging 0.75
R7873:Psd3 UTSW 8 68,335,634 (GRCm39) missense possibly damaging 0.95
R8110:Psd3 UTSW 8 68,573,708 (GRCm39) missense probably damaging 1.00
R8765:Psd3 UTSW 8 68,416,093 (GRCm39) missense possibly damaging 0.69
R8768:Psd3 UTSW 8 68,417,003 (GRCm39) missense probably damaging 1.00
R8817:Psd3 UTSW 8 68,413,135 (GRCm39) missense possibly damaging 0.95
R8837:Psd3 UTSW 8 68,172,596 (GRCm39) missense probably damaging 0.99
R8878:Psd3 UTSW 8 68,210,750 (GRCm39) missense probably benign 0.28
R8903:Psd3 UTSW 8 68,165,945 (GRCm39) missense unknown
R8955:Psd3 UTSW 8 68,416,461 (GRCm39) missense probably benign 0.08
R9216:Psd3 UTSW 8 68,573,539 (GRCm39) missense probably benign 0.00
R9241:Psd3 UTSW 8 68,415,967 (GRCm39) missense probably benign 0.00
R9351:Psd3 UTSW 8 68,413,301 (GRCm39) missense probably benign 0.18
R9449:Psd3 UTSW 8 68,165,833 (GRCm39) missense unknown
R9451:Psd3 UTSW 8 68,363,487 (GRCm39) missense unknown
R9709:Psd3 UTSW 8 68,194,414 (GRCm39) missense probably null 0.99
R9797:Psd3 UTSW 8 68,210,778 (GRCm39) missense probably damaging 0.99
Z1088:Psd3 UTSW 8 68,358,912 (GRCm39) splice site silent
Predicted Primers PCR Primer
(F):5'- GGGTTTCACACAAAGCAGGTC -3'
(R):5'- AAACTAAGTTTTGCCTCCCCTG -3'

Sequencing Primer
(F):5'- ACAAAGCAGGTCAGACAACTG -3'
(R):5'- TCTAGAGTTGTGCAGCCCAAC -3'
Posted On 2019-09-13