Incidental Mutation 'R8371:Pcdha6'
ID 646424
Institutional Source Beutler Lab
Gene Symbol Pcdha6
Ensembl Gene ENSMUSG00000103707
Gene Name protocadherin alpha 6
Synonyms Cnr2, Crnr2
MMRRC Submission 067740-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.172) question?
Stock # R8371 (G1)
Quality Score 225.009
Status Not validated
Chromosome 18
Chromosomal Location 37100684-37320710 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 37102920 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Stop codon at position 704 (C704*)
Ref Sequence ENSEMBL: ENSMUSP00000141587 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000193777] [ENSMUST00000192631] [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 null
Transcript: ENSMUST00000193777
AA Change: C704*
SMART Domains Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: C704*

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: 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
Predicted Effect probably null
Transcript: ENSMUST00000193389
AA Change: C704*
SMART Domains Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: C704*

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: 99.6%
  • 20x: 98.7%
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8a G T 11: 109,945,473 (GRCm39) Q1050K probably benign Het
B4galt5 A G 2: 167,151,145 (GRCm39) M121T probably damaging Het
Birc2 A G 9: 7,849,427 (GRCm39) L549P probably damaging Het
Cacna1b T C 2: 24,610,036 (GRCm39) N368S possibly damaging Het
Cbr1 A G 16: 93,406,779 (GRCm39) E165G probably damaging Het
Ccdc178 T C 18: 21,944,561 (GRCm39) D866G possibly damaging Het
Cd40 G A 2: 164,908,458 (GRCm39) G178E probably damaging Het
Cers1 T A 8: 70,782,223 (GRCm39) L349H probably benign Het
Chd8 T C 14: 52,470,275 (GRCm39) K445R probably benign Het
Clca3a2 G T 3: 144,513,114 (GRCm39) S477* probably null Het
Clec4a1 T A 6: 122,910,882 (GRCm39) *246R probably null Het
CN725425 T C 15: 91,124,973 (GRCm39) I171T probably benign Het
Crybg3 A G 16: 59,377,414 (GRCm39) M1280T probably benign Het
Csf1r A T 18: 61,250,663 (GRCm39) Q458L probably benign Het
Cyp3a11 A T 5: 145,805,438 (GRCm39) V193E possibly damaging Het
Cys1 A G 12: 24,718,694 (GRCm39) I53T probably benign Het
Dhrs3 A C 4: 144,645,953 (GRCm39) probably null Het
Dhx57 T C 17: 80,582,919 (GRCm39) R229G probably benign Het
Dhx9 T C 1: 153,331,961 (GRCm39) N1336D unknown Het
Dmgdh T A 13: 93,845,238 (GRCm39) H410Q probably benign Het
Dmxl1 T A 18: 50,031,781 (GRCm39) M2225K probably benign Het
Eif4g3 T G 4: 137,824,156 (GRCm39) Y80D probably damaging Het
Ephx4 A T 5: 107,561,384 (GRCm39) I164F possibly damaging Het
Eppk1 C T 15: 75,994,319 (GRCm39) R854Q probably benign Het
Fhl4 G A 10: 84,934,637 (GRCm39) A48V probably benign Het
Fmn2 T C 1: 174,437,173 (GRCm39) L1048S unknown Het
Gemin5 T C 11: 58,017,384 (GRCm39) M1212V probably benign Het
Gm9195 C T 14: 72,697,899 (GRCm39) V1294I probably benign Het
Gpr55 A T 1: 85,868,849 (GRCm39) V244E probably damaging Het
Hgfac T A 5: 35,202,787 (GRCm39) F429Y probably damaging Het
Jade2 T A 11: 51,715,959 (GRCm39) E415D probably benign Het
Kcnj4 T A 15: 79,369,342 (GRCm39) I213F probably damaging Het
Kcnq5 G A 1: 21,549,648 (GRCm39) R360C probably damaging Het
Klhl33 C T 14: 51,129,689 (GRCm39) R312Q probably damaging Het
Krt82 T C 15: 101,453,546 (GRCm39) E280G probably benign Het
Lemd1 C A 1: 132,156,687 (GRCm39) Q40K probably damaging Het
Lmo7 T C 14: 102,124,444 (GRCm39) L423P possibly damaging Het
Lrp8 A G 4: 107,726,268 (GRCm39) Y773C probably damaging Het
Miga2 AAGAG AAG 2: 30,265,755 (GRCm39) probably null Het
Mroh8 A T 2: 157,094,896 (GRCm39) Y363* probably null Het
Or2n1c G A 17: 38,519,189 (GRCm39) A18T probably benign Het
Or51a25 C A 7: 102,372,790 (GRCm39) K302N probably damaging Het
Or5p61 G A 7: 107,758,435 (GRCm39) T215I probably benign Het
Pcdha2 T C 18: 37,073,316 (GRCm39) Y316H possibly damaging Het
Pik3c2g G A 6: 139,881,782 (GRCm39) V923M unknown Het
Rhd A G 4: 134,603,694 (GRCm39) S72G probably benign Het
Rhot1 T C 11: 80,134,292 (GRCm39) L295P probably damaging Het
Rrp1b A G 17: 32,268,458 (GRCm39) E139G possibly damaging Het
Scnn1a T G 6: 125,320,806 (GRCm39) Y620D possibly damaging Het
Serpinb12 A T 1: 106,884,135 (GRCm39) I294L probably benign Het
Serpinb3d T C 1: 107,008,469 (GRCm39) D132G probably damaging Het
Slc26a3 A T 12: 31,502,541 (GRCm39) D254V probably damaging Het
Srrm1 A T 4: 135,052,532 (GRCm39) I614N unknown Het
Stt3b A G 9: 115,095,243 (GRCm39) Y263H probably damaging Het
Taf7 T A 18: 37,776,552 (GRCm39) K5I probably damaging Het
Tbck C A 3: 132,458,285 (GRCm39) H638Q possibly damaging Het
Tnfsf9 A C 17: 57,412,541 (GRCm39) D37A probably benign Het
Trim71 C A 9: 114,344,857 (GRCm39) V354F probably benign Het
Tspoap1 T G 11: 87,669,127 (GRCm39) C1467G probably benign Het
Xirp1 C T 9: 119,848,499 (GRCm39) R128Q possibly damaging Het
Zc3h12d GCCC GCC 10: 7,715,735 (GRCm39) probably null Het
Zfhx2 T C 14: 55,301,549 (GRCm39) D2145G probably damaging Het
Zfy2 T C Y: 2,117,168 (GRCm39) T220A probably benign 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
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'- TCGCCTATTAGTGCTGGTGAAG -3'
(R):5'- TCAAATCCTGATGCTCACCC -3'

Sequencing Primer
(F):5'- AAGGACCACGGGGAGCC -3'
(R):5'- AAGGCCATGAGATCGGTTTTG -3'
Posted On 2020-09-02