Incidental Mutation 'R2363:Pcdhb20'
ID 247252
Institutional Source Beutler Lab
Gene Symbol Pcdhb20
Ensembl Gene ENSMUSG00000046191
Gene Name protocadherin beta 20
Synonyms Pcdhb14, PcdhbT
MMRRC Submission 040344-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.083) question?
Stock # R2363 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 37637332-37640713 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 37638725 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 417 (Y417C)
Ref Sequence ENSEMBL: ENSMUSP00000137038 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000052179] [ENSMUST00000059571] [ENSMUST00000115661] [ENSMUST00000194544]
AlphaFold Q91XZ9
Predicted Effect probably damaging
Transcript: ENSMUST00000052179
AA Change: Y417C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000137038
Gene: ENSMUSG00000046191
AA Change: Y417C

DomainStartEndE-ValueType
Pfam:Cadherin_2 30 112 8.3e-36 PFAM
low complexity region 136 148 N/A INTRINSIC
CA 155 240 1.41e-19 SMART
CA 264 345 2.91e-21 SMART
CA 368 449 1.12e-22 SMART
CA 473 559 3.41e-27 SMART
CA 589 670 6.34e-13 SMART
Pfam:Cadherin_C_2 686 769 7.1e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000059571
SMART Domains Protein: ENSMUSP00000053326
Gene: ENSMUSG00000043313

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
CA 45 131 4.8e-1 SMART
CA 155 240 6.58e-20 SMART
CA 264 345 1.03e-21 SMART
CA 368 449 4.21e-18 SMART
CA 473 559 3.36e-26 SMART
CA 589 670 6.69e-12 SMART
Pfam:Cadherin_C_2 686 769 1.9e-25 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
Meta Mutation Damage Score 0.8166 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency 98% (51/52)
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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abtb2 T C 2: 103,397,528 (GRCm39) C153R probably damaging Het
Adam23 A G 1: 63,596,650 (GRCm39) probably null Het
Adpgk G T 9: 59,222,136 (GRCm39) M354I probably benign Het
Atmin G T 8: 117,681,653 (GRCm39) probably null Het
C1rl G A 6: 124,486,069 (GRCm39) G480D probably benign Het
C4b G A 17: 34,955,032 (GRCm39) probably benign Het
Cacnb1 G A 11: 97,903,672 (GRCm39) T127I possibly damaging Het
Cmya5 A T 13: 93,230,210 (GRCm39) V1626E probably benign Het
Cndp2 C T 18: 84,686,694 (GRCm39) G443S probably damaging Het
Crb1 A G 1: 139,265,016 (GRCm39) I134T possibly damaging Het
Dnaaf3 T C 7: 4,535,276 (GRCm39) probably null Het
Enam C T 5: 88,651,008 (GRCm39) P764L probably benign Het
Fat3 G A 9: 15,909,567 (GRCm39) S2145F probably damaging Het
Fbln1 G A 15: 85,111,341 (GRCm39) probably null Het
Flnb A G 14: 7,945,950 (GRCm38) I2452V possibly damaging Het
Fmo3 A T 1: 162,781,884 (GRCm39) W490R probably damaging Het
Gabrb1 C T 5: 72,026,916 (GRCm39) R106* probably null Het
Galnt4 C T 10: 98,944,923 (GRCm39) T216I probably damaging Het
Gkn3 C T 6: 87,360,507 (GRCm39) A163T probably damaging Het
Golph3 A G 15: 12,349,649 (GRCm39) D223G probably benign Het
Herc4 T A 10: 63,151,473 (GRCm39) F905I possibly damaging Het
Il23r T C 6: 67,429,401 (GRCm39) T314A probably benign Het
Lrrtm4 T C 6: 79,998,857 (GRCm39) W90R probably damaging Het
Maml2 C T 9: 13,532,541 (GRCm39) T585I probably damaging Het
Mpp3 G A 11: 101,911,312 (GRCm39) A170V probably damaging Het
Naip6 T A 13: 100,452,928 (GRCm39) K44N possibly damaging Het
Or10aa3 C T 1: 173,878,814 (GRCm39) R292C probably damaging Het
Or10ak7 C T 4: 118,791,230 (GRCm39) E272K probably benign Het
Or1e17 A G 11: 73,831,182 (GRCm39) T37A possibly damaging Het
Or4k51 C T 2: 111,585,139 (GRCm39) P182S probably damaging Het
Or51b6 T A 7: 103,556,267 (GRCm39) M207K probably benign Het
Or6f2 A G 7: 139,756,878 (GRCm39) T282A probably damaging Het
Or7e165 T G 9: 19,694,892 (GRCm39) I154M probably benign Het
Or8c10 T C 9: 38,279,394 (GRCm39) I174T probably damaging Het
Pak1 T A 7: 97,535,521 (GRCm39) V204E probably benign Het
Pcdhb10 T A 18: 37,547,190 (GRCm39) C755* probably null Het
Pkd1l3 G T 8: 110,355,341 (GRCm39) W723L probably benign Het
Plin1 C T 7: 79,376,139 (GRCm39) probably null Het
Polr3a A T 14: 24,525,960 (GRCm39) probably null Het
Ranbp2 A T 10: 58,314,758 (GRCm39) K1826I possibly damaging Het
Rapgef1 A G 2: 29,626,608 (GRCm39) I970V possibly damaging Het
Rdx C A 9: 51,980,173 (GRCm39) F255L probably damaging Het
Rp1l1 A T 14: 64,267,447 (GRCm39) H1011L possibly damaging Het
Serpina6 T C 12: 103,614,868 (GRCm39) D326G probably benign Het
Sh3tc2 A G 18: 62,123,966 (GRCm39) E909G probably benign Het
Shprh T A 10: 11,047,697 (GRCm39) V1015D probably damaging Het
Slfn8 A T 11: 82,894,920 (GRCm39) Y629N probably damaging Het
Triml1 A G 8: 43,594,408 (GRCm39) S8P probably damaging Het
Other mutations in Pcdhb20
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01071:Pcdhb20 APN 18 37,637,738 (GRCm39) missense possibly damaging 0.87
IGL01373:Pcdhb20 APN 18 37,639,621 (GRCm39) missense probably benign 0.10
IGL01556:Pcdhb20 APN 18 37,637,852 (GRCm39) missense possibly damaging 0.88
IGL01621:Pcdhb20 APN 18 37,637,860 (GRCm39) missense possibly damaging 0.49
IGL01768:Pcdhb20 APN 18 37,639,768 (GRCm39) missense possibly damaging 0.80
IGL01859:Pcdhb20 APN 18 37,637,616 (GRCm39) missense probably damaging 0.98
IGL02492:Pcdhb20 APN 18 37,639,453 (GRCm39) missense probably benign 0.43
IGL03057:Pcdhb20 APN 18 37,637,851 (GRCm39) missense possibly damaging 0.74
IGL02991:Pcdhb20 UTSW 18 37,639,264 (GRCm39) missense probably damaging 1.00
R0799:Pcdhb20 UTSW 18 37,638,938 (GRCm39) missense probably damaging 1.00
R1465:Pcdhb20 UTSW 18 37,637,750 (GRCm39) missense probably damaging 0.99
R1465:Pcdhb20 UTSW 18 37,637,750 (GRCm39) missense probably damaging 0.99
R2012:Pcdhb20 UTSW 18 37,638,127 (GRCm39) missense probably damaging 0.99
R2079:Pcdhb20 UTSW 18 37,638,224 (GRCm39) missense probably benign 0.07
R2350:Pcdhb20 UTSW 18 37,637,563 (GRCm39) missense probably benign 0.01
R2364:Pcdhb20 UTSW 18 37,638,991 (GRCm39) missense probably damaging 1.00
R2870:Pcdhb20 UTSW 18 37,638,833 (GRCm39) missense possibly damaging 0.82
R2870:Pcdhb20 UTSW 18 37,638,833 (GRCm39) missense possibly damaging 0.82
R4060:Pcdhb20 UTSW 18 37,639,217 (GRCm39) missense probably damaging 1.00
R4609:Pcdhb20 UTSW 18 37,638,849 (GRCm39) missense probably benign 0.02
R4750:Pcdhb20 UTSW 18 37,639,184 (GRCm39) missense possibly damaging 0.48
R4897:Pcdhb20 UTSW 18 37,639,298 (GRCm39) missense possibly damaging 0.70
R4970:Pcdhb20 UTSW 18 37,639,824 (GRCm39) missense probably benign 0.00
R5098:Pcdhb20 UTSW 18 37,637,858 (GRCm39) missense probably damaging 1.00
R5616:Pcdhb20 UTSW 18 37,637,585 (GRCm39) missense probably damaging 0.97
R5890:Pcdhb20 UTSW 18 37,638,286 (GRCm39) missense probably benign 0.00
R6225:Pcdhb20 UTSW 18 37,638,047 (GRCm39) missense probably damaging 1.00
R6248:Pcdhb20 UTSW 18 37,639,285 (GRCm39) missense probably damaging 0.99
R6419:Pcdhb20 UTSW 18 37,638,608 (GRCm39) missense probably damaging 1.00
R6814:Pcdhb20 UTSW 18 37,639,218 (GRCm39) missense probably benign 0.22
R6821:Pcdhb20 UTSW 18 37,639,175 (GRCm39) missense probably damaging 1.00
R6824:Pcdhb20 UTSW 18 37,638,752 (GRCm39) missense probably benign 0.06
R6872:Pcdhb20 UTSW 18 37,639,218 (GRCm39) missense probably benign 0.22
R7040:Pcdhb20 UTSW 18 37,637,770 (GRCm39) missense probably benign 0.00
R7145:Pcdhb20 UTSW 18 37,638,142 (GRCm39) missense probably damaging 1.00
R7165:Pcdhb20 UTSW 18 37,638,123 (GRCm39) missense probably damaging 1.00
R7215:Pcdhb20 UTSW 18 37,638,439 (GRCm39) missense probably benign 0.24
R7265:Pcdhb20 UTSW 18 37,638,616 (GRCm39) missense possibly damaging 0.95
R7372:Pcdhb20 UTSW 18 37,639,840 (GRCm39) missense probably benign 0.00
R7402:Pcdhb20 UTSW 18 37,638,005 (GRCm39) missense probably benign 0.05
R7718:Pcdhb20 UTSW 18 37,638,704 (GRCm39) missense probably damaging 1.00
R7794:Pcdhb20 UTSW 18 37,637,485 (GRCm39) missense probably benign 0.00
R7842:Pcdhb20 UTSW 18 37,638,112 (GRCm39) missense possibly damaging 0.94
R8084:Pcdhb20 UTSW 18 37,639,226 (GRCm39) missense possibly damaging 0.95
R8133:Pcdhb20 UTSW 18 37,639,663 (GRCm39) nonsense probably null
R8422:Pcdhb20 UTSW 18 37,637,849 (GRCm39) missense probably damaging 1.00
R8477:Pcdhb20 UTSW 18 37,638,307 (GRCm39) missense probably benign 0.12
R8727:Pcdhb20 UTSW 18 37,638,437 (GRCm39) missense probably damaging 1.00
R8733:Pcdhb20 UTSW 18 37,638,437 (GRCm39) missense probably damaging 1.00
R8951:Pcdhb20 UTSW 18 37,639,146 (GRCm39) missense probably damaging 1.00
R9196:Pcdhb20 UTSW 18 37,638,024 (GRCm39) missense probably benign 0.00
R9384:Pcdhb20 UTSW 18 37,638,024 (GRCm39) missense probably benign 0.00
R9388:Pcdhb20 UTSW 18 37,638,853 (GRCm39) missense probably benign 0.02
R9462:Pcdhb20 UTSW 18 37,639,799 (GRCm39) missense probably benign 0.30
R9667:Pcdhb20 UTSW 18 37,637,839 (GRCm39) missense probably benign 0.00
Z1177:Pcdhb20 UTSW 18 37,637,641 (GRCm39) missense possibly damaging 0.95
Predicted Primers PCR Primer
(F):5'- TGTCGTCGGTTACAAAGGC -3'
(R):5'- CATTGGAGCCTGAGTCTTTGTC -3'

Sequencing Primer
(F):5'- GTCGTCGGTTACAAAGGCAATTCC -3'
(R):5'- CCTGAGTCTTTGTCTGTGGCAC -3'
Posted On 2014-10-30