Incidental Mutation 'R8881:Pcdha6'
ID 676950
Institutional Source Beutler Lab
Gene Symbol Pcdha6
Ensembl Gene ENSMUSG00000103707
Gene Name protocadherin alpha 6
Synonyms Cnr2, Crnr2
MMRRC Submission 068749-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.156) question?
Stock # R8881 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 37100684-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 37101484 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Phenylalanine at position 226 (V226F)
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: V226F

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: V226F

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: V226F

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: V226F

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
Meta Mutation Damage Score 0.4511 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.5%
Validation Efficiency 100% (69/69)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 G A 7: 120,074,794 (GRCm39) C612Y probably benign Het
Adam21 T C 12: 81,606,650 (GRCm39) T371A probably benign Het
Akap9 T C 5: 4,011,279 (GRCm39) S661P Het
Anxa11 C T 14: 25,874,687 (GRCm39) R233C probably damaging Het
Capza3 A C 6: 139,987,521 (GRCm39) D40A probably damaging Het
Caskin1 C A 17: 24,718,273 (GRCm39) N294K probably damaging Het
Cdh1 T C 8: 107,392,904 (GRCm39) V796A probably benign Het
Cfap251 C T 5: 123,462,438 (GRCm39) P1249L probably damaging Het
Cped1 A T 6: 22,119,578 (GRCm39) T346S possibly damaging Het
Crisp4 A T 1: 18,185,902 (GRCm39) V278D probably damaging Het
Ddx60 A C 8: 62,474,343 (GRCm39) D1477A possibly damaging Het
Dmrtb1 T C 4: 107,537,922 (GRCm39) D82G possibly damaging Het
Dnah11 T C 12: 118,077,647 (GRCm39) N1282S probably benign Het
Dnah11 C T 12: 118,090,550 (GRCm39) V1104M probably benign Het
Dot1l A G 10: 80,621,429 (GRCm39) E630G probably damaging Het
Dppa4 C A 16: 48,108,299 (GRCm39) T28K Het
Dusp5 T A 19: 53,529,745 (GRCm39) S383T probably benign Het
Eef2k C T 7: 120,472,548 (GRCm39) A87V probably damaging Het
Epha1 T C 6: 42,337,961 (GRCm39) Y828C probably damaging Het
Erbb4 A C 1: 68,382,997 (GRCm39) probably null Het
Fam151b T A 13: 92,604,630 (GRCm39) M120L probably benign Het
Fam237b A C 5: 5,625,379 (GRCm39) D25A possibly damaging Het
Fez2 T C 17: 78,689,051 (GRCm39) D366G probably damaging Het
Frmd4b G T 6: 97,272,735 (GRCm39) H886N probably benign Het
Galnt17 T C 5: 130,906,635 (GRCm39) H511R probably benign Het
Grpel1 C A 5: 36,626,816 (GRCm39) Q33K possibly damaging Het
Gzmm A C 10: 79,530,819 (GRCm39) probably null Het
Hmcn1 C A 1: 150,525,723 (GRCm39) L3333F probably damaging Het
Il21r A T 7: 125,231,498 (GRCm39) T309S probably benign Het
Itgal G A 7: 126,929,541 (GRCm39) V1153M probably benign Het
Kdf1 G A 4: 133,257,654 (GRCm39) A390T possibly damaging Het
Lcn11 G T 2: 25,669,296 (GRCm39) R151L probably benign Het
Lgi3 T A 14: 70,770,282 (GRCm39) Y116N probably damaging Het
Llgl2 A G 11: 115,743,866 (GRCm39) H731R probably benign Het
Lrp5 A T 19: 3,641,015 (GRCm39) S1482T probably damaging Het
Meis2 T C 2: 115,889,116 (GRCm39) D212G probably benign Het
Mrgpra9 A G 7: 46,885,242 (GRCm39) C142R possibly damaging Het
Mrgprf A G 7: 144,861,999 (GRCm39) H187R probably benign Het
Mvd A G 8: 123,164,564 (GRCm39) probably null Het
Neb T C 2: 52,096,999 (GRCm39) I4938M possibly damaging Het
Nipal4 A T 11: 46,042,177 (GRCm39) M168K probably benign Het
Nr1h4 A G 10: 89,319,351 (GRCm39) Y158H probably damaging Het
Nrxn2 T C 19: 6,554,920 (GRCm39) I1133T probably benign Het
Numa1 T C 7: 101,650,684 (GRCm39) Y1472H probably benign Het
Or10ak8 A G 4: 118,774,571 (GRCm39) V31A probably benign Het
Or12j3 A G 7: 139,952,698 (GRCm39) V275A probably benign Het
Or2y10 G A 11: 49,455,209 (GRCm39) V154M probably benign Het
Or3a1d T C 11: 74,237,471 (GRCm39) D313G probably benign Het
Or52h7 A G 7: 104,213,619 (GRCm39) M64V possibly damaging Het
Pate7 T A 9: 35,689,384 (GRCm39) probably benign Het
Pnpla6 G A 8: 3,581,489 (GRCm39) M605I probably benign Het
Ppp1r13l G A 7: 19,105,194 (GRCm39) R322H probably damaging Het
Sgtb T C 13: 104,258,046 (GRCm39) probably null Het
Skint6 T C 4: 112,672,716 (GRCm39) K1086E possibly damaging Het
Slc4a11 T C 2: 130,527,457 (GRCm39) E646G probably damaging Het
Speg G T 1: 75,377,795 (GRCm39) R851L possibly damaging Het
Spns3 T G 11: 72,429,912 (GRCm39) D172A probably damaging Het
Srgap3 A G 6: 112,700,098 (GRCm39) V984A probably benign Het
Syne1 A T 10: 5,223,639 (GRCm39) D3080E probably damaging Het
Taf5l T C 8: 124,730,101 (GRCm39) H196R possibly damaging Het
Tmem229a G C 6: 24,955,587 (GRCm39) R56G probably damaging Het
Tmprss6 A C 15: 78,327,987 (GRCm39) *582G probably null Het
Trip13 C A 13: 74,077,795 (GRCm39) R173L possibly damaging Het
Trpm7 A T 2: 126,661,883 (GRCm39) V1055E probably damaging Het
Utrn A G 10: 12,423,737 (GRCm39) I2T possibly damaging Het
V1rd19 T A 7: 23,703,081 (GRCm39) S182R possibly damaging Het
Vmn2r58 C A 7: 41,486,609 (GRCm39) G762V probably benign Het
Zfp874b T C 13: 67,622,141 (GRCm39) K386E probably 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
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'- TCTTTGTTTCCACTAGAGGGC -3'
(R):5'- GGCACCAGTCTATTAAAAGAGTACG -3'

Sequencing Primer
(F):5'- TTTCCACTAGAGGGCGCATCAG -3'
(R):5'- GAGTACGAAATTGCTGAATTCGTCCC -3'
Posted On 2021-07-15