Incidental Mutation 'R4378:Phc1'
ID 325193
Institutional Source Beutler Lab
Gene Symbol Phc1
Ensembl Gene ENSMUSG00000040669
Gene Name polyhomeotic 1
Synonyms rae28, Mph1, Rae-28, Edr1
MMRRC Submission 041121-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4378 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 122294690-122317520 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 122311966 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 64 (N64S)
Ref Sequence ENSEMBL: ENSMUSP00000125030 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000079560] [ENSMUST00000081849] [ENSMUST00000112600] [ENSMUST00000159252] [ENSMUST00000159384] [ENSMUST00000159657] [ENSMUST00000161210] [ENSMUST00000160163] [ENSMUST00000160696] [ENSMUST00000160843] [ENSMUST00000161054] [ENSMUST00000161149] [ENSMUST00000161739]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000079560
AA Change: N64S

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000078514
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
low complexity region 182 196 N/A INTRINSIC
low complexity region 240 303 N/A INTRINSIC
low complexity region 330 341 N/A INTRINSIC
low complexity region 373 416 N/A INTRINSIC
coiled coil region 420 446 N/A INTRINSIC
low complexity region 448 480 N/A INTRINSIC
low complexity region 485 506 N/A INTRINSIC
low complexity region 524 535 N/A INTRINSIC
low complexity region 543 556 N/A INTRINSIC
low complexity region 575 587 N/A INTRINSIC
low complexity region 617 628 N/A INTRINSIC
low complexity region 704 722 N/A INTRINSIC
Pfam:zf-FCS 798 833 4.9e-8 PFAM
low complexity region 855 869 N/A INTRINSIC
SAM 943 1010 9.57e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000081849
AA Change: N64S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000080532
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
low complexity region 188 251 N/A INTRINSIC
low complexity region 278 289 N/A INTRINSIC
low complexity region 321 364 N/A INTRINSIC
coiled coil region 368 394 N/A INTRINSIC
low complexity region 396 428 N/A INTRINSIC
low complexity region 433 454 N/A INTRINSIC
low complexity region 472 483 N/A INTRINSIC
low complexity region 491 504 N/A INTRINSIC
low complexity region 523 535 N/A INTRINSIC
low complexity region 565 576 N/A INTRINSIC
low complexity region 652 670 N/A INTRINSIC
Pfam:zf-FCS 746 781 4.6e-8 PFAM
low complexity region 803 817 N/A INTRINSIC
SAM 891 958 9.57e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112600
AA Change: N64S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000108219
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
low complexity region 188 251 N/A INTRINSIC
low complexity region 278 289 N/A INTRINSIC
low complexity region 321 364 N/A INTRINSIC
coiled coil region 368 394 N/A INTRINSIC
low complexity region 396 428 N/A INTRINSIC
low complexity region 433 454 N/A INTRINSIC
low complexity region 472 483 N/A INTRINSIC
low complexity region 491 504 N/A INTRINSIC
low complexity region 523 535 N/A INTRINSIC
low complexity region 565 576 N/A INTRINSIC
low complexity region 652 670 N/A INTRINSIC
Pfam:zf-FCS 746 781 4.6e-8 PFAM
low complexity region 803 817 N/A INTRINSIC
SAM 891 958 9.57e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000159252
SMART Domains Protein: ENSMUSP00000124678
Gene: ENSMUSG00000040669

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 46 65 N/A INTRINSIC
low complexity region 137 151 N/A INTRINSIC
low complexity region 195 258 N/A INTRINSIC
low complexity region 285 296 N/A INTRINSIC
low complexity region 328 371 N/A INTRINSIC
coiled coil region 375 401 N/A INTRINSIC
low complexity region 403 435 N/A INTRINSIC
low complexity region 440 461 N/A INTRINSIC
low complexity region 479 490 N/A INTRINSIC
low complexity region 498 511 N/A INTRINSIC
low complexity region 530 542 N/A INTRINSIC
low complexity region 572 583 N/A INTRINSIC
low complexity region 659 677 N/A INTRINSIC
Pfam:zf-FCS 753 788 2.2e-8 PFAM
low complexity region 810 824 N/A INTRINSIC
SAM 898 965 9.57e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000159384
AA Change: N64S

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000124744
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000159657
AA Change: N64S

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000123957
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161210
AA Change: N64S

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000124795
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000160163
AA Change: N64S

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000125545
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000160696
AA Change: N64S

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000125580
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
low complexity region 182 196 N/A INTRINSIC
low complexity region 240 303 N/A INTRINSIC
low complexity region 330 341 N/A INTRINSIC
low complexity region 373 416 N/A INTRINSIC
coiled coil region 420 446 N/A INTRINSIC
low complexity region 448 480 N/A INTRINSIC
low complexity region 485 506 N/A INTRINSIC
low complexity region 524 535 N/A INTRINSIC
low complexity region 543 556 N/A INTRINSIC
low complexity region 575 587 N/A INTRINSIC
low complexity region 617 628 N/A INTRINSIC
low complexity region 704 722 N/A INTRINSIC
Pfam:PHC2_SAM_assoc 834 941 3.4e-31 PFAM
SAM 943 1010 9.57e-15 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000160843
AA Change: N64S

PolyPhen 2 Score 0.659 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000125030
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
low complexity region 182 196 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160863
Predicted Effect probably benign
Transcript: ENSMUST00000161054
AA Change: N64S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000123911
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
low complexity region 188 251 N/A INTRINSIC
low complexity region 278 289 N/A INTRINSIC
low complexity region 321 364 N/A INTRINSIC
coiled coil region 368 394 N/A INTRINSIC
low complexity region 396 428 N/A INTRINSIC
low complexity region 433 454 N/A INTRINSIC
low complexity region 472 483 N/A INTRINSIC
low complexity region 491 504 N/A INTRINSIC
low complexity region 523 535 N/A INTRINSIC
low complexity region 565 576 N/A INTRINSIC
low complexity region 652 670 N/A INTRINSIC
Pfam:zf-FCS 746 781 4.6e-8 PFAM
low complexity region 803 817 N/A INTRINSIC
SAM 891 958 9.57e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000161149
AA Change: N64S

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000125717
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161290
AA Change: N46S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000125110
Gene: ENSMUSG00000040669
AA Change: N46S

DomainStartEndE-ValueType
low complexity region 17 29 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161739
AA Change: N64S

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000125568
Gene: ENSMUSG00000040669
AA Change: N64S

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
low complexity region 83 102 N/A INTRINSIC
low complexity region 182 196 N/A INTRINSIC
low complexity region 240 303 N/A INTRINSIC
low complexity region 330 341 N/A INTRINSIC
low complexity region 373 416 N/A INTRINSIC
coiled coil region 420 446 N/A INTRINSIC
low complexity region 448 480 N/A INTRINSIC
low complexity region 485 506 N/A INTRINSIC
low complexity region 524 535 N/A INTRINSIC
low complexity region 543 556 N/A INTRINSIC
low complexity region 575 587 N/A INTRINSIC
low complexity region 617 628 N/A INTRINSIC
low complexity region 704 722 N/A INTRINSIC
Pfam:zf-FCS 798 833 4.9e-8 PFAM
low complexity region 855 869 N/A INTRINSIC
SAM 943 1010 9.57e-15 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161877
SMART Domains Protein: ENSMUSP00000123854
Gene: ENSMUSG00000040669

DomainStartEndE-ValueType
low complexity region 3 22 N/A INTRINSIC
low complexity region 34 46 N/A INTRINSIC
Meta Mutation Damage Score 0.0600 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 96% (47/49)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a homolog of the Drosophila polyhomeotic gene, which is a member of the Polycomb group of genes. The gene product is a component of a multimeric protein complex that contains EDR2 and the vertebrate Polycomb protein BMH1. The gene product, the EDR2 protein, and the Drosophila polyhomeotic protein share 2 highly conserved domains, named homology domains I and II. These domains are involved in protein-protein interactions and may mediate heterodimerization of the protein encoded by this gene and the EDR2 protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice exhibit perinatal lethality, posterior skeletal transformations and defects in neural crest derived tissues, including ocular abnormalities, cleft palate, parathyroid and thymic hypoplasia and cardiac anomalies. Hematopoiesis is impaired in fetal livers. [provided by MGI curators]
Allele List at MGI

All alleles(147) : Targeted, knock-out(1) Gene trapped(146)

Other mutations in this stock
Total: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 A G 11: 9,243,644 (GRCm39) K1836E probably benign Het
Adora1 A G 1: 134,130,948 (GRCm39) F241S probably damaging Het
Akt1s1 C T 7: 44,503,384 (GRCm39) T168M probably damaging Het
Amigo1 C T 3: 108,099,069 (GRCm39) probably benign Het
Amigo2 A G 15: 97,143,859 (GRCm39) F188L possibly damaging Het
Armc2 T C 10: 41,869,078 (GRCm39) T29A possibly damaging Het
Axl G A 7: 25,458,262 (GRCm39) A822V probably benign Het
Borcs5 T C 6: 134,621,292 (GRCm39) V21A probably benign Het
Cdc42ep3 A G 17: 79,642,408 (GRCm39) S171P probably benign Het
Cmas T C 6: 142,718,011 (GRCm39) probably benign Het
Cyp4f40 A G 17: 32,887,003 (GRCm39) N158S probably null Het
Dnah6 G T 6: 73,095,009 (GRCm39) N2139K probably benign Het
Elmo1 A T 13: 20,557,286 (GRCm39) H409L possibly damaging Het
Exoc1l A G 5: 76,648,380 (GRCm39) K62R probably damaging Het
Exoc4 T A 6: 33,792,622 (GRCm39) V584E probably damaging Het
Gm9116 A G 3: 93,817,786 (GRCm39) noncoding transcript Het
Gxylt2 A G 6: 100,710,161 (GRCm39) S101G probably benign Het
Hsph1 C A 5: 149,559,472 (GRCm39) E24* probably null Het
Ighv1-56 C T 12: 115,206,568 (GRCm39) E50K probably benign Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Lrriq1 A T 10: 103,038,225 (GRCm39) D859E probably damaging Het
Mapk7 G A 11: 61,384,493 (GRCm39) S71L probably damaging Het
Nars1 A G 18: 64,634,424 (GRCm39) Y500H probably damaging Het
Or1j1 T C 2: 36,702,481 (GRCm39) M208V probably benign Het
Or5d20-ps1 G T 2: 87,931,829 (GRCm39) N167K unknown Het
Ppp4r3b T A 11: 29,159,450 (GRCm39) N180K possibly damaging Het
Primpol G A 8: 47,029,218 (GRCm39) probably benign Het
Prtg T C 9: 72,750,042 (GRCm39) S149P possibly damaging Het
Qrich2 T C 11: 116,337,741 (GRCm39) S1916G probably damaging Het
Rps6ka5 A T 12: 100,564,196 (GRCm39) Y218N probably damaging Het
Setbp1 T C 18: 78,899,833 (GRCm39) D1278G possibly damaging Het
Sirt1 C T 10: 63,174,728 (GRCm39) A8T probably benign Het
Sobp C T 10: 42,897,300 (GRCm39) V762I probably damaging Het
Sptan1 T C 2: 29,915,581 (GRCm39) S1994P probably damaging Het
Taok3 T C 5: 117,347,636 (GRCm39) I87T probably damaging Het
Tecta T C 9: 42,278,004 (GRCm39) Y1168C probably damaging Het
Trhr A G 15: 44,061,023 (GRCm39) Y181C probably damaging Het
Ube4b C T 4: 149,468,255 (GRCm39) D174N probably damaging Het
Ubr4 C T 4: 139,137,751 (GRCm39) H1067Y possibly damaging Het
Vmn2r86 A G 10: 130,288,469 (GRCm39) I344T possibly damaging Het
Vmn2r88 T A 14: 51,650,746 (GRCm39) L153* probably null Het
Zfp516 T A 18: 83,005,305 (GRCm39) D736E probably benign Het
Zfp612 G T 8: 110,815,683 (GRCm39) V258F possibly damaging Het
Other mutations in Phc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00340:Phc1 APN 6 122,299,958 (GRCm39) splice site probably benign
IGL01354:Phc1 APN 6 122,311,042 (GRCm39) missense probably damaging 1.00
IGL01786:Phc1 APN 6 122,296,479 (GRCm39) missense possibly damaging 0.82
IGL02110:Phc1 APN 6 122,298,994 (GRCm39) missense possibly damaging 0.91
IGL02479:Phc1 APN 6 122,300,676 (GRCm39) unclassified probably benign
IGL02861:Phc1 APN 6 122,300,748 (GRCm39) unclassified probably benign
IGL03106:Phc1 APN 6 122,300,428 (GRCm39) unclassified probably benign
3-1:Phc1 UTSW 6 122,315,423 (GRCm39) intron probably benign
FR4737:Phc1 UTSW 6 122,300,557 (GRCm39) small insertion probably benign
FR4976:Phc1 UTSW 6 122,300,559 (GRCm39) small insertion probably benign
R0452:Phc1 UTSW 6 122,299,995 (GRCm39) missense probably damaging 1.00
R1146:Phc1 UTSW 6 122,300,416 (GRCm39) unclassified probably benign
R1146:Phc1 UTSW 6 122,300,416 (GRCm39) unclassified probably benign
R1301:Phc1 UTSW 6 122,302,833 (GRCm39) missense probably benign 0.03
R1738:Phc1 UTSW 6 122,295,525 (GRCm39) missense probably damaging 1.00
R2056:Phc1 UTSW 6 122,310,299 (GRCm39) missense probably damaging 0.99
R2164:Phc1 UTSW 6 122,299,296 (GRCm39) missense possibly damaging 0.82
R2183:Phc1 UTSW 6 122,300,284 (GRCm39) missense probably damaging 1.00
R2424:Phc1 UTSW 6 122,297,002 (GRCm39) missense probably damaging 0.98
R4648:Phc1 UTSW 6 122,298,872 (GRCm39) missense possibly damaging 0.95
R4831:Phc1 UTSW 6 122,313,964 (GRCm39) start gained probably benign
R5244:Phc1 UTSW 6 122,298,938 (GRCm39) missense probably damaging 1.00
R5475:Phc1 UTSW 6 122,311,051 (GRCm39) missense possibly damaging 0.95
R6491:Phc1 UTSW 6 122,311,923 (GRCm39)
R6701:Phc1 UTSW 6 122,302,733 (GRCm39) missense probably damaging 0.96
R6733:Phc1 UTSW 6 122,313,845 (GRCm39) missense possibly damaging 0.77
R7022:Phc1 UTSW 6 122,311,990 (GRCm39) missense probably damaging 0.98
R7383:Phc1 UTSW 6 122,300,317 (GRCm39) missense unknown
R7707:Phc1 UTSW 6 122,300,739 (GRCm39) missense unknown
R7825:Phc1 UTSW 6 122,299,340 (GRCm39) missense probably benign 0.26
R7846:Phc1 UTSW 6 122,310,329 (GRCm39) missense probably damaging 1.00
R8314:Phc1 UTSW 6 122,297,937 (GRCm39) missense unknown
R8346:Phc1 UTSW 6 122,302,774 (GRCm39) missense probably damaging 0.98
R8534:Phc1 UTSW 6 122,315,539 (GRCm39) intron probably benign
RF036:Phc1 UTSW 6 122,300,539 (GRCm39) small insertion probably benign
RF041:Phc1 UTSW 6 122,300,559 (GRCm39) small insertion probably benign
RF044:Phc1 UTSW 6 122,300,559 (GRCm39) small insertion probably benign
RF064:Phc1 UTSW 6 122,300,539 (GRCm39) small insertion probably benign
X0024:Phc1 UTSW 6 122,300,588 (GRCm39) small deletion probably benign
X0026:Phc1 UTSW 6 122,296,497 (GRCm39) missense possibly damaging 0.66
Predicted Primers PCR Primer
(F):5'- AAGAGTCTCCCACAGTTCATAC -3'
(R):5'- TCAGATGCTGTGATAGTCGTC -3'

Sequencing Primer
(F):5'- TCATACTGCAACCTTAATCTAAGAAC -3'
(R):5'- CAGATGCTGTGATAGTCGTCCTTTG -3'
Posted On 2015-07-06