Incidental Mutation 'R4490:Prdm4'
ID 330688
Institutional Source Beutler Lab
Gene Symbol Prdm4
Ensembl Gene ENSMUSG00000035529
Gene Name PR domain containing 4
Synonyms SC-1, SC1, 1700031E19Rik, 2810470D21Rik
MMRRC Submission 041746-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4490 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 85727828-85752958 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 85736763 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Serine at position 626 (C626S)
Ref Sequence ENSEMBL: ENSMUSP00000151931 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000037646] [ENSMUST00000219370] [ENSMUST00000220032]
AlphaFold Q80V63
Predicted Effect probably damaging
Transcript: ENSMUST00000037646
AA Change: C619S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000041942
Gene: ENSMUSG00000035529
AA Change: C619S

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: ENSMUST00000218743
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219112
Predicted Effect probably benign
Transcript: ENSMUST00000219370
Predicted Effect probably damaging
Transcript: ENSMUST00000220032
AA Change: C626S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.9673 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.1%
Validation Efficiency 100% (45/45)
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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abl2 T C 1: 156,461,349 (GRCm39) V417A probably damaging Het
Adgrb2 T C 4: 129,906,121 (GRCm39) V881A possibly damaging Het
Arl5c G A 11: 97,886,662 (GRCm39) R10* probably null Het
Atad1 A G 19: 32,673,197 (GRCm39) C229R probably benign Het
Atp6v0a2 T C 5: 124,784,674 (GRCm39) V319A probably damaging Het
Cage1 A G 13: 38,207,393 (GRCm39) S257P possibly damaging Het
Ccndbp1 A G 2: 120,842,876 (GRCm39) D179G probably damaging Het
Cngb3 T C 4: 19,415,684 (GRCm39) I398T probably benign Het
Crmp1 A G 5: 37,433,675 (GRCm39) D178G probably damaging Het
Csmd3 C T 15: 48,177,429 (GRCm39) V370I possibly damaging Het
Dapk1 A G 13: 60,865,942 (GRCm39) T180A probably benign Het
Dmtf1 A G 5: 9,190,379 (GRCm39) probably benign Het
Dnah12 T C 14: 26,455,758 (GRCm39) L827S possibly damaging Het
F5 T C 1: 164,044,964 (GRCm39) V2084A probably benign Het
Fan1 A T 7: 64,018,928 (GRCm39) S476T possibly damaging Het
Far2 T C 6: 148,074,907 (GRCm39) L380P possibly damaging Het
Gbp2 A G 3: 142,329,525 (GRCm39) N24S probably benign Het
Gm14325 T C 2: 177,474,776 (GRCm39) H101R possibly damaging Het
Gpr55 C T 1: 85,869,540 (GRCm39) V14M probably damaging Het
Herc6 A T 6: 57,631,480 (GRCm39) Y724F probably damaging Het
Impg1 T A 9: 80,301,341 (GRCm39) Q195L probably damaging Het
Inf2 T C 12: 112,566,638 (GRCm39) F68L probably damaging Het
Kcnh8 T C 17: 53,268,905 (GRCm39) probably null Het
Klb A G 5: 65,533,137 (GRCm39) N482S probably benign Het
Kpnb1 A G 11: 97,062,424 (GRCm39) V447A probably benign Het
Nckap5l G A 15: 99,324,011 (GRCm39) P831S probably benign Het
Ncor2 A G 5: 125,113,879 (GRCm39) probably null Het
Or4b1d A T 2: 89,969,261 (GRCm39) V74D probably damaging Het
Pgm3 T C 9: 86,443,893 (GRCm39) Y337C probably damaging Het
Prdm1 G T 10: 44,322,903 (GRCm39) Y197* probably null Het
Prex2 T A 1: 11,232,487 (GRCm39) S851R probably benign Het
Ranbp6 A G 19: 29,787,733 (GRCm39) L873P probably damaging Het
Rin2 A G 2: 145,664,194 (GRCm39) T23A possibly damaging Het
Rxra G T 2: 27,631,207 (GRCm39) R118L probably damaging Het
Spice1 T C 16: 44,202,476 (GRCm39) L750P probably damaging Het
Trpm1 C T 7: 63,858,660 (GRCm39) Q228* probably null Het
Tsc1 A G 2: 28,560,937 (GRCm39) D265G probably damaging Het
Usp29 T C 7: 6,964,949 (GRCm39) I264T possibly damaging Het
Vmn2r26 T C 6: 124,027,697 (GRCm39) L479P possibly damaging Het
Zfp9 A G 6: 118,442,273 (GRCm39) S130P 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
R0366:Prdm4 UTSW 10 85,743,868 (GRCm39) missense probably damaging 1.00
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
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'- GCTTACAGGCCAATGACATCC -3'
(R):5'- TTCAAAGCTCATCTGACCAGCC -3'

Sequencing Primer
(F):5'- ATGACATCCCATAGCTATGTGC -3'
(R):5'- GCTCATCTGACCAGCCATATC -3'
Posted On 2015-07-21