Incidental Mutation 'R7116:Psd3'
ID 551777
Institutional Source Beutler Lab
Gene Symbol Psd3
Ensembl Gene ENSMUSG00000030465
Gene Name pleckstrin and Sec7 domain containing 3
Synonyms EFA6D, 4931420C21Rik
MMRRC Submission 045207-MU
Accession Numbers

Ncbi RefSeq: NM_030263.5, NM_027626.1; MGI:1918215

Essential gene? Probably non essential (E-score: 0.077) question?
Stock # R7116 (G1)
Quality Score 225.009
Status Not validated
Chromosome 8
Chromosomal Location 67689082-68212027 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 67713738 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 915 (V915A)
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 probably benign
Transcript: ENSMUST00000038959
AA Change: V916A

PolyPhen 2 Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: V916A

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 possibly damaging
Transcript: ENSMUST00000059374
AA Change: V287A

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000060306
Gene: ENSMUSG00000030465
AA Change: V287A

DomainStartEndE-ValueType
PH 114 228 3.85e-15 SMART
Blast:Sec7 247 305 1e-8 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000093468
AA Change: V429A

PolyPhen 2 Score 0.849 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000091178
Gene: ENSMUSG00000030465
AA Change: V429A

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 probably benign
Transcript: ENSMUST00000093469
AA Change: V915A

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: V915A

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 benign
Transcript: ENSMUST00000098696
AA Change: V915A

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: V915A

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 benign
Transcript: ENSMUST00000120071
AA Change: V287A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000112545
Gene: ENSMUSG00000030465
AA Change: V287A

DomainStartEndE-ValueType
PH 114 228 3.85e-15 SMART
Blast:Sec7 247 309 3e-11 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000212505
AA Change: V946A

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
Predicted Effect probably benign
Transcript: ENSMUST00000212960
AA Change: V1200A

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actn1 A G 12: 80,204,977 (GRCm38) S109P probably damaging Het
Afg3l1 T G 8: 123,489,862 (GRCm38) L280R probably damaging Het
Akap13 T A 7: 75,720,195 (GRCm38) S129T probably benign Het
Ankrd11 A G 8: 122,896,130 (GRCm38) S328P probably damaging Het
Aox3 A T 1: 58,153,530 (GRCm38) E554D probably benign Het
Bcl11a T C 11: 24,163,839 (GRCm38) V394A probably damaging Het
Cass4 A G 2: 172,427,969 (GRCm38) Y657C unknown Het
Ccdc88a C T 11: 29,504,051 (GRCm38) A1738V probably benign Het
Cfap74 T C 4: 155,455,061 (GRCm38) F948L unknown Het
Chgb A T 2: 132,781,317 (GRCm38) probably benign Het
Coro1c C T 5: 113,852,206 (GRCm38) W138* probably null Het
Dgkb A G 12: 37,981,990 (GRCm38) Q17R probably benign Het
Esco2 A G 14: 65,826,557 (GRCm38) Y393H probably damaging Het
Eya3 T A 4: 132,694,799 (GRCm38) D228E probably benign Het
Fat2 T C 11: 55,282,336 (GRCm38) D2517G probably damaging Het
Fry T A 5: 150,395,869 (GRCm38) probably null Het
Gal3st2b A T 1: 93,940,776 (GRCm38) Q243L possibly damaging Het
Gimap9 C T 6: 48,678,055 (GRCm38) A192V probably benign Het
Glg1 T A 8: 111,178,957 (GRCm38) Q564L probably benign Het
H2-Aa A T 17: 34,283,627 (GRCm38) Y188* probably null Het
Hira T C 16: 18,912,114 (GRCm38) Y188H probably damaging Het
Ighv8-8 C T 12: 115,294,194 (GRCm38) D76N probably benign Het
Irf6 T C 1: 193,167,597 (GRCm38) F276L probably damaging Het
Itpr1 T C 6: 108,481,268 (GRCm38) C2000R probably damaging Het
Jakmip3 T C 7: 139,020,250 (GRCm38) V293A possibly damaging Het
Kcnh7 A G 2: 62,877,270 (GRCm38) V132A probably benign Het
Kcnj1 A G 9: 32,396,981 (GRCm38) T234A possibly damaging Het
Kpna3 T A 14: 61,368,186 (GRCm38) N470I probably benign Het
Lamb2 T C 9: 108,487,323 (GRCm38) F1121L probably damaging Het
Lingo1 T C 9: 56,620,627 (GRCm38) D232G probably benign Het
Lpxn T A 19: 12,811,258 (GRCm38) N70K probably benign Het
Ltbp4 T A 7: 27,305,427 (GRCm38) H1657L probably damaging Het
Luzp2 C A 7: 55,265,330 (GRCm38) F334L possibly damaging Het
Mgat5b A T 11: 116,944,959 (GRCm38) S142C possibly damaging Het
Mroh7 G A 4: 106,711,320 (GRCm38) T396I probably benign Het
Muc5b T C 7: 141,863,750 (GRCm38) S3478P probably benign Het
Nfatc2 A T 2: 168,507,349 (GRCm38) M626K probably benign Het
Nlrp14 A G 7: 107,183,048 (GRCm38) D484G possibly damaging Het
Npc1 T C 18: 12,211,544 (GRCm38) Y423C probably damaging Het
Nrsn1 A G 13: 25,253,405 (GRCm38) I180T probably damaging Het
Olfr570 T A 7: 102,900,635 (GRCm38) N89K probably benign Het
Olfr741 A T 14: 50,485,568 (GRCm38) I37F probably benign Het
Osbpl6 A T 2: 76,595,881 (GRCm38) I935F probably benign Het
Otog T C 7: 46,298,265 (GRCm38) F96L probably damaging Het
Pde1b T C 15: 103,528,318 (GRCm38) L534P possibly damaging Het
Pdzd8 C T 19: 59,299,693 (GRCm38) E1092K probably damaging Het
Pfkl T C 10: 78,001,415 (GRCm38) H108R probably benign Het
Pkhd1l1 G A 15: 44,557,976 (GRCm38) V3047I probably benign Het
Plag1 A T 4: 3,904,812 (GRCm38) C126* probably null Het
Pphln1 T A 15: 93,455,525 (GRCm38) S229T probably benign Het
Pramel5 C T 4: 144,273,881 (GRCm38) D42N possibly damaging Het
Ptdss1 T A 13: 66,945,327 (GRCm38) I77N probably benign Het
Rsbn1 T A 3: 103,914,576 (GRCm38) C3* probably null Het
Shank1 C T 7: 44,327,161 (GRCm38) A561V unknown Het
Stip1 C T 19: 7,021,810 (GRCm38) G467S possibly damaging Het
Sv2c A T 13: 95,976,644 (GRCm38) V599E probably damaging Het
Vmn2r37 T C 7: 9,217,899 (GRCm38) T322A probably benign Het
Vmn2r60 T A 7: 42,137,063 (GRCm38) M430K probably benign Het
Wipf3 T A 6: 54,481,919 (GRCm38) probably null Het
Other mutations in Psd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00769:Psd3 APN 8 67,908,679 (GRCm38) splice site probably benign
IGL01095:Psd3 APN 8 67,908,513 (GRCm38) missense probably damaging 1.00
IGL01139:Psd3 APN 8 67,908,535 (GRCm38) missense probably damaging 1.00
IGL01330:Psd3 APN 8 67,697,178 (GRCm38) missense probably damaging 1.00
IGL01350:Psd3 APN 8 67,720,892 (GRCm38) missense probably damaging 1.00
IGL01487:Psd3 APN 8 67,697,114 (GRCm38) missense probably benign 0.01
IGL01780:Psd3 APN 8 67,963,869 (GRCm38) missense probably benign
IGL02020:Psd3 APN 8 67,974,170 (GRCm38) intron probably benign
IGL02232:Psd3 APN 8 67,904,145 (GRCm38) missense probably damaging 1.00
IGL02350:Psd3 APN 8 67,963,869 (GRCm38) missense probably benign
IGL02357:Psd3 APN 8 67,963,869 (GRCm38) missense probably benign
PIT4495001:Psd3 UTSW 8 67,963,913 (GRCm38) missense probably benign 0.00
R0052:Psd3 UTSW 8 67,882,979 (GRCm38) critical splice donor site probably null
R0052:Psd3 UTSW 8 67,882,979 (GRCm38) critical splice donor site probably null
R0242:Psd3 UTSW 8 67,758,086 (GRCm38) missense probably damaging 0.99
R0242:Psd3 UTSW 8 67,758,086 (GRCm38) missense probably damaging 0.99
R0581:Psd3 UTSW 8 67,720,946 (GRCm38) missense probably damaging 1.00
R0655:Psd3 UTSW 8 67,963,689 (GRCm38) missense probably benign 0.19
R1740:Psd3 UTSW 8 68,120,839 (GRCm38) missense probably damaging 1.00
R1789:Psd3 UTSW 8 67,960,565 (GRCm38) missense probably benign 0.26
R1847:Psd3 UTSW 8 67,720,004 (GRCm38) missense possibly damaging 0.93
R1951:Psd3 UTSW 8 67,963,487 (GRCm38) missense probably benign 0.00
R1954:Psd3 UTSW 8 67,697,075 (GRCm38) missense probably damaging 1.00
R2143:Psd3 UTSW 8 67,964,351 (GRCm38) missense probably damaging 1.00
R4387:Psd3 UTSW 8 68,000,761 (GRCm38) missense probably damaging 1.00
R4801:Psd3 UTSW 8 68,121,148 (GRCm38) missense probably benign
R4802:Psd3 UTSW 8 68,121,148 (GRCm38) missense probably benign
R4913:Psd3 UTSW 8 68,121,169 (GRCm38) missense probably damaging 0.99
R5045:Psd3 UTSW 8 67,713,825 (GRCm38) missense probably damaging 0.99
R5173:Psd3 UTSW 8 67,696,989 (GRCm38) missense probably damaging 1.00
R5264:Psd3 UTSW 8 67,713,725 (GRCm38) missense probably benign 0.23
R5350:Psd3 UTSW 8 67,908,861 (GRCm38) missense probably benign 0.00
R5816:Psd3 UTSW 8 67,960,510 (GRCm38) missense possibly damaging 0.90
R5994:Psd3 UTSW 8 67,719,968 (GRCm38) missense probably damaging 1.00
R6157:Psd3 UTSW 8 68,121,527 (GRCm38) start codon destroyed probably benign 0.14
R6241:Psd3 UTSW 8 67,818,139 (GRCm38) intron probably benign
R6586:Psd3 UTSW 8 67,963,545 (GRCm38) missense probably damaging 0.96
R6735:Psd3 UTSW 8 68,120,746 (GRCm38) critical splice donor site probably null
R6908:Psd3 UTSW 8 67,964,177 (GRCm38) missense probably benign 0.00
R6984:Psd3 UTSW 8 67,818,045 (GRCm38) missense possibly damaging 0.85
R7082:Psd3 UTSW 8 67,904,148 (GRCm38) missense probably benign 0.03
R7297:Psd3 UTSW 8 68,121,034 (GRCm38) missense probably damaging 0.98
R7334:Psd3 UTSW 8 67,908,705 (GRCm38) missense possibly damaging 0.94
R7348:Psd3 UTSW 8 67,790,931 (GRCm38) missense possibly damaging 0.65
R7357:Psd3 UTSW 8 68,121,497 (GRCm38) missense probably benign 0.01
R7369:Psd3 UTSW 8 67,904,166 (GRCm38) missense possibly damaging 0.95
R7385:Psd3 UTSW 8 68,000,756 (GRCm38) missense probably damaging 1.00
R7733:Psd3 UTSW 8 68,120,916 (GRCm38) missense possibly damaging 0.75
R7873:Psd3 UTSW 8 67,882,982 (GRCm38) missense possibly damaging 0.95
R8110:Psd3 UTSW 8 68,121,056 (GRCm38) missense probably damaging 1.00
R8765:Psd3 UTSW 8 67,963,441 (GRCm38) missense possibly damaging 0.69
R8768:Psd3 UTSW 8 67,964,351 (GRCm38) missense probably damaging 1.00
R8817:Psd3 UTSW 8 67,960,483 (GRCm38) missense possibly damaging 0.95
R8837:Psd3 UTSW 8 67,719,944 (GRCm38) missense probably damaging 0.99
R8878:Psd3 UTSW 8 67,758,098 (GRCm38) missense probably benign 0.28
R8903:Psd3 UTSW 8 67,713,293 (GRCm38) missense unknown
R8955:Psd3 UTSW 8 67,963,809 (GRCm38) missense probably benign 0.08
R9216:Psd3 UTSW 8 68,120,887 (GRCm38) missense probably benign 0.00
R9241:Psd3 UTSW 8 67,963,315 (GRCm38) missense probably benign 0.00
R9351:Psd3 UTSW 8 67,960,649 (GRCm38) missense probably benign 0.18
R9449:Psd3 UTSW 8 67,713,181 (GRCm38) missense unknown
R9451:Psd3 UTSW 8 67,910,835 (GRCm38) missense unknown
R9709:Psd3 UTSW 8 67,741,762 (GRCm38) missense probably null 0.99
R9797:Psd3 UTSW 8 67,758,126 (GRCm38) missense probably damaging 0.99
Z1088:Psd3 UTSW 8 67,906,260 (GRCm38) splice site silent
Predicted Primers PCR Primer
(F):5'- GGGCTCCTGTCATATTAGGATGTC -3'
(R):5'- TTGGAAGGACTTAGGACCAATG -3'

Sequencing Primer
(F):5'- TGTCCTAAATTGGAGCCAGGAC -3'
(R):5'- GGACTTAGGACCAATGATAAATGTTG -3'
Posted On 2019-05-15