Incidental Mutation 'R4678:Pcdha1'
ID 349812
Institutional Source Beutler Lab
Gene Symbol Pcdha1
Ensembl Gene ENSMUSG00000103442
Gene Name protocadherin alpha 1
Synonyms
MMRRC Submission 041931-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4678 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37063338-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 37063965 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Lysine at position 210 (Q210K)
Ref Sequence ENSEMBL: ENSMUSP00000142308 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000193839]
AlphaFold Q91Y21
Predicted Effect probably benign
Transcript: ENSMUST00000070797
AA Change: Q210K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442
AA Change: Q210K

DomainStartEndE-ValueType
CA 22 132 3.09e-2 SMART
CA 156 241 6.14e-20 SMART
CA 265 349 3.92e-27 SMART
CA 373 454 4.94e-24 SMART
CA 478 564 1e-24 SMART
CA 592 672 4.55e-14 SMART
transmembrane domain 694 716 N/A INTRINSIC
Pfam:Cadherin_tail 797 931 5.3e-58 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192440
Predicted Effect probably benign
Transcript: ENSMUST00000193839
AA Change: Q210K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442
AA Change: Q210K

DomainStartEndE-ValueType
CA 22 132 3.09e-2 SMART
CA 156 241 6.14e-20 SMART
CA 265 349 3.92e-27 SMART
CA 373 454 4.94e-24 SMART
CA 478 564 1e-24 SMART
CA 592 672 4.55e-14 SMART
transmembrane domain 694 716 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.1%
Validation Efficiency
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 alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele are viable and fertile. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 105 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110025L11Rik T C 16: 88,860,873 (GRCm39) probably benign Het
Abcc4 A G 14: 118,865,103 (GRCm39) S308P probably damaging Het
Agr3 G T 12: 35,997,832 (GRCm39) V115L probably damaging Het
Ahr A T 12: 35,557,463 (GRCm39) I319N probably damaging Het
Alpk1 A T 3: 127,473,507 (GRCm39) V832D probably damaging Het
Ano1 T C 7: 144,223,289 (GRCm39) T78A probably benign Het
Apob G A 12: 8,045,585 (GRCm39) G897D probably damaging Het
Arfgef1 A G 1: 10,212,891 (GRCm39) F1677L probably benign Het
Arhgap40 G T 2: 158,374,226 (GRCm39) G217W probably benign Het
Arhgef4 A G 1: 34,761,749 (GRCm39) E335G unknown Het
Calcoco2 T C 11: 95,994,374 (GRCm39) T60A probably damaging Het
Catsperg1 A T 7: 28,889,721 (GRCm39) S741T probably benign Het
Ccdc181 T G 1: 164,105,846 (GRCm39) I27S probably damaging Het
Ceacam9 A T 7: 16,459,334 (GRCm39) Y211F probably damaging Het
Cep41 T C 6: 30,671,318 (GRCm39) probably null Het
Cercam T A 2: 29,759,689 (GRCm39) L45Q probably damaging Het
Cnnm2 G A 19: 46,751,685 (GRCm39) V492M possibly damaging Het
Cntn3 A G 6: 102,180,981 (GRCm39) V738A probably damaging Het
Coq8a T C 1: 179,997,646 (GRCm39) E351G probably damaging Het
Cyp3a57 T C 5: 145,307,538 (GRCm39) probably null Het
Dbn1 T C 13: 55,623,071 (GRCm39) I471V probably benign Het
Ddx21 G T 10: 62,429,782 (GRCm39) Q321K probably benign Het
Dhx8 T C 11: 101,630,634 (GRCm39) V347A probably damaging Het
Dkc1 A G X: 74,144,598 (GRCm39) I215V probably benign Homo
Dlg2 A G 7: 92,077,788 (GRCm39) I685V possibly damaging Het
Dusp11 A C 6: 85,930,363 (GRCm39) N140K probably damaging Het
Ece2 A G 16: 20,459,468 (GRCm39) K454R probably damaging Het
Eno4 T A 19: 58,935,181 (GRCm39) V131E probably damaging Het
Enpep A G 3: 129,097,362 (GRCm39) probably null Het
Etv1 T C 12: 38,885,219 (GRCm39) Y236H probably damaging Het
F2rl2 A G 13: 95,837,140 (GRCm39) T62A probably benign Het
Fbxl21 T C 13: 56,684,862 (GRCm39) V296A probably damaging Het
Fig4 T C 10: 41,148,994 (GRCm39) I153V probably benign Het
Fis1 T A 5: 136,991,951 (GRCm39) N41K possibly damaging Het
Fras1 T A 5: 96,848,427 (GRCm39) M1814K probably benign Het
Frem2 T A 3: 53,451,792 (GRCm39) I2266F probably benign Het
Gm10330 A T 12: 23,829,843 (GRCm39) *113R probably null Het
Gm12185 T A 11: 48,806,367 (GRCm39) I275F probably benign Het
Gsdme A T 6: 50,206,304 (GRCm39) C180S possibly damaging Het
Herc1 A G 9: 66,323,551 (GRCm39) E1355G probably benign Het
Hnrnpm A T 17: 33,869,185 (GRCm39) I453N possibly damaging Het
Hspb9 T C 11: 100,604,896 (GRCm39) L74P probably damaging Het
Ift46 C A 9: 44,695,260 (GRCm39) Y85* probably null Het
Insyn2b T G 11: 34,353,227 (GRCm39) L423R probably damaging Het
Ints3 T C 3: 90,315,817 (GRCm39) T316A possibly damaging Het
Isg20 C T 7: 78,564,076 (GRCm39) probably benign Het
Itga11 T A 9: 62,642,639 (GRCm39) N187K probably damaging Het
Klhl9 G A 4: 88,639,161 (GRCm39) T360I probably damaging Het
Krt39 T A 11: 99,411,826 (GRCm39) I87F probably benign Het
Krtap19-4 G A 16: 88,681,734 (GRCm39) S74F unknown Het
Lgi1 G A 19: 38,289,737 (GRCm39) V268I probably damaging Het
Lrrc46 G A 11: 96,925,719 (GRCm39) P248S probably benign Het
Lrrn4 C T 2: 132,721,488 (GRCm39) V110I probably benign Het
Mamstr C A 7: 45,294,116 (GRCm39) probably benign Het
Micu3 T A 8: 40,833,718 (GRCm39) F451I probably damaging Het
Mid1 C A X: 168,768,044 (GRCm39) D130E possibly damaging Het
Mkks T C 2: 136,722,201 (GRCm39) T319A probably benign Het
Mob3c A G 4: 115,690,968 (GRCm39) probably null Het
Muc6 T C 7: 141,230,554 (GRCm39) E1192G probably benign Het
Ndc80 A G 17: 71,827,753 (GRCm39) probably null Het
Nfx1 A G 4: 41,012,070 (GRCm39) K807E probably benign Het
Nrxn1 A T 17: 90,930,850 (GRCm39) L181Q probably damaging Het
Nsun7 A G 5: 66,418,407 (GRCm39) S46G probably benign Het
Nup98 A T 7: 101,834,038 (GRCm39) L308H probably damaging Het
Or4c115 C A 2: 88,927,860 (GRCm39) W137L probably benign Het
Or52j3 T C 7: 102,836,098 (GRCm39) F97L probably damaging Het
Or6f2 T C 7: 139,756,141 (GRCm39) V36A probably benign Het
Or8k32 T C 2: 86,369,077 (GRCm39) M61V possibly damaging Het
Palb2 T C 7: 121,726,589 (GRCm39) K427R probably damaging Het
Pcdhb2 T C 18: 37,429,260 (GRCm39) L411P probably damaging Het
Pde4dip C A 3: 97,602,321 (GRCm39) D2252Y probably damaging Het
Plekhg4 T A 8: 106,107,003 (GRCm39) Y899* probably null Het
Plxnb2 G T 15: 89,045,131 (GRCm39) T1105K probably benign Het
Psmd2 T C 16: 20,478,719 (GRCm39) V606A probably damaging Het
Ptprq A T 10: 107,521,043 (GRCm39) F710I probably benign Het
Rad51ap2 A G 12: 11,506,552 (GRCm39) E158G probably damaging Het
Rasip1 T A 7: 45,277,247 (GRCm39) H18Q possibly damaging Het
Rassf8 A G 6: 145,760,808 (GRCm39) K45E probably damaging Het
Rrn3 T A 16: 13,613,940 (GRCm39) M284K probably damaging Het
Rsf1 GGCG GGCGACGGCTGCG 7: 97,229,113 (GRCm39) probably benign Het
Rtn2 C A 7: 19,027,820 (GRCm39) N403K probably damaging Het
Rusc1 A G 3: 88,997,027 (GRCm39) W462R probably damaging Het
Sdc3 T A 4: 130,545,907 (GRCm39) probably benign Het
Secisbp2l C T 2: 125,582,657 (GRCm39) G933D possibly damaging Het
Slc12a2 T A 18: 58,039,032 (GRCm39) C537* probably null Het
Slc4a2 G A 5: 24,639,238 (GRCm39) probably null Het
Spsb4 T A 9: 96,877,744 (GRCm39) D193V probably damaging Het
Strn A C 17: 78,984,780 (GRCm39) F288V probably damaging Het
Stx18 G A 5: 38,293,712 (GRCm39) probably benign Het
Tfcp2l1 T A 1: 118,596,378 (GRCm39) M371K probably benign Het
Thnsl1 A G 2: 21,216,352 (GRCm39) probably null Het
Tlr11 C T 14: 50,598,439 (GRCm39) H142Y possibly damaging Het
Tor1aip2 T A 1: 155,940,780 (GRCm39) I362K probably damaging Het
Trmt13 T C 3: 116,383,404 (GRCm39) K125E probably damaging Het
Trpm8 T C 1: 88,264,851 (GRCm39) V320A probably benign Het
Ubr3 A T 2: 69,766,263 (GRCm39) H377L probably damaging Het
Usp8 A G 2: 126,567,349 (GRCm39) R123G probably null Het
Vim T A 2: 13,579,775 (GRCm39) L178Q probably damaging Het
Vmn1r231 A C 17: 21,110,489 (GRCm39) V142G possibly damaging Het
Vmn1r83 A G 7: 12,055,697 (GRCm39) M120T possibly damaging Het
Vwce G T 19: 10,642,012 (GRCm39) V913F possibly damaging Het
Zbtb18 C A 1: 177,275,285 (GRCm39) T215K probably benign Het
Zeb2 A T 2: 44,886,353 (GRCm39) D857E probably damaging Het
Zfp106 G A 2: 120,364,221 (GRCm39) H729Y probably damaging Het
Zfp977 C A 7: 42,229,437 (GRCm39) A363S probably benign Het
Other mutations in Pcdha1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00714:Pcdha1 APN 18 37,065,228 (GRCm39) missense probably damaging 0.99
R0062:Pcdha1 UTSW 18 37,139,681 (GRCm39) missense probably benign 0.08
R0108:Pcdha1 UTSW 18 37,131,809 (GRCm39) missense probably benign
R0543:Pcdha1 UTSW 18 37,318,121 (GRCm39) missense probably damaging 1.00
R1599:Pcdha1 UTSW 18 37,318,290 (GRCm39) missense probably damaging 1.00
R1717:Pcdha1 UTSW 18 37,065,237 (GRCm39) missense probably benign 0.01
R2301:Pcdha1 UTSW 18 37,289,236 (GRCm39) missense probably damaging 1.00
R3038:Pcdha1 UTSW 18 37,064,064 (GRCm39) missense probably damaging 1.00
R3086:Pcdha1 UTSW 18 37,064,001 (GRCm39) missense possibly damaging 0.95
R3693:Pcdha1 UTSW 18 37,065,361 (GRCm39) missense possibly damaging 0.95
R3783:Pcdha1 UTSW 18 37,063,855 (GRCm39) missense probably damaging 1.00
R3881:Pcdha1 UTSW 18 37,064,454 (GRCm39) missense possibly damaging 0.91
R4012:Pcdha1 UTSW 18 37,064,189 (GRCm39) missense probably benign 0.02
R4540:Pcdha1 UTSW 18 37,064,680 (GRCm39) missense probably damaging 1.00
R4597:Pcdha1 UTSW 18 37,064,959 (GRCm39) missense possibly damaging 0.64
R4998:Pcdha1 UTSW 18 37,065,469 (GRCm39) missense probably damaging 1.00
R5466:Pcdha1 UTSW 18 37,065,312 (GRCm39) missense possibly damaging 0.73
R5518:Pcdha1 UTSW 18 37,065,415 (GRCm39) missense probably benign 0.23
R5673:Pcdha1 UTSW 18 37,063,726 (GRCm39) missense probably damaging 1.00
R5925:Pcdha1 UTSW 18 37,063,724 (GRCm39) missense probably damaging 1.00
R5942:Pcdha1 UTSW 18 37,063,444 (GRCm39) missense probably damaging 1.00
R5963:Pcdha1 UTSW 18 37,064,224 (GRCm39) missense probably damaging 0.99
R6034:Pcdha1 UTSW 18 37,063,651 (GRCm39) missense probably damaging 1.00
R6034:Pcdha1 UTSW 18 37,063,651 (GRCm39) missense probably damaging 1.00
R6107:Pcdha1 UTSW 18 37,065,354 (GRCm39) missense probably benign 0.00
R6329:Pcdha1 UTSW 18 37,065,301 (GRCm39) missense probably damaging 1.00
R6479:Pcdha1 UTSW 18 37,064,509 (GRCm39) missense probably benign 0.28
R6503:Pcdha1 UTSW 18 37,064,724 (GRCm39) missense probably damaging 1.00
R6907:Pcdha1 UTSW 18 37,064,124 (GRCm39) missense probably benign 0.01
R7011:Pcdha1 UTSW 18 37,063,588 (GRCm39) missense probably damaging 1.00
R7030:Pcdha1 UTSW 18 37,292,326 (GRCm39) missense probably damaging 0.97
R7314:Pcdha1 UTSW 18 37,064,553 (GRCm39) missense probably damaging 0.99
R7343:Pcdha1 UTSW 18 37,063,702 (GRCm39) missense probably damaging 1.00
R7699:Pcdha1 UTSW 18 37,064,115 (GRCm39) missense probably damaging 0.98
R7700:Pcdha1 UTSW 18 37,064,115 (GRCm39) missense probably damaging 0.98
R7768:Pcdha1 UTSW 18 37,065,220 (GRCm39) missense probably damaging 1.00
R7780:Pcdha1 UTSW 18 37,065,511 (GRCm39) missense probably benign 0.28
R7800:Pcdha1 UTSW 18 37,064,426 (GRCm39) missense probably damaging 1.00
R7917:Pcdha1 UTSW 18 37,065,254 (GRCm39) missense possibly damaging 0.64
R8325:Pcdha1 UTSW 18 37,063,867 (GRCm39) missense possibly damaging 0.47
R8699:Pcdha1 UTSW 18 37,064,076 (GRCm39) missense probably benign 0.00
R9400:Pcdha1 UTSW 18 37,064,760 (GRCm39) missense probably benign 0.43
R9513:Pcdha1 UTSW 18 37,065,286 (GRCm39) missense probably benign 0.26
R9746:Pcdha1 UTSW 18 37,065,713 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- CCAGTTTTCAAAGGCGCAGAG -3'
(R):5'- AACGTCGTCACTAATGTCCC -3'

Sequencing Primer
(F):5'- CTAGATTCACGGTTTCCACTAGAGG -3'
(R):5'- GTCACTAATGTCCCATTCACTGTAG -3'
Posted On 2015-10-08