Incidental Mutation 'ANU05:Psd'
ID 262519
Institutional Source Beutler Lab
Gene Symbol Psd
Ensembl Gene ENSMUSG00000037126
Gene Name pleckstrin and Sec7 domain containing
Synonyms Efa6, Psdl, Efa6a, 1110007H17Rik
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # ANU05
Quality Score 192
Status Not validated
Chromosome 19
Chromosomal Location 46300526-46315595 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 46303186 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 100 (V100A)
Ref Sequence ENSEMBL: ENSMUSP00000153381 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041391] [ENSMUST00000073116] [ENSMUST00000096029] [ENSMUST00000111881] [ENSMUST00000224556] [ENSMUST00000225323]
AlphaFold Q5DTT2
Predicted Effect probably benign
Transcript: ENSMUST00000041391
AA Change: V731A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: V731A

DomainStartEndE-ValueType
low complexity region 48 63 N/A INTRINSIC
low complexity region 79 99 N/A INTRINSIC
low complexity region 329 368 N/A INTRINSIC
low complexity region 419 431 N/A INTRINSIC
low complexity region 445 466 N/A INTRINSIC
Sec7 519 708 5.08e-75 SMART
low complexity region 714 724 N/A INTRINSIC
low complexity region 736 744 N/A INTRINSIC
PH 757 871 1.87e-13 SMART
Blast:Sec7 900 952 1e-6 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000073116
SMART Domains Protein: ENSMUSP00000072859
Gene: ENSMUSG00000025225

DomainStartEndE-ValueType
Pfam:RHD_DNA_bind 40 220 1.3e-67 PFAM
IPT 227 326 3.48e-27 SMART
low complexity region 351 382 N/A INTRINSIC
low complexity region 391 409 N/A INTRINSIC
ANK 487 522 5.58e1 SMART
ANK 526 555 9.78e-4 SMART
ANK 559 591 3.74e0 SMART
ANK 599 628 3.36e-2 SMART
ANK 633 663 1.3e1 SMART
ANK 667 696 4.26e-4 SMART
low complexity region 707 721 N/A INTRINSIC
ANK 729 758 2.35e3 SMART
DEATH 764 851 5.52e-16 SMART
low complexity region 879 894 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000096029
AA Change: V732A

PolyPhen 2 Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: V732A

DomainStartEndE-ValueType
low complexity region 48 63 N/A INTRINSIC
low complexity region 79 99 N/A INTRINSIC
low complexity region 329 368 N/A INTRINSIC
low complexity region 419 431 N/A INTRINSIC
low complexity region 445 466 N/A INTRINSIC
Sec7 520 709 5.08e-75 SMART
low complexity region 715 725 N/A INTRINSIC
low complexity region 737 745 N/A INTRINSIC
PH 758 872 1.87e-13 SMART
Blast:Sec7 901 953 1e-6 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000111881
SMART Domains Protein: ENSMUSP00000107512
Gene: ENSMUSG00000025225

DomainStartEndE-ValueType
Pfam:RHD 40 220 1.3e-67 PFAM
IPT 227 326 3.48e-27 SMART
low complexity region 351 382 N/A INTRINSIC
low complexity region 391 409 N/A INTRINSIC
ANK 487 522 5.58e1 SMART
ANK 526 555 9.78e-4 SMART
ANK 559 591 3.74e0 SMART
ANK 599 628 3.36e-2 SMART
ANK 633 663 1.3e1 SMART
ANK 667 696 4.26e-4 SMART
low complexity region 707 721 N/A INTRINSIC
ANK 729 758 2.35e3 SMART
DEATH 764 851 5.52e-16 SMART
low complexity region 879 894 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000224556
AA Change: V100A

PolyPhen 2 Score 0.766 (Sensitivity: 0.85; Specificity: 0.92)
Predicted Effect probably benign
Transcript: ENSMUST00000225323
AA Change: V732A

PolyPhen 2 Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000226062
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225748
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.5%
  • 20x: 93.3%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110038F14Rik G A 15: 76,834,475 (GRCm39) V124I probably damaging Het
Acaca A G 11: 84,206,678 (GRCm39) K1513E probably damaging Het
Acacb T A 5: 114,363,931 (GRCm39) F1464Y probably benign Het
Adgrg6 G A 10: 14,286,274 (GRCm39) A1114V possibly damaging Het
Agl A G 3: 116,566,438 (GRCm39) I975T possibly damaging Het
Akap7 T C 10: 25,147,451 (GRCm39) H93R probably damaging Het
Arhgef11 T C 3: 87,640,481 (GRCm39) W1213R probably benign Het
Ccar1 T A 10: 62,592,428 (GRCm39) E708V probably damaging Het
Cfap206 C T 4: 34,721,562 (GRCm39) S162N probably damaging Het
Cilp T C 9: 65,186,265 (GRCm39) S787P possibly damaging Het
Col6a3 G A 1: 90,730,014 (GRCm39) T1157I probably damaging Het
D630003M21Rik T C 2: 158,038,308 (GRCm39) Y1046C probably benign Het
Dock3 A G 9: 106,772,862 (GRCm39) S464P probably benign Het
Dusp19 A G 2: 80,454,618 (GRCm39) T113A probably benign Het
Dync1h1 A C 12: 110,615,538 (GRCm39) Y2957S probably benign Het
Epdr1 T C 13: 19,778,814 (GRCm39) Y94C probably damaging Het
Fcho1 A T 8: 72,165,191 (GRCm39) L422Q probably benign Het
Gca T A 2: 62,520,787 (GRCm39) Y210* probably null Het
Gpnmb T C 6: 49,032,615 (GRCm39) V513A probably benign Het
Irx4 A G 13: 73,415,786 (GRCm39) T192A probably damaging Het
Isca1 T C 13: 59,906,785 (GRCm39) T54A probably benign Het
Kif12 GGGGC GGGGCCTCCACCCGGCGGGC 4: 63,089,660 (GRCm39) probably benign Het
L3mbtl1 T C 2: 162,812,100 (GRCm39) V715A probably benign Het
Lama1 G A 17: 68,045,865 (GRCm39) D257N probably damaging Het
Lgr5 T C 10: 115,314,439 (GRCm39) H166R probably damaging Het
M6pr A G 6: 122,289,218 (GRCm39) R9G probably benign Het
Nmt2 T G 2: 3,315,731 (GRCm39) S240R probably benign Het
Npas3 A G 12: 54,114,857 (GRCm39) E593G possibly damaging Het
Or8k30 G A 2: 86,339,513 (GRCm39) A237T possibly damaging Het
Pank4 T C 4: 155,059,103 (GRCm39) M412T probably damaging Het
Rab11fip3 T C 17: 26,235,087 (GRCm39) T28A probably damaging Het
Rnpepl1 A T 1: 92,847,468 (GRCm39) D685V probably benign Het
Rrad T C 8: 105,357,283 (GRCm39) E88G probably benign Het
Sdk2 T A 11: 113,733,906 (GRCm39) M846L probably benign Het
Sparcl1 A T 5: 104,242,581 (GRCm39) V36E possibly damaging Het
Spmip5 A T 19: 58,777,545 (GRCm39) H80Q probably damaging Het
Srrm4 C T 5: 116,605,628 (GRCm39) E210K unknown Het
Stk25 A T 1: 93,551,145 (GRCm39) probably null Het
Tacr3 A T 3: 134,635,810 (GRCm39) Y338F probably damaging Het
Tap2 A T 17: 34,428,184 (GRCm39) Q286L probably benign Het
Tedc1 C T 12: 113,126,808 (GRCm39) R357* probably null Het
Tubgcp5 C A 7: 55,458,277 (GRCm39) A396E possibly damaging Het
Ube2o T C 11: 116,430,960 (GRCm39) D980G probably damaging Het
Vmn1r86 T C 7: 12,836,433 (GRCm39) M98V probably benign Het
Vmn2r58 T A 7: 41,513,935 (GRCm39) H236L probably benign Het
Zfp521 T C 18: 13,950,303 (GRCm39) H1217R probably damaging Het
Zfyve1 A T 12: 83,601,779 (GRCm39) F110I probably benign Het
Other mutations in Psd
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01291:Psd APN 19 46,303,186 (GRCm39) missense possibly damaging 0.77
IGL01307:Psd APN 19 46,303,097 (GRCm39) missense probably damaging 1.00
IGL02329:Psd APN 19 46,308,098 (GRCm39) missense possibly damaging 0.66
IGL02423:Psd APN 19 46,302,943 (GRCm39) missense possibly damaging 0.95
IGL02644:Psd APN 19 46,311,834 (GRCm39) missense probably damaging 1.00
IGL02724:Psd APN 19 46,307,984 (GRCm39) missense probably benign 0.04
IGL03117:Psd APN 19 46,311,561 (GRCm39) unclassified probably benign
G1Funyon:Psd UTSW 19 46,309,541 (GRCm39) intron probably benign
P0035:Psd UTSW 19 46,309,400 (GRCm39) missense possibly damaging 0.56
R0054:Psd UTSW 19 46,311,781 (GRCm39) missense probably damaging 1.00
R0054:Psd UTSW 19 46,311,781 (GRCm39) missense probably damaging 1.00
R0403:Psd UTSW 19 46,309,411 (GRCm39) unclassified probably benign
R0499:Psd UTSW 19 46,310,600 (GRCm39) missense probably damaging 0.98
R0542:Psd UTSW 19 46,302,649 (GRCm39) missense probably damaging 1.00
R0543:Psd UTSW 19 46,307,956 (GRCm39) missense possibly damaging 0.62
R0894:Psd UTSW 19 46,301,880 (GRCm39) missense probably damaging 1.00
R1449:Psd UTSW 19 46,313,250 (GRCm39) missense probably damaging 0.99
R1586:Psd UTSW 19 46,303,237 (GRCm39) missense probably damaging 0.98
R2096:Psd UTSW 19 46,313,088 (GRCm39) splice site probably null
R2504:Psd UTSW 19 46,313,352 (GRCm39) missense possibly damaging 0.90
R2857:Psd UTSW 19 46,312,859 (GRCm39) missense probably benign 0.00
R2863:Psd UTSW 19 46,303,201 (GRCm39) missense probably damaging 0.97
R3897:Psd UTSW 19 46,313,024 (GRCm39) missense possibly damaging 0.93
R3967:Psd UTSW 19 46,312,845 (GRCm39) missense probably benign
R3970:Psd UTSW 19 46,312,845 (GRCm39) missense probably benign
R4435:Psd UTSW 19 46,302,933 (GRCm39) missense probably damaging 1.00
R4612:Psd UTSW 19 46,301,778 (GRCm39) missense probably benign 0.15
R4940:Psd UTSW 19 46,310,856 (GRCm39) missense probably damaging 1.00
R5055:Psd UTSW 19 46,310,907 (GRCm39) missense probably benign 0.00
R5485:Psd UTSW 19 46,304,528 (GRCm39) splice site probably null
R5768:Psd UTSW 19 46,301,178 (GRCm39) missense possibly damaging 0.84
R5775:Psd UTSW 19 46,303,211 (GRCm39) nonsense probably null
R6057:Psd UTSW 19 46,311,753 (GRCm39) missense possibly damaging 0.77
R6349:Psd UTSW 19 46,301,826 (GRCm39) splice site probably null
R6496:Psd UTSW 19 46,308,753 (GRCm39) missense probably damaging 1.00
R6614:Psd UTSW 19 46,301,851 (GRCm39) missense probably benign 0.11
R6820:Psd UTSW 19 46,309,283 (GRCm39) missense probably damaging 1.00
R6849:Psd UTSW 19 46,306,185 (GRCm39) missense probably damaging 0.97
R6860:Psd UTSW 19 46,310,858 (GRCm39) missense probably damaging 1.00
R7286:Psd UTSW 19 46,303,240 (GRCm39) missense probably damaging 0.98
R7326:Psd UTSW 19 46,312,893 (GRCm39) missense probably benign 0.01
R7351:Psd UTSW 19 46,310,869 (GRCm39) missense probably benign 0.27
R7593:Psd UTSW 19 46,301,352 (GRCm39) missense possibly damaging 0.47
R7614:Psd UTSW 19 46,301,877 (GRCm39) missense probably damaging 1.00
R7943:Psd UTSW 19 46,313,169 (GRCm39) missense possibly damaging 0.54
R8301:Psd UTSW 19 46,309,541 (GRCm39) intron probably benign
R8498:Psd UTSW 19 46,312,788 (GRCm39) missense probably damaging 1.00
R8712:Psd UTSW 19 46,301,775 (GRCm39) missense probably damaging 1.00
R8952:Psd UTSW 19 46,310,900 (GRCm39) missense probably damaging 1.00
R8980:Psd UTSW 19 46,310,657 (GRCm39) missense possibly damaging 0.95
R9168:Psd UTSW 19 46,309,233 (GRCm39) missense probably damaging 1.00
R9322:Psd UTSW 19 46,301,880 (GRCm39) missense probably damaging 1.00
R9512:Psd UTSW 19 46,306,154 (GRCm39) missense possibly damaging 0.79
R9569:Psd UTSW 19 46,308,717 (GRCm39) missense possibly damaging 0.94
R9638:Psd UTSW 19 46,301,841 (GRCm39) frame shift probably null
R9645:Psd UTSW 19 46,301,841 (GRCm39) frame shift probably null
R9721:Psd UTSW 19 46,311,628 (GRCm39) missense probably benign 0.00
Z1177:Psd UTSW 19 46,313,100 (GRCm39) missense probably benign 0.16
Predicted Primers PCR Primer
(F):5'- AGCTACCTAATCCCCTCTGGCAAG -3'
(R):5'- CGTGTCTGTCCAGGAGAAAAGTGTG -3'

Sequencing Primer
(F):5'- AGGTAGAGGATCATGCCCTTG -3'
(R):5'- AGCCCTACTCGGAGATAGCAG -3'
Posted On 2015-02-04