Incidental Mutation 'R9413:Psd4'
ID 711884
Institutional Source Beutler Lab
Gene Symbol Psd4
Ensembl Gene ENSMUSG00000026979
Gene Name pleckstrin and Sec7 domain containing 4
Synonyms SEC7 homolog, EFA6B
MMRRC Submission
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9413 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 24257571-24299882 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 24287472 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 468 (T468I)
Ref Sequence ENSEMBL: ENSMUSP00000062415 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056641] [ENSMUST00000102942] [ENSMUST00000127242] [ENSMUST00000131930] [ENSMUST00000140303] [ENSMUST00000140547] [ENSMUST00000142522] [ENSMUST00000166388]
AlphaFold Q8BLR5
Predicted Effect probably benign
Transcript: ENSMUST00000056641
AA Change: T468I

PolyPhen 2 Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000062415
Gene: ENSMUSG00000026979
AA Change: T468I

DomainStartEndE-ValueType
low complexity region 156 176 N/A INTRINSIC
low complexity region 350 361 N/A INTRINSIC
low complexity region 420 438 N/A INTRINSIC
low complexity region 458 474 N/A INTRINSIC
Sec7 497 688 9.39e-47 SMART
PH 727 843 1.1e-10 SMART
low complexity region 883 893 N/A INTRINSIC
low complexity region 897 920 N/A INTRINSIC
low complexity region 961 973 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102942
AA Change: T468I

PolyPhen 2 Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000100006
Gene: ENSMUSG00000026979
AA Change: T468I

DomainStartEndE-ValueType
low complexity region 156 176 N/A INTRINSIC
low complexity region 350 361 N/A INTRINSIC
low complexity region 420 438 N/A INTRINSIC
low complexity region 458 474 N/A INTRINSIC
Sec7 497 688 9.39e-47 SMART
PH 727 843 1.1e-10 SMART
low complexity region 883 893 N/A INTRINSIC
low complexity region 897 920 N/A INTRINSIC
low complexity region 961 973 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000127242
Predicted Effect probably benign
Transcript: ENSMUST00000131930
Predicted Effect probably benign
Transcript: ENSMUST00000140303
Predicted Effect probably benign
Transcript: ENSMUST00000140547
Predicted Effect probably benign
Transcript: ENSMUST00000142522
Predicted Effect probably benign
Transcript: ENSMUST00000166388
AA Change: T468I

PolyPhen 2 Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000132395
Gene: ENSMUSG00000026979
AA Change: T468I

DomainStartEndE-ValueType
low complexity region 156 176 N/A INTRINSIC
low complexity region 350 361 N/A INTRINSIC
low complexity region 420 438 N/A INTRINSIC
low complexity region 458 474 N/A INTRINSIC
Sec7 497 688 9.39e-47 SMART
PH 727 843 1.1e-10 SMART
low complexity region 883 893 N/A INTRINSIC
low complexity region 897 920 N/A INTRINSIC
low complexity region 961 973 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 97% (35/36)
Allele List at MGI
Other mutations in this stock
Total: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 A T 7: 120,126,422 (GRCm39) T1194S probably benign Het
Akr7a5 A T 4: 139,038,059 (GRCm39) probably benign Het
Ap3b2 G T 7: 81,127,757 (GRCm39) P140T possibly damaging Het
Ap3s1 T C 18: 46,887,531 (GRCm39) probably null Het
Arrdc2 C T 8: 71,288,892 (GRCm39) R381H probably damaging Het
Atg13 T C 2: 91,511,970 (GRCm39) D286G probably benign Het
C1qtnf4 T C 2: 90,720,648 (GRCm39) F307S probably damaging Het
Cdk5rap1 A T 2: 154,207,880 (GRCm39) probably null Het
Chsy3 C T 18: 59,309,170 (GRCm39) A141V possibly damaging Het
Creb3l1 C T 2: 91,822,231 (GRCm39) probably null Het
D5Ertd579e A G 5: 36,772,278 (GRCm39) S706P probably damaging Het
Ell2 A G 13: 75,917,705 (GRCm39) D545G Het
Ephb6 T C 6: 41,591,509 (GRCm39) L222P Het
Flnc G A 6: 29,441,484 (GRCm39) R422Q probably benign Het
Gm6619 A T 6: 131,468,370 (GRCm39) D167V unknown Het
Gucy2c T C 6: 136,700,771 (GRCm39) D581G possibly damaging Het
Hectd1 G A 12: 51,792,880 (GRCm39) R2471* probably null Het
Kif1a A T 1: 92,949,019 (GRCm39) M1501K probably benign Het
Mycbpap A G 11: 94,392,321 (GRCm39) V390A probably damaging Het
Or2n1d A T 17: 38,646,320 (GRCm39) T91S possibly damaging Het
Pex3 A G 10: 13,410,454 (GRCm39) Y236H probably damaging Het
Pglyrp3 G T 3: 91,930,106 (GRCm39) A91S probably damaging Het
Ppp1ca T C 19: 4,244,897 (GRCm39) S292P probably damaging Het
Prkci T C 3: 31,097,915 (GRCm39) V455A probably damaging Het
Prrx1 A G 1: 163,140,182 (GRCm39) V8A probably benign Het
Rnf213 A G 11: 119,357,059 (GRCm39) E4203G Het
Snrnp27 T C 6: 86,653,255 (GRCm39) D121G possibly damaging Het
Spag6 A T 2: 18,739,029 (GRCm39) M320L probably benign Het
Spata16 T A 3: 26,978,486 (GRCm39) M484K possibly damaging Het
Trim69 G A 2: 122,009,083 (GRCm39) W381* probably null Het
Tubgcp3 A C 8: 12,674,885 (GRCm39) I745S probably damaging Het
Ubxn2b A G 4: 6,204,607 (GRCm39) D156G probably damaging Het
Vmn2r103 A G 17: 20,032,158 (GRCm39) N644S possibly damaging Het
Other mutations in Psd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00850:Psd4 APN 2 24,284,298 (GRCm39) missense probably benign 0.25
IGL01302:Psd4 APN 2 24,286,799 (GRCm39) critical splice donor site probably null
IGL01446:Psd4 APN 2 24,295,407 (GRCm39) missense probably damaging 1.00
IGL01577:Psd4 APN 2 24,293,234 (GRCm39) missense probably damaging 0.96
IGL01823:Psd4 APN 2 24,284,444 (GRCm39) missense probably benign 0.27
IGL02103:Psd4 APN 2 24,290,540 (GRCm39) nonsense probably null
IGL02212:Psd4 APN 2 24,295,326 (GRCm39) nonsense probably null
IGL02240:Psd4 APN 2 24,286,389 (GRCm39) missense probably benign 0.00
IGL02261:Psd4 APN 2 24,291,756 (GRCm39) missense probably damaging 1.00
IGL02345:Psd4 APN 2 24,291,835 (GRCm39) critical splice donor site probably null
IGL03272:Psd4 APN 2 24,295,692 (GRCm39) splice site probably benign
bitcoin UTSW 2 24,291,569 (GRCm39) missense probably damaging 1.00
crypto UTSW 2 24,287,259 (GRCm39) missense probably benign
Ethereum UTSW 2 24,296,996 (GRCm39) missense probably damaging 1.00
underworld UTSW 2 24,295,363 (GRCm39) missense probably damaging 1.00
PIT4469001:Psd4 UTSW 2 24,284,306 (GRCm39) missense probably benign 0.08
R0131:Psd4 UTSW 2 24,295,363 (GRCm39) missense probably damaging 1.00
R0131:Psd4 UTSW 2 24,295,363 (GRCm39) missense probably damaging 1.00
R0132:Psd4 UTSW 2 24,295,363 (GRCm39) missense probably damaging 1.00
R0278:Psd4 UTSW 2 24,284,450 (GRCm39) missense probably damaging 1.00
R1303:Psd4 UTSW 2 24,285,030 (GRCm39) missense probably benign 0.00
R1551:Psd4 UTSW 2 24,293,292 (GRCm39) missense probably benign 0.02
R1715:Psd4 UTSW 2 24,295,344 (GRCm39) missense probably damaging 1.00
R1854:Psd4 UTSW 2 24,287,468 (GRCm39) missense probably benign 0.26
R1942:Psd4 UTSW 2 24,295,805 (GRCm39) missense probably damaging 1.00
R2392:Psd4 UTSW 2 24,284,679 (GRCm39) missense probably damaging 0.98
R2420:Psd4 UTSW 2 24,291,253 (GRCm39) missense probably damaging 1.00
R4509:Psd4 UTSW 2 24,286,347 (GRCm39) missense probably benign
R4512:Psd4 UTSW 2 24,292,901 (GRCm39) missense probably damaging 1.00
R4558:Psd4 UTSW 2 24,294,806 (GRCm39) missense probably damaging 1.00
R4995:Psd4 UTSW 2 24,287,259 (GRCm39) missense probably benign
R5120:Psd4 UTSW 2 24,295,450 (GRCm39) missense probably benign
R5314:Psd4 UTSW 2 24,290,528 (GRCm39) missense possibly damaging 0.89
R5563:Psd4 UTSW 2 24,284,897 (GRCm39) missense probably benign
R5638:Psd4 UTSW 2 24,287,427 (GRCm39) missense probably benign 0.14
R6191:Psd4 UTSW 2 24,284,499 (GRCm39) missense probably damaging 1.00
R6224:Psd4 UTSW 2 24,291,569 (GRCm39) missense probably damaging 1.00
R7024:Psd4 UTSW 2 24,284,555 (GRCm39) missense possibly damaging 0.76
R7046:Psd4 UTSW 2 24,284,985 (GRCm39) missense probably benign 0.05
R7209:Psd4 UTSW 2 24,287,357 (GRCm39) missense probably damaging 1.00
R7483:Psd4 UTSW 2 24,294,768 (GRCm39) missense possibly damaging 0.65
R7498:Psd4 UTSW 2 24,296,996 (GRCm39) missense probably damaging 1.00
R7571:Psd4 UTSW 2 24,297,023 (GRCm39) missense probably damaging 1.00
R7741:Psd4 UTSW 2 24,291,108 (GRCm39) critical splice donor site probably null
R7978:Psd4 UTSW 2 24,294,867 (GRCm39) missense probably damaging 1.00
R8133:Psd4 UTSW 2 24,286,701 (GRCm39) missense probably benign
R8254:Psd4 UTSW 2 24,293,223 (GRCm39) missense probably damaging 0.99
R8786:Psd4 UTSW 2 24,295,444 (GRCm39) missense probably benign 0.08
R8797:Psd4 UTSW 2 24,287,440 (GRCm39) missense probably benign 0.02
R9015:Psd4 UTSW 2 24,287,492 (GRCm39) missense
X0009:Psd4 UTSW 2 24,291,537 (GRCm39) missense probably damaging 1.00
X0064:Psd4 UTSW 2 24,294,750 (GRCm39) missense probably damaging 0.99
Z1177:Psd4 UTSW 2 24,284,943 (GRCm39) frame shift probably null
Z1177:Psd4 UTSW 2 24,284,924 (GRCm39) missense possibly damaging 0.95
Predicted Primers PCR Primer
(F):5'- AGCCCGTGTTCTGCACTTTG -3'
(R):5'- ATGCTCTACCCAAAGCAGG -3'

Sequencing Primer
(F):5'- GGAGCCAAACCTCTTTACTGGAG -3'
(R):5'- GCAGGGTATTCTTATCACAACAC -3'
Posted On 2022-05-16