Incidental Mutation 'R5773:Pcdha6'
ID 445535
Institutional Source Beutler Lab
Gene Symbol Pcdha6
Ensembl Gene ENSMUSG00000103707
Gene Name protocadherin alpha 6
Synonyms Cnr2, Crnr2
MMRRC Submission 043372-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.156) question?
Stock # R5773 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37100684-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 37102643 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Leucine at position 612 (H612L)
Ref Sequence ENSEMBL: ENSMUSP00000141459 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000193389] [ENSMUST00000193777] [ENSMUST00000194751] [ENSMUST00000193839] [ENSMUST00000195590] [ENSMUST00000192512] [ENSMUST00000194544] [ENSMUST00000192631]
AlphaFold Q91Y14
Predicted Effect probably benign
Transcript: ENSMUST00000070797
SMART Domains Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442

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 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: ENSMUST00000115662
SMART Domains Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148

DomainStartEndE-ValueType
CA 45 131 6.34e-2 SMART
CA 155 240 2.98e-18 SMART
CA 264 348 2.17e-29 SMART
CA 372 453 2.84e-24 SMART
CA 477 563 5.02e-25 SMART
CA 594 675 8.16e-16 SMART
transmembrane domain 695 717 N/A INTRINSIC
low complexity region 916 940 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192168
SMART Domains Protein: ENSMUSP00000142293
Gene: ENSMUSG00000103092

DomainStartEndE-ValueType
CA 21 131 2.2e-2 SMART
CA 155 240 2.05e-21 SMART
CA 264 348 8.81e-21 SMART
CA 372 453 2.01e-24 SMART
CA 477 563 1.42e-24 SMART
CA 591 673 1.63e-15 SMART
transmembrane domain 693 715 N/A INTRINSIC
low complexity region 902 926 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192178
Predicted Effect probably benign
Transcript: ENSMUST00000192295
SMART Domains Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252

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 477 568 5.38e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000192503
SMART Domains Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312

DomainStartEndE-ValueType
low complexity region 11 17 N/A INTRINSIC
CA 42 128 3.78e-2 SMART
CA 152 237 8.94e-22 SMART
CA 261 345 3.74e-24 SMART
CA 369 450 1.09e-25 SMART
CA 474 560 1.42e-24 SMART
CA 588 670 2.96e-13 SMART
transmembrane domain 692 714 N/A INTRINSIC
low complexity region 910 934 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193389
AA Change: H612L

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: H612L

DomainStartEndE-ValueType
CA 21 131 5.67e-2 SMART
CA 155 240 4.72e-21 SMART
CA 264 348 1.9e-25 SMART
CA 372 453 3.31e-25 SMART
CA 477 563 1.42e-24 SMART
CA 594 676 5.91e-13 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000193777
AA Change: H612L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: H612L

DomainStartEndE-ValueType
CA 21 131 5.67e-2 SMART
CA 155 240 4.72e-21 SMART
CA 264 348 1.9e-25 SMART
CA 372 453 3.31e-25 SMART
CA 477 563 1.42e-24 SMART
CA 594 676 5.91e-13 SMART
low complexity region 914 938 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194751
SMART Domains Protein: ENSMUSP00000142285
Gene: ENSMUSG00000103707

DomainStartEndE-ValueType
low complexity region 15 21 N/A INTRINSIC
Pfam:Cadherin_2 29 112 4.5e-32 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000193839
SMART Domains Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442

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
Predicted Effect probably benign
Transcript: ENSMUST00000195590
SMART Domains Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148

DomainStartEndE-ValueType
CA 45 131 6.34e-2 SMART
CA 155 240 2.98e-18 SMART
CA 264 348 2.17e-29 SMART
CA 372 453 2.84e-24 SMART
CA 477 563 5.02e-25 SMART
CA 594 675 8.16e-16 SMART
transmembrane domain 695 717 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192512
SMART Domains Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252

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
low complexity region 915 939 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194544
SMART Domains Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

DomainStartEndE-ValueType
Blast:CA 18 66 5e-20 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000192631
SMART Domains Protein: ENSMUSP00000142156
Gene: ENSMUSG00000104318

DomainStartEndE-ValueType
CA 21 131 2.58e-2 SMART
CA 155 240 4.27e-19 SMART
CA 264 348 1.42e-24 SMART
CA 372 453 9.36e-25 SMART
CA 477 563 1.42e-24 SMART
CA 594 671 4.03e-6 SMART
transmembrane domain 696 718 N/A INTRINSIC
low complexity region 905 929 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.8%
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]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acss2 G A 2: 155,416,614 (GRCm39) probably null Het
Akna C T 4: 63,313,307 (GRCm39) S272N probably benign Het
Ap2m1 T C 16: 20,362,140 (GRCm39) V416A probably damaging Het
Atp7b A G 8: 22,517,879 (GRCm39) F320L probably benign Het
Brd1 T C 15: 88,573,752 (GRCm39) K1116E probably benign Het
Ccdc186 T C 19: 56,801,919 (GRCm39) D66G probably benign Het
Cdh4 A G 2: 179,527,789 (GRCm39) Y503C probably damaging Het
Cfb C A 17: 35,076,248 (GRCm39) E166* probably null Het
Cmtm1 A T 8: 105,031,808 (GRCm39) F90I probably damaging Het
Col1a1 A T 11: 94,830,255 (GRCm39) K160N probably benign Het
Cradd T C 10: 95,011,823 (GRCm39) I106V probably benign Het
Defa17 A G 8: 22,146,574 (GRCm39) R67G probably damaging Het
Dgkh T C 14: 78,832,895 (GRCm39) N765S probably damaging Het
Dock5 A G 14: 68,033,507 (GRCm39) V954A possibly damaging Het
Eif2d A G 1: 131,086,040 (GRCm39) probably null Het
Epg5 T A 18: 78,004,040 (GRCm39) F683I probably damaging Het
Fhad1 T G 4: 141,656,881 (GRCm39) K91T probably damaging Het
Fut11 A T 14: 20,748,383 (GRCm39) D476V probably damaging Het
Gldn T C 9: 54,241,775 (GRCm39) probably null Het
Gm7247 C T 14: 51,601,805 (GRCm39) S26F probably benign Het
Gm8674 T A 13: 50,055,912 (GRCm39) noncoding transcript Het
Gtpbp6 C A 5: 110,254,757 (GRCm39) E168D possibly damaging Het
Hinfp T A 9: 44,210,533 (GRCm39) H163L probably benign Het
Igkv6-29 C A 6: 70,115,584 (GRCm39) G70V possibly damaging Het
Ing3 T A 6: 21,971,834 (GRCm39) C368S probably damaging Het
Itih1 A G 14: 30,657,356 (GRCm39) V489A possibly damaging Het
Itsn2 T C 12: 4,757,089 (GRCm39) L1393P probably damaging Het
Kcnj13 T C 1: 87,314,389 (GRCm39) T278A probably damaging Het
Kntc1 G A 5: 123,932,220 (GRCm39) R1338Q probably damaging Het
Lipi T A 16: 75,370,813 (GRCm39) T135S probably damaging Het
Map7 A G 10: 20,122,390 (GRCm39) K152R probably benign Het
Mmp24 A G 2: 155,641,829 (GRCm39) Y219C probably damaging Het
Nup188 T C 2: 30,212,208 (GRCm39) V565A possibly damaging Het
Nup210 T C 6: 91,062,865 (GRCm39) K265E probably damaging Het
Or10ak9 A G 4: 118,726,718 (GRCm39) T247A probably damaging Het
Pgpep1 G A 8: 71,105,101 (GRCm39) T53M probably damaging Het
Pld2 G T 11: 70,446,758 (GRCm39) S778I probably damaging Het
Ppef2 A C 5: 92,398,420 (GRCm39) Y33D probably damaging Het
Ppfibp2 A T 7: 107,285,079 (GRCm39) T129S possibly damaging Het
Prickle1 G T 15: 93,406,478 (GRCm39) H182N probably damaging Het
R3hdm2 T A 10: 127,280,172 (GRCm39) probably benign Het
Rbm12b1 A T 4: 12,145,765 (GRCm39) E579V probably damaging Het
Rsf1 GGC GGCGGCGGCTGC 7: 97,229,140 (GRCm39) probably benign Het
Slc1a6 T G 10: 78,629,111 (GRCm39) probably null Het
Slc27a6 G T 18: 58,715,245 (GRCm39) A283S probably damaging Het
Spats2l T A 1: 57,918,708 (GRCm39) N27K possibly damaging Het
Srgap1 T C 10: 121,732,614 (GRCm39) M155V probably benign Het
Stxbp5l C A 16: 37,028,459 (GRCm39) A535S probably damaging Het
Svep1 C A 4: 58,099,985 (GRCm39) C1353F possibly damaging Het
Taar4 T A 10: 23,837,056 (GRCm39) I222N probably damaging Het
Tlr6 A G 5: 65,111,846 (GRCm39) F354L probably benign Het
Trp53bp1 A G 2: 121,074,395 (GRCm39) S452P probably damaging Het
Ttll5 GCCCTGCGGGGCTGCCACGCTGTCGATCCGGCAGCTAC G 12: 85,980,329 (GRCm39) probably null Het
Usp42 A T 5: 143,699,467 (GRCm39) M1264K probably benign Het
Zfp865 A T 7: 5,037,693 (GRCm39) probably benign Het
Zfyve26 A T 12: 79,334,511 (GRCm39) L169Q probably damaging Het
Zmym4 A T 4: 126,799,163 (GRCm39) N383K possibly damaging Het
Other mutations in Pcdha6
AlleleSourceChrCoordTypePredicted EffectPPH Score
R3734:Pcdha6 UTSW 18 37,102,454 (GRCm39) missense probably damaging 1.00
R3859:Pcdha6 UTSW 18 37,102,984 (GRCm39) missense possibly damaging 0.89
R3875:Pcdha6 UTSW 18 37,101,119 (GRCm39) missense probably damaging 1.00
R4446:Pcdha6 UTSW 18 37,100,813 (GRCm39) missense probably benign 0.28
R4647:Pcdha6 UTSW 18 37,102,189 (GRCm39) missense probably damaging 0.98
R4659:Pcdha6 UTSW 18 37,102,292 (GRCm39) missense probably damaging 1.00
R4780:Pcdha6 UTSW 18 37,102,906 (GRCm39) missense probably damaging 1.00
R4839:Pcdha6 UTSW 18 37,101,485 (GRCm39) missense possibly damaging 0.73
R4915:Pcdha6 UTSW 18 37,101,510 (GRCm39) missense probably damaging 1.00
R5011:Pcdha6 UTSW 18 37,100,960 (GRCm39) missense probably damaging 1.00
R5084:Pcdha6 UTSW 18 37,102,016 (GRCm39) missense probably damaging 1.00
R5090:Pcdha6 UTSW 18 37,101,770 (GRCm39) missense probably benign 0.15
R5189:Pcdha6 UTSW 18 37,101,844 (GRCm39) missense probably damaging 1.00
R5652:Pcdha6 UTSW 18 37,101,889 (GRCm39) splice site probably null
R5890:Pcdha6 UTSW 18 37,102,121 (GRCm39) missense possibly damaging 0.94
R6135:Pcdha6 UTSW 18 37,102,269 (GRCm39) missense probably damaging 1.00
R6276:Pcdha6 UTSW 18 37,102,820 (GRCm39) splice site probably null
R6346:Pcdha6 UTSW 18 37,101,113 (GRCm39) missense probably damaging 1.00
R6889:Pcdha6 UTSW 18 37,101,396 (GRCm39) missense probably damaging 1.00
R7295:Pcdha6 UTSW 18 37,101,189 (GRCm39) missense probably damaging 1.00
R7776:Pcdha6 UTSW 18 37,103,034 (GRCm39) missense probably benign 0.27
R7944:Pcdha6 UTSW 18 37,101,965 (GRCm39) missense possibly damaging 0.55
R7950:Pcdha6 UTSW 18 37,102,479 (GRCm39) missense probably damaging 1.00
R8371:Pcdha6 UTSW 18 37,102,920 (GRCm39) nonsense probably null
R8513:Pcdha6 UTSW 18 37,102,229 (GRCm39) missense probably damaging 1.00
R8549:Pcdha6 UTSW 18 37,101,594 (GRCm39) missense possibly damaging 0.83
R8735:Pcdha6 UTSW 18 37,101,203 (GRCm39) missense possibly damaging 0.55
R8827:Pcdha6 UTSW 18 37,102,802 (GRCm39) missense probably damaging 1.00
R8881:Pcdha6 UTSW 18 37,101,484 (GRCm39) missense probably damaging 1.00
R9094:Pcdha6 UTSW 18 37,101,593 (GRCm39) missense probably damaging 0.98
R9357:Pcdha6 UTSW 18 37,102,226 (GRCm39) missense probably benign 0.16
Z1088:Pcdha6 UTSW 18 37,102,270 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ATGAGAACGACAATGCGCC -3'
(R):5'- AACGAAACTTCCTGGCCAG -3'

Sequencing Primer
(F):5'- CCACGCTGCTTGGACCTTG -3'
(R):5'- GGAGTCTGGCTGTTCTCAACC -3'
Posted On 2016-11-21