Incidental Mutation 'R5779:Pcdhb3'
ID 446903
Institutional Source Beutler Lab
Gene Symbol Pcdhb3
Ensembl Gene ENSMUSG00000045498
Gene Name protocadherin beta 3
Synonyms PcdhbC
MMRRC Submission 043377-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.064) question?
Stock # R5779 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 37433852-37437638 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 37434520 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 162 (V162A)
Ref Sequence ENSEMBL: ENSMUSP00000059180 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051754] [ENSMUST00000056522] [ENSMUST00000115661] [ENSMUST00000194544]
AlphaFold Q91XZ7
Predicted Effect probably benign
Transcript: ENSMUST00000051754
AA Change: V162A

PolyPhen 2 Score 0.265 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000059180
Gene: ENSMUSG00000045498
AA Change: V162A

DomainStartEndE-ValueType
low complexity region 14 28 N/A INTRINSIC
CA 44 131 6.29e-1 SMART
CA 155 240 7.16e-21 SMART
CA 264 345 1.22e-23 SMART
CA 368 449 2.86e-20 SMART
CA 473 559 2.55e-26 SMART
CA 589 670 1.11e-8 SMART
Pfam:Cadherin_C_2 687 770 9.9e-25 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000056522
SMART Domains Protein: ENSMUSP00000057921
Gene: ENSMUSG00000051599

DomainStartEndE-ValueType
Pfam:Cadherin_2 32 114 5.2e-33 PFAM
CA 157 242 1.74e-19 SMART
CA 266 347 5.99e-23 SMART
CA 370 451 1.16e-20 SMART
CA 475 561 5.94e-27 SMART
CA 591 672 2.03e-11 SMART
Pfam:Cadherin_C_2 688 771 3.5e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000115661
SMART Domains Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458

DomainStartEndE-ValueType
CA 20 131 5.3e-2 SMART
CA 155 240 1.51e-19 SMART
CA 264 348 7.6e-25 SMART
CA 372 453 1.42e-24 SMART
CA 477 563 1.42e-24 SMART
CA 594 674 4.12e-12 SMART
low complexity region 706 721 N/A INTRINSIC
Pfam:Cadherin_tail 796 930 3.9e-58 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193025
Predicted Effect probably benign
Transcript: ENSMUST00000193984
Predicted Effect probably benign
Transcript: ENSMUST00000194544
SMART Domains Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

DomainStartEndE-ValueType
Blast:CA 18 66 5e-20 BLAST
Meta Mutation Damage Score 0.0741 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 88% (52/59)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca6 T C 11: 110,075,496 (GRCm39) M1332V probably benign Het
Acsbg3 A T 17: 57,188,061 (GRCm39) N190Y probably benign Het
Afg3l2 T C 18: 67,573,513 (GRCm39) K132R probably null Het
Antkmt A G 17: 26,009,631 (GRCm39) V194A probably benign Het
Arap3 T C 18: 38,117,418 (GRCm39) D886G probably damaging Het
B3gntl1 G T 11: 121,542,502 (GRCm39) probably null Het
Cdk12 T A 11: 98,109,900 (GRCm39) S640R probably benign Het
Ceacam12 C A 7: 17,803,079 (GRCm39) P162T probably benign Het
Chrna5 C A 9: 54,905,388 (GRCm39) H67N probably benign Het
Copb1 T A 7: 113,818,807 (GRCm39) D837V probably damaging Het
Dcaf5 C T 12: 80,385,606 (GRCm39) R840H probably benign Het
Ect2l T A 10: 18,039,186 (GRCm39) Q324L probably benign Het
Eef1e1 T C 13: 38,830,249 (GRCm39) N141S probably damaging Het
Eif2ak4 A C 2: 118,243,444 (GRCm39) N208T possibly damaging Het
Ext1 A G 15: 53,207,949 (GRCm39) Y271H probably damaging Het
Fbxo5 G A 10: 5,750,303 (GRCm39) R323C possibly damaging Het
Fpr-rs3 C A 17: 20,844,488 (GRCm39) A218S possibly damaging Het
Gm20499 G A 5: 114,955,082 (GRCm39) probably benign Het
Gm57859 A G 11: 113,578,818 (GRCm39) D71G probably benign Het
Gucy1b2 C A 14: 62,651,750 (GRCm39) L400F possibly damaging Het
Hgd T A 16: 37,413,733 (GRCm39) L24H probably benign Het
Hmx3 C A 7: 131,146,057 (GRCm39) S255* probably null Het
Ifrd1 A T 12: 40,253,369 (GRCm39) F448I probably damaging Het
Igfn1 T A 1: 135,894,578 (GRCm39) E1996V probably benign Het
Itpr1 G A 6: 108,329,104 (GRCm39) G173R probably damaging Het
Kbtbd8 T C 6: 95,095,515 (GRCm39) S26P probably benign Het
Kctd17 A T 15: 78,321,333 (GRCm39) probably benign Het
Matr3 T C 18: 35,717,575 (GRCm39) S258P possibly damaging Het
Mpp4 G A 1: 59,190,825 (GRCm39) A90V probably benign Het
Mrpl20 G A 4: 155,891,378 (GRCm39) R34Q probably damaging Het
Neb A T 2: 52,135,313 (GRCm39) S3266T probably damaging Het
Nipal3 A G 4: 135,179,650 (GRCm39) probably benign Het
Npas2 A T 1: 39,326,652 (GRCm39) T46S possibly damaging Het
Nsd3 G T 8: 26,172,685 (GRCm39) E815* probably null Het
Nup98 C A 7: 101,801,568 (GRCm39) V786L probably benign Het
Or4k2 A T 14: 50,424,203 (GRCm39) M157K possibly damaging Het
Pcgf2 G A 11: 97,581,117 (GRCm39) P58L probably damaging Het
Penk A G 4: 4,134,318 (GRCm39) F110L probably damaging Het
Relch T G 1: 105,615,072 (GRCm39) N246K probably damaging Het
Scfd1 A G 12: 51,478,312 (GRCm39) N508S probably benign Het
Scn2a T C 2: 65,594,827 (GRCm39) V1892A probably benign Het
Sema6a G A 18: 47,381,893 (GRCm39) R885C probably damaging Het
Sik2 T C 9: 50,807,145 (GRCm39) H755R probably benign Het
Slc36a3 A T 11: 55,026,094 (GRCm39) Y241* probably null Het
Smg5 T C 3: 88,258,925 (GRCm39) probably benign Het
Spag9 A G 11: 94,005,079 (GRCm39) T1049A probably benign Het
Tas2r103 T C 6: 133,013,908 (GRCm39) M53V probably benign Het
Tpr C T 1: 150,299,292 (GRCm39) A1090V probably damaging Het
Traf5 T A 1: 191,729,633 (GRCm39) R473W probably damaging Het
Ush2a T C 1: 188,175,707 (GRCm39) probably null Het
Vit A G 17: 78,853,855 (GRCm39) T34A probably benign Het
Other mutations in Pcdhb3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00976:Pcdhb3 APN 18 37,436,001 (GRCm39) missense probably benign 0.12
IGL01568:Pcdhb3 APN 18 37,435,054 (GRCm39) missense possibly damaging 0.74
IGL02541:Pcdhb3 APN 18 37,435,198 (GRCm39) missense probably damaging 0.99
IGL02852:Pcdhb3 APN 18 37,435,150 (GRCm39) missense probably damaging 1.00
IGL03140:Pcdhb3 APN 18 37,434,272 (GRCm39) missense probably benign 0.00
IGL03336:Pcdhb3 APN 18 37,436,014 (GRCm39) missense possibly damaging 0.86
R0380:Pcdhb3 UTSW 18 37,435,210 (GRCm39) missense possibly damaging 0.48
R1558:Pcdhb3 UTSW 18 37,434,634 (GRCm39) missense probably damaging 1.00
R1713:Pcdhb3 UTSW 18 37,436,375 (GRCm39) missense probably benign
R1728:Pcdhb3 UTSW 18 37,434,931 (GRCm39) missense probably damaging 1.00
R1784:Pcdhb3 UTSW 18 37,434,931 (GRCm39) missense probably damaging 1.00
R1838:Pcdhb3 UTSW 18 37,434,370 (GRCm39) missense probably benign 0.00
R2079:Pcdhb3 UTSW 18 37,436,362 (GRCm39) missense possibly damaging 0.93
R2164:Pcdhb3 UTSW 18 37,435,239 (GRCm39) missense possibly damaging 0.78
R2513:Pcdhb3 UTSW 18 37,434,294 (GRCm39) missense probably benign 0.17
R2513:Pcdhb3 UTSW 18 37,434,292 (GRCm39) nonsense probably null
R2513:Pcdhb3 UTSW 18 37,434,293 (GRCm39) missense probably damaging 1.00
R3080:Pcdhb3 UTSW 18 37,434,535 (GRCm39) missense probably damaging 1.00
R3755:Pcdhb3 UTSW 18 37,435,878 (GRCm39) missense probably damaging 0.97
R3756:Pcdhb3 UTSW 18 37,435,878 (GRCm39) missense probably damaging 0.97
R3862:Pcdhb3 UTSW 18 37,436,329 (GRCm39) missense probably damaging 1.00
R3863:Pcdhb3 UTSW 18 37,436,329 (GRCm39) missense probably damaging 1.00
R3864:Pcdhb3 UTSW 18 37,436,329 (GRCm39) missense probably damaging 1.00
R4114:Pcdhb3 UTSW 18 37,435,093 (GRCm39) missense probably benign 0.03
R4895:Pcdhb3 UTSW 18 37,434,759 (GRCm39) missense probably damaging 1.00
R4917:Pcdhb3 UTSW 18 37,435,452 (GRCm39) missense probably damaging 0.99
R5508:Pcdhb3 UTSW 18 37,434,179 (GRCm39) missense probably damaging 1.00
R5848:Pcdhb3 UTSW 18 37,434,700 (GRCm39) missense probably benign 0.39
R5991:Pcdhb3 UTSW 18 37,434,561 (GRCm39) missense probably benign 0.07
R6014:Pcdhb3 UTSW 18 37,435,706 (GRCm39) missense probably damaging 1.00
R6111:Pcdhb3 UTSW 18 37,435,242 (GRCm39) missense probably benign 0.00
R6282:Pcdhb3 UTSW 18 37,434,699 (GRCm39) missense probably damaging 1.00
R6339:Pcdhb3 UTSW 18 37,433,998 (GRCm39) intron probably benign
R6425:Pcdhb3 UTSW 18 37,435,528 (GRCm39) missense possibly damaging 0.64
R6860:Pcdhb3 UTSW 18 37,434,763 (GRCm39) missense probably benign 0.01
R6896:Pcdhb3 UTSW 18 37,434,265 (GRCm39) missense probably damaging 1.00
R6946:Pcdhb3 UTSW 18 37,435,672 (GRCm39) missense probably damaging 1.00
R7110:Pcdhb3 UTSW 18 37,435,975 (GRCm39) missense possibly damaging 0.87
R7236:Pcdhb3 UTSW 18 37,434,505 (GRCm39) missense probably damaging 1.00
R7402:Pcdhb3 UTSW 18 37,434,657 (GRCm39) missense probably benign
R7469:Pcdhb3 UTSW 18 37,434,388 (GRCm39) missense probably benign 0.02
R7723:Pcdhb3 UTSW 18 37,435,565 (GRCm39) missense probably damaging 0.98
R7738:Pcdhb3 UTSW 18 37,436,012 (GRCm39) missense probably benign 0.00
R7800:Pcdhb3 UTSW 18 37,434,974 (GRCm39) missense probably benign 0.00
R7817:Pcdhb3 UTSW 18 37,435,982 (GRCm39) missense probably benign
R8157:Pcdhb3 UTSW 18 37,436,292 (GRCm39) missense probably damaging 1.00
R9264:Pcdhb3 UTSW 18 37,435,166 (GRCm39) missense probably benign 0.03
R9482:Pcdhb3 UTSW 18 37,434,736 (GRCm39) missense probably damaging 1.00
R9488:Pcdhb3 UTSW 18 37,435,416 (GRCm39) missense possibly damaging 0.62
X0026:Pcdhb3 UTSW 18 37,434,817 (GRCm39) missense probably damaging 0.96
X0066:Pcdhb3 UTSW 18 37,435,392 (GRCm39) nonsense probably null
Z1177:Pcdhb3 UTSW 18 37,435,089 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TGTGCTGCACTTTCAGATATTG -3'
(R):5'- TGTGTCTAAGACCAGGATGTG -3'

Sequencing Primer
(F):5'- GCACTTTCAGATATTGCTGCATG -3'
(R):5'- TGGGTAGTTCCAGAACGAGGC -3'
Posted On 2016-12-15