Incidental Mutation 'R0366:Prdm4'
ID 36426
Institutional Source Beutler Lab
Gene Symbol Prdm4
Ensembl Gene ENSMUSG00000035529
Gene Name PR domain containing 4
Synonyms SC-1, SC1, 1700031E19Rik, 2810470D21Rik
MMRRC Submission 038572-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0366 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 85727828-85752958 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 85743868 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 129 (D129G)
Ref Sequence ENSEMBL: ENSMUSP00000151931 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000037646] [ENSMUST00000218969] [ENSMUST00000219370] [ENSMUST00000220032]
AlphaFold Q80V63
Predicted Effect probably damaging
Transcript: ENSMUST00000037646
AA Change: D129G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000041942
Gene: ENSMUSG00000035529
AA Change: D129G

DomainStartEndE-ValueType
low complexity region 14 28 N/A INTRINSIC
low complexity region 33 44 N/A INTRINSIC
low complexity region 51 69 N/A INTRINSIC
low complexity region 339 353 N/A INTRINSIC
PDB:3DB5|B 386 543 2e-98 PDB
Blast:SET 408 538 5e-82 BLAST
ZnF_C2H2 548 569 7.77e1 SMART
low complexity region 575 588 N/A INTRINSIC
ZnF_C2H2 593 615 3.78e-1 SMART
ZnF_C2H2 621 643 2.27e-4 SMART
ZnF_C2H2 649 671 8.02e-5 SMART
ZnF_C2H2 677 699 3.63e-3 SMART
ZnF_C2H2 705 727 3.11e-2 SMART
ZnF_C2H2 733 753 1.81e1 SMART
low complexity region 759 780 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218289
Predicted Effect probably damaging
Transcript: ENSMUST00000218969
AA Change: D129G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219112
Predicted Effect probably benign
Transcript: ENSMUST00000219370
Predicted Effect probably damaging
Transcript: ENSMUST00000220032
AA Change: D129G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.7736 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 91.9%
Validation Efficiency 99% (68/69)
MGI Phenotype FUNCTION: This gene encodes a member of the PR/SET family of zinc finger proteins. This protein has been shown to bind DNA in a sequence-specific manner and has been implicated in neural stem cell proliferation and differentiation. Pseudogenes have been identified on chromosomes 14 and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
PHENOTYPE: Mice homozygous for alleles lacking the zinc finger domain or PR/SET domain exhibit no abnormal phenotype. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc10 G T 17: 46,635,724 (GRCm39) S93* probably null Het
Ackr2 T C 9: 121,738,426 (GRCm39) L267P probably damaging Het
Adgre4 T A 17: 56,099,001 (GRCm39) L169* probably null Het
Ankrd12 T A 17: 66,291,501 (GRCm39) S1311C possibly damaging Het
Arid2 T A 15: 96,259,601 (GRCm39) probably benign Het
Atp9b A T 18: 80,805,317 (GRCm39) V747E probably damaging Het
Best1 T C 19: 9,969,417 (GRCm39) probably null Het
Brwd1 C A 16: 95,839,164 (GRCm39) E836* probably null Het
Cachd1 A G 4: 100,851,934 (GRCm39) S1177G possibly damaging Het
Cacna1e C T 1: 154,291,884 (GRCm39) E1766K probably benign Het
Cckar A G 5: 53,857,507 (GRCm39) I301T probably benign Het
Cdc27 T G 11: 104,396,474 (GRCm39) T816P probably damaging Het
Cep162 T G 9: 87,102,537 (GRCm39) Q708H probably damaging Het
Cep250 C A 2: 155,830,321 (GRCm39) D1301E probably benign Het
D430041D05Rik G A 2: 104,085,685 (GRCm39) H955Y probably damaging Het
Dcdc2a T A 13: 25,240,417 (GRCm39) V55E probably damaging Het
Efcab12 A G 6: 115,800,209 (GRCm39) probably benign Het
Ep400 A G 5: 110,849,537 (GRCm39) V1428A unknown Het
Erbb3 T C 10: 128,408,439 (GRCm39) E825G possibly damaging Het
Evl A T 12: 108,652,307 (GRCm39) probably null Het
Fuca2 G A 10: 13,381,507 (GRCm39) R140H probably benign Het
Gm5581 T C 6: 131,143,410 (GRCm39) noncoding transcript Het
Gm7052 T C 17: 22,259,498 (GRCm39) probably benign Het
Gpd1 T G 15: 99,617,151 (GRCm39) I119S probably damaging Het
Gzmc A T 14: 56,470,193 (GRCm39) Y101* probably null Het
Hmcn2 G T 2: 31,314,218 (GRCm39) A3588S possibly damaging Het
Ikbkb A G 8: 23,185,276 (GRCm39) probably benign Het
Itgax G T 7: 127,748,261 (GRCm39) probably benign Het
Kif24 C A 4: 41,428,717 (GRCm39) S81I possibly damaging Het
Lct G A 1: 128,214,199 (GRCm39) P1858S probably benign Het
Map2k1 C A 9: 64,100,984 (GRCm39) probably null Het
Mdga1 A G 17: 30,076,682 (GRCm39) V30A possibly damaging Het
Meiosin T A 7: 18,840,964 (GRCm39) I57F probably damaging Het
Mtcl1 G A 17: 66,645,124 (GRCm39) P1441L probably damaging Het
N4bp2 T A 5: 65,963,739 (GRCm39) F596Y possibly damaging Het
Notch4 A T 17: 34,800,473 (GRCm39) probably benign Het
Or2l5 A G 16: 19,333,598 (GRCm39) S263P probably benign Het
Or4c12 A C 2: 89,774,162 (GRCm39) V99G possibly damaging Het
Or6c1 A G 10: 129,517,840 (GRCm39) M256T possibly damaging Het
Or8b44 T A 9: 38,410,450 (GRCm39) C162S possibly damaging Het
Or8k25 A G 2: 86,244,369 (GRCm39) V9A possibly damaging Het
Pbld2 A G 10: 62,889,736 (GRCm39) probably benign Het
Phip T C 9: 82,808,460 (GRCm39) Y505C probably damaging Het
Plcb2 A G 2: 118,554,928 (GRCm39) F58L probably benign Het
Plcd1 T A 9: 118,910,204 (GRCm39) I72F probably damaging Het
Ppp5c A T 7: 16,756,508 (GRCm39) Y63* probably null Het
Prkcq C A 2: 11,251,649 (GRCm39) probably benign Het
Rab5b C T 10: 128,518,772 (GRCm39) R120Q probably benign Het
Rab7b T A 1: 131,626,242 (GRCm39) V90D probably damaging Het
Ripk3 T C 14: 56,024,292 (GRCm39) T193A probably damaging Het
Rnf167 C T 11: 70,540,143 (GRCm39) R88* probably null Het
Robo1 A G 16: 72,539,133 (GRCm39) T59A possibly damaging Het
Scd2 G A 19: 44,289,685 (GRCm39) V227I probably benign Het
Scg3 T A 9: 75,582,620 (GRCm39) probably benign Het
Sec31a A T 5: 100,530,625 (GRCm39) L677H probably damaging Het
Sema6a G A 18: 47,423,112 (GRCm39) probably null Het
Setd7 T C 3: 51,457,741 (GRCm39) T29A probably benign Het
Shoc1 A C 4: 59,099,410 (GRCm39) M94R probably benign Het
Slc4a5 A G 6: 83,272,854 (GRCm39) Y942C probably benign Het
Slit1 T A 19: 41,599,470 (GRCm39) Y1027F probably damaging Het
Sptan1 G A 2: 29,882,764 (GRCm39) probably null Het
Tdrd12 T C 7: 35,208,227 (GRCm39) Q249R probably benign Het
Tmem171 T A 13: 98,828,736 (GRCm39) D138V possibly damaging Het
Ttll10 G A 4: 156,119,612 (GRCm39) R596W probably damaging Het
Usp53 G T 3: 122,742,850 (GRCm39) N695K probably damaging Het
Vmn2r25 A T 6: 123,800,581 (GRCm39) L587* probably null Het
Zglp1 C T 9: 20,974,675 (GRCm39) C171Y probably benign Het
Other mutations in Prdm4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01864:Prdm4 APN 10 85,729,100 (GRCm39) missense probably benign 0.08
IGL02514:Prdm4 APN 10 85,743,781 (GRCm39) missense probably damaging 0.99
IGL02576:Prdm4 APN 10 85,736,801 (GRCm39) missense possibly damaging 0.86
IGL02674:Prdm4 APN 10 85,729,263 (GRCm39) missense probably damaging 0.99
IGL03002:Prdm4 APN 10 85,729,016 (GRCm39) missense probably benign 0.08
IGL03153:Prdm4 APN 10 85,743,860 (GRCm39) missense probably benign
IGL03278:Prdm4 APN 10 85,743,622 (GRCm39) missense probably damaging 0.99
IGL03338:Prdm4 APN 10 85,743,685 (GRCm39) missense possibly damaging 0.90
R0020:Prdm4 UTSW 10 85,743,487 (GRCm39) missense probably benign
R0133:Prdm4 UTSW 10 85,746,085 (GRCm39) critical splice donor site probably null
R0633:Prdm4 UTSW 10 85,743,767 (GRCm39) missense probably damaging 1.00
R1132:Prdm4 UTSW 10 85,735,145 (GRCm39) missense probably damaging 1.00
R1460:Prdm4 UTSW 10 85,743,686 (GRCm39) missense probably benign 0.28
R1477:Prdm4 UTSW 10 85,740,129 (GRCm39) missense probably benign 0.00
R1680:Prdm4 UTSW 10 85,735,087 (GRCm39) missense possibly damaging 0.96
R1772:Prdm4 UTSW 10 85,729,256 (GRCm39) missense probably damaging 0.99
R1983:Prdm4 UTSW 10 85,743,817 (GRCm39) missense probably damaging 1.00
R2136:Prdm4 UTSW 10 85,729,215 (GRCm39) nonsense probably null
R3426:Prdm4 UTSW 10 85,746,153 (GRCm39) missense probably damaging 1.00
R3723:Prdm4 UTSW 10 85,735,145 (GRCm39) missense probably damaging 1.00
R4490:Prdm4 UTSW 10 85,736,763 (GRCm39) missense probably damaging 1.00
R4750:Prdm4 UTSW 10 85,735,085 (GRCm39) missense probably damaging 1.00
R5561:Prdm4 UTSW 10 85,728,987 (GRCm39) makesense probably null
R5601:Prdm4 UTSW 10 85,728,987 (GRCm39) makesense probably null
R5602:Prdm4 UTSW 10 85,728,987 (GRCm39) makesense probably null
R5604:Prdm4 UTSW 10 85,728,987 (GRCm39) makesense probably null
R5972:Prdm4 UTSW 10 85,743,365 (GRCm39) missense probably damaging 1.00
R6272:Prdm4 UTSW 10 85,743,694 (GRCm39) missense possibly damaging 0.82
R6300:Prdm4 UTSW 10 85,746,085 (GRCm39) critical splice donor site probably null
R6457:Prdm4 UTSW 10 85,743,896 (GRCm39) missense probably damaging 1.00
R6605:Prdm4 UTSW 10 85,740,002 (GRCm39) missense probably benign 0.00
R6642:Prdm4 UTSW 10 85,743,682 (GRCm39) missense probably benign 0.00
R7663:Prdm4 UTSW 10 85,735,145 (GRCm39) missense probably damaging 1.00
R9064:Prdm4 UTSW 10 85,737,678 (GRCm39) missense probably damaging 0.98
R9071:Prdm4 UTSW 10 85,729,076 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- ATCATTAGGATGAAGACTTTGGGCACC -3'
(R):5'- ACCACAGCTTTGGATTTGGGATGTAG -3'

Sequencing Primer
(F):5'- CACCATGTGTGTTTACAGAGC -3'
(R):5'- taGAGCAAATTTTAGCATCTTTGGAC -3'
Posted On 2013-05-09