Incidental Mutation 'R6397:Pcdhb5'
ID 516048
Institutional Source Beutler Lab
Gene Symbol Pcdhb5
Ensembl Gene ENSMUSG00000063687
Gene Name protocadherin beta 5
Synonyms PcdhbE, Pcdhb4A
MMRRC Submission 044545-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.083) question?
Stock # R6397 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 37453434-37456966 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 37454558 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 313 (S313T)
Ref Sequence ENSEMBL: ENSMUSP00000077389 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000078271] [ENSMUST00000115661] [ENSMUST00000194544]
AlphaFold Q91XZ5
Predicted Effect probably benign
Transcript: ENSMUST00000078271
AA Change: S313T

PolyPhen 2 Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000077389
Gene: ENSMUSG00000063687
AA Change: S313T

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
CA 46 130 1.55e0 SMART
CA 154 239 2.42e-18 SMART
CA 263 344 1.27e-26 SMART
CA 367 448 1.14e-23 SMART
CA 472 558 2.38e-26 SMART
CA 588 669 7.06e-11 SMART
Pfam:Cadherin_C_2 686 769 3.1e-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 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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.2%
  • 20x: 97.5%
Validation Efficiency 94% (29/31)
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: 31 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arfgef3 G T 10: 18,483,413 (GRCm39) S1437* probably null Het
Cdh1 T C 8: 107,330,922 (GRCm39) S18P possibly damaging Het
Dipk1a T A 5: 108,059,504 (GRCm39) K105* probably null Het
Dmbt1 T C 7: 130,705,308 (GRCm39) V1137A possibly damaging Het
Dnase1l1 C T X: 73,320,644 (GRCm39) probably null Homo
Gm3486 G A 14: 41,208,343 (GRCm39) L123F probably benign Het
Ifi203 C A 1: 173,754,770 (GRCm39) V654L probably benign Het
Kalrn A G 16: 33,813,355 (GRCm39) L787P probably damaging Het
Kazald1 A G 19: 45,065,317 (GRCm39) E66G probably benign Het
Map4 T A 9: 109,856,784 (GRCm39) D151E possibly damaging Het
Msrb3 G A 10: 120,627,356 (GRCm39) T42I probably damaging Het
Nfatc1 C T 18: 80,679,156 (GRCm39) C744Y probably damaging Het
Nlgn1 T A 3: 25,487,827 (GRCm39) H836L possibly damaging Het
Nrxn2 A G 19: 6,582,152 (GRCm39) N653D probably damaging Het
Oprk1 A G 1: 5,668,971 (GRCm39) Y139C probably damaging Het
Or2ab1 A G 11: 58,488,338 (GRCm39) T39A probably benign Het
Pcdhb8 C T 18: 37,488,516 (GRCm39) R65* probably null Het
Phf8-ps T C 17: 33,285,219 (GRCm39) N528D probably benign Het
Pstpip2 T G 18: 77,961,079 (GRCm39) C221G probably benign Het
Sall2 T A 14: 52,552,610 (GRCm39) H195L probably damaging Het
Snx7 A G 3: 117,640,272 (GRCm39) I79T probably benign Het
Sptbn2 A T 19: 4,792,446 (GRCm39) E1367V possibly damaging Het
Stau1 A G 2: 166,792,927 (GRCm39) V346A possibly damaging Het
Tchh A G 3: 93,353,173 (GRCm39) E871G unknown Het
Tlr9 A G 9: 106,102,305 (GRCm39) N532S probably damaging Het
Tuba1c G A 15: 98,935,738 (GRCm39) A400T probably benign Het
Vmn2r86 A T 10: 130,282,131 (GRCm39) Y828* probably null Het
Vps45 A G 3: 95,950,164 (GRCm39) I255T probably benign Het
Yap1 T C 9: 8,001,467 (GRCm39) Y173C probably damaging Het
Zc3h7b A T 15: 81,677,055 (GRCm39) I821F probably benign Het
Zftraf1 A T 15: 76,532,391 (GRCm39) I239N probably damaging Het
Other mutations in Pcdhb5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00504:Pcdhb5 APN 18 37,455,162 (GRCm39) missense probably damaging 1.00
IGL00895:Pcdhb5 APN 18 37,454,036 (GRCm39) missense probably benign 0.42
IGL00896:Pcdhb5 APN 18 37,455,838 (GRCm39) splice site probably null
IGL01385:Pcdhb5 APN 18 37,455,267 (GRCm39) missense probably benign 0.00
IGL01619:Pcdhb5 APN 18 37,455,992 (GRCm39) missense probably damaging 1.00
IGL01712:Pcdhb5 APN 18 37,454,306 (GRCm39) missense probably damaging 1.00
IGL01716:Pcdhb5 APN 18 37,454,075 (GRCm39) missense probably benign
IGL01719:Pcdhb5 APN 18 37,454,075 (GRCm39) missense probably benign
IGL01720:Pcdhb5 APN 18 37,454,075 (GRCm39) missense probably benign
IGL01723:Pcdhb5 APN 18 37,454,075 (GRCm39) missense probably benign
IGL01724:Pcdhb5 APN 18 37,454,075 (GRCm39) missense probably benign
IGL01839:Pcdhb5 APN 18 37,454,502 (GRCm39) missense probably damaging 0.98
IGL01884:Pcdhb5 APN 18 37,454,387 (GRCm39) missense probably benign 0.00
IGL01962:Pcdhb5 APN 18 37,454,093 (GRCm39) missense probably damaging 1.00
IGL02088:Pcdhb5 APN 18 37,455,012 (GRCm39) missense probably benign 0.11
IGL02299:Pcdhb5 APN 18 37,453,943 (GRCm39) missense probably benign
IGL02444:Pcdhb5 APN 18 37,454,103 (GRCm39) missense probably benign 0.01
IGL03372:Pcdhb5 APN 18 37,453,713 (GRCm39) missense probably benign 0.22
R0034:Pcdhb5 UTSW 18 37,455,137 (GRCm39) missense probably damaging 1.00
R0047:Pcdhb5 UTSW 18 37,454,321 (GRCm39) missense possibly damaging 0.87
R0179:Pcdhb5 UTSW 18 37,455,612 (GRCm39) missense probably damaging 1.00
R0466:Pcdhb5 UTSW 18 37,455,596 (GRCm39) missense probably damaging 1.00
R0471:Pcdhb5 UTSW 18 37,454,359 (GRCm39) nonsense probably null
R0565:Pcdhb5 UTSW 18 37,453,820 (GRCm39) missense possibly damaging 0.91
R0646:Pcdhb5 UTSW 18 37,454,675 (GRCm39) missense probably benign
R1014:Pcdhb5 UTSW 18 37,455,303 (GRCm39) missense probably damaging 1.00
R1617:Pcdhb5 UTSW 18 37,454,455 (GRCm39) nonsense probably null
R1676:Pcdhb5 UTSW 18 37,453,805 (GRCm39) missense probably benign 0.01
R1774:Pcdhb5 UTSW 18 37,455,725 (GRCm39) missense probably damaging 0.99
R1826:Pcdhb5 UTSW 18 37,454,522 (GRCm39) nonsense probably null
R1854:Pcdhb5 UTSW 18 37,455,393 (GRCm39) missense possibly damaging 0.94
R2355:Pcdhb5 UTSW 18 37,455,169 (GRCm39) missense probably benign
R4290:Pcdhb5 UTSW 18 37,455,734 (GRCm39) missense possibly damaging 0.90
R4292:Pcdhb5 UTSW 18 37,455,734 (GRCm39) missense possibly damaging 0.90
R4293:Pcdhb5 UTSW 18 37,455,734 (GRCm39) missense possibly damaging 0.90
R4294:Pcdhb5 UTSW 18 37,455,734 (GRCm39) missense possibly damaging 0.90
R4295:Pcdhb5 UTSW 18 37,455,734 (GRCm39) missense possibly damaging 0.90
R4391:Pcdhb5 UTSW 18 37,455,789 (GRCm39) missense possibly damaging 0.88
R4411:Pcdhb5 UTSW 18 37,455,050 (GRCm39) missense possibly damaging 0.80
R4480:Pcdhb5 UTSW 18 37,453,805 (GRCm39) missense probably benign 0.43
R4852:Pcdhb5 UTSW 18 37,455,524 (GRCm39) missense probably benign 0.04
R5121:Pcdhb5 UTSW 18 37,454,170 (GRCm39) missense probably benign 0.11
R5133:Pcdhb5 UTSW 18 37,453,943 (GRCm39) missense probably benign
R5630:Pcdhb5 UTSW 18 37,454,208 (GRCm39) missense possibly damaging 0.88
R5833:Pcdhb5 UTSW 18 37,454,155 (GRCm39) missense probably damaging 0.99
R5896:Pcdhb5 UTSW 18 37,455,732 (GRCm39) nonsense probably null
R5942:Pcdhb5 UTSW 18 37,453,838 (GRCm39) nonsense probably null
R5945:Pcdhb5 UTSW 18 37,454,523 (GRCm39) missense probably benign 0.08
R5970:Pcdhb5 UTSW 18 37,454,826 (GRCm39) missense probably damaging 1.00
R6045:Pcdhb5 UTSW 18 37,454,628 (GRCm39) missense probably damaging 1.00
R6054:Pcdhb5 UTSW 18 37,454,133 (GRCm39) missense probably damaging 0.98
R6147:Pcdhb5 UTSW 18 37,453,779 (GRCm39) missense probably damaging 1.00
R6152:Pcdhb5 UTSW 18 37,455,886 (GRCm39) nonsense probably null
R6193:Pcdhb5 UTSW 18 37,455,080 (GRCm39) missense probably damaging 1.00
R6505:Pcdhb5 UTSW 18 37,453,933 (GRCm39) missense probably benign 0.00
R6608:Pcdhb5 UTSW 18 37,454,876 (GRCm39) missense probably damaging 0.98
R6737:Pcdhb5 UTSW 18 37,455,723 (GRCm39) missense probably damaging 1.00
R7146:Pcdhb5 UTSW 18 37,454,409 (GRCm39) missense probably damaging 1.00
R7162:Pcdhb5 UTSW 18 37,454,739 (GRCm39) missense probably benign 0.16
R7584:Pcdhb5 UTSW 18 37,455,425 (GRCm39) missense possibly damaging 0.90
R8214:Pcdhb5 UTSW 18 37,454,636 (GRCm39) missense probably benign 0.37
R8327:Pcdhb5 UTSW 18 37,453,953 (GRCm39) missense probably benign 0.00
R8676:Pcdhb5 UTSW 18 37,454,129 (GRCm39) missense probably benign 0.01
R9234:Pcdhb5 UTSW 18 37,453,695 (GRCm39) missense probably benign
R9424:Pcdhb5 UTSW 18 37,454,120 (GRCm39) missense probably damaging 1.00
R9505:Pcdhb5 UTSW 18 37,454,664 (GRCm39) missense possibly damaging 0.87
R9635:Pcdhb5 UTSW 18 37,454,510 (GRCm39) missense probably benign 0.06
Predicted Primers PCR Primer
(F):5'- ATGCTCCTGAGTTTGTGAACAAC -3'
(R):5'- CGTATTCGGATGATAGCGACCAC -3'

Sequencing Primer
(F):5'- TTGTGAACAACCCCTATGAGGTG -3'
(R):5'- ATAGCGACCACAGTTTCTGG -3'
Posted On 2018-05-04