Incidental Mutation 'R9094:Pcdha6'
ID 691248
Institutional Source Beutler Lab
Gene Symbol Pcdha6
Ensembl Gene ENSMUSG00000103707
Gene Name protocadherin alpha 6
Synonyms Cnr2, Crnr2
MMRRC Submission 068909-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.156) question?
Stock # R9094 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 37100684-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 37101593 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 262 (I262N)
Ref Sequence ENSEMBL: ENSMUSP00000141587 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000193777] [ENSMUST00000193389] [ENSMUST00000193839] [ENSMUST00000194544] [ENSMUST00000194751] [ENSMUST00000195590]
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 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: 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 damaging
Transcript: ENSMUST00000193777
AA Change: I262N

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: I262N

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 damaging
Transcript: ENSMUST00000193389
AA Change: I262N

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: I262N

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: 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: ENSMUST00000194544
SMART Domains Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

DomainStartEndE-ValueType
Blast:CA 18 66 5e-20 BLAST
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: 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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency 96% (67/70)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3110021N24Rik T C 4: 108,637,744 (GRCm39) V37A unknown Het
3425401B19Rik G A 14: 32,382,614 (GRCm39) S1117L possibly damaging Het
Abi3bp A G 16: 56,456,590 (GRCm39) I1021V probably benign Het
Agrn C A 4: 156,253,264 (GRCm39) K1848N probably benign Het
Anln A G 9: 22,249,283 (GRCm39) V1005A probably benign Het
Arb2a A G 13: 78,311,725 (GRCm39) K356R possibly damaging Het
Arid3b A G 9: 57,741,327 (GRCm39) Y40H probably damaging Het
Bco1 A C 8: 117,859,917 (GRCm39) D540A probably benign Het
Blnk A G 19: 40,982,482 (GRCm39) I7T probably benign Het
Brca2 T G 5: 150,475,770 (GRCm39) D2493E probably benign Het
Bsn T A 9: 107,988,052 (GRCm39) M2567L unknown Het
Cacna1e T A 1: 154,355,064 (GRCm39) Y693F possibly damaging Het
Catsperg1 G C 7: 28,884,152 (GRCm39) T987R probably damaging Het
Cpa4 G T 6: 30,574,393 (GRCm39) D61Y possibly damaging Het
Cpne1 A C 2: 155,921,080 (GRCm39) V70G probably damaging Het
Dnase1l3 A T 14: 7,987,306 (GRCm38) N81K probably damaging Het
Duxf3 GCCC GCC 10: 58,066,944 (GRCm39) probably null Het
Fbxo31 G A 8: 122,281,136 (GRCm39) R337C probably damaging Het
Fbxo34 C G 14: 47,767,928 (GRCm39) H480Q probably benign Het
Frmd4b T C 6: 97,398,559 (GRCm39) E96G Het
Gdpgp1 T A 7: 79,888,216 (GRCm39) D82E probably benign Het
Gjb3 GCCAGATGCGCCCA GCCAGATGCGCCCAGATGCGCCCA 4: 127,220,458 (GRCm39) probably null Het
Grpel1 A G 5: 36,626,823 (GRCm39) N35S probably benign Het
Il12rb1 A G 8: 71,273,291 (GRCm39) T665A possibly damaging Het
Il16 T C 7: 83,301,559 (GRCm39) T886A probably benign Het
Insig1 T A 5: 28,278,570 (GRCm39) C128* probably null Het
Kcnk10 T A 12: 98,484,775 (GRCm39) E120D probably benign Het
Kctd1 T C 18: 15,195,369 (GRCm39) N418S possibly damaging Het
Kifbp A G 10: 62,395,037 (GRCm39) V535A probably damaging Het
Klhl20 T A 1: 160,933,055 (GRCm39) H251L probably damaging Het
Ldlrad3 T C 2: 101,888,326 (GRCm39) D127G probably damaging Het
Lrp3 T C 7: 34,903,182 (GRCm39) Y388C probably damaging Het
Lrrc4 G A 6: 28,830,206 (GRCm39) R47W possibly damaging Het
Luzp1 A T 4: 136,272,562 (GRCm39) D1022V probably damaging Het
Mllt1 C A 17: 57,212,737 (GRCm39) R132L probably damaging Het
Ncoa1 G T 12: 4,345,494 (GRCm39) H618N possibly damaging Het
Nelfcd T C 2: 174,265,861 (GRCm39) S318P probably damaging Het
Ngly1 A C 14: 16,280,721 (GRCm38) T301P probably damaging Het
Npy5r G A 8: 67,133,560 (GRCm39) T411I probably damaging Het
Or55b10 T C 7: 102,143,568 (GRCm39) E138G possibly damaging Het
Or5d46 A G 2: 88,170,248 (GRCm39) N113S probably benign Het
Peg10 GAT GATCAT 6: 4,756,449 (GRCm39) probably benign Het
Pm20d1 C A 1: 131,730,481 (GRCm39) A245D possibly damaging Het
Rars1 T C 11: 35,718,182 (GRCm39) probably benign Het
Rbms2 T A 10: 127,987,107 (GRCm39) I62F probably damaging Het
Rev3l A T 10: 39,700,809 (GRCm39) T1769S probably benign Het
Rexo1 A G 10: 80,378,854 (GRCm39) Y1061H probably damaging Het
Rgs3 A T 4: 62,500,240 (GRCm39) I26F probably damaging Het
Rsf1 G GACGGCGGCC 7: 97,229,116 (GRCm39) probably benign Het
Rtkn A T 6: 83,128,018 (GRCm39) N406Y possibly damaging Het
Rtn4r A T 16: 17,969,708 (GRCm39) I379F possibly damaging Het
Sez6 G A 11: 77,865,121 (GRCm39) E623K possibly damaging Het
Slmap T C 14: 26,137,355 (GRCm39) probably benign Het
Sorl1 A T 9: 41,975,050 (GRCm39) N519K possibly damaging Het
Srebf2 A T 15: 82,056,975 (GRCm39) I237F possibly damaging Het
Szt2 T C 4: 118,242,651 (GRCm39) S1479G possibly damaging Het
Tbc1d24 C A 17: 24,400,274 (GRCm39) E537* probably null Het
Ttf1 T A 2: 28,957,080 (GRCm39) I450K probably benign Het
Ube2e2 A G 14: 18,893,288 (GRCm38) S2P unknown Het
Utp20 T C 10: 88,611,180 (GRCm39) N1379S probably damaging Het
Vmn2r25 C T 6: 123,805,391 (GRCm39) V489I probably benign Het
Wfdc8 C T 2: 164,439,245 (GRCm39) R379H unknown Het
Zeb2 C T 2: 45,003,136 (GRCm39) probably benign Het
Zfp3 C T 11: 70,663,241 (GRCm39) T400I probably benign Het
Zfp760 T C 17: 21,941,932 (GRCm39) I369T 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
R5773:Pcdha6 UTSW 18 37,102,643 (GRCm39) missense probably benign 0.00
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
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'- CTTGGACAGAGAGGATGCTC -3'
(R):5'- CTAAAACAGTGCAATGGCCC -3'

Sequencing Primer
(F):5'- GCTCCTGAGCATAAGCTA -3'
(R):5'- CGCATCAACGTGGATTTTGTAGAC -3'
Posted On 2021-12-30