Incidental Mutation 'R5487:Pcdha9'
ID 430433
Institutional Source Beutler Lab
Gene Symbol Pcdha9
Ensembl Gene ENSMUSG00000103770
Gene Name protocadherin alpha 9
Synonyms
MMRRC Submission 043048-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.690) question?
Stock # R5487 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37130933-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 37132703 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Tyrosine at position 591 (N591Y)
Ref Sequence ENSEMBL: ENSMUSP00000111323 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115659] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000194544] [ENSMUST00000194751] [ENSMUST00000193389] [ENSMUST00000192631] [ENSMUST00000193839] [ENSMUST00000192512] [ENSMUST00000195590] [ENSMUST00000194038] [ENSMUST00000193777]
AlphaFold Q91Y11
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 damaging
Transcript: ENSMUST00000115659
AA Change: N591Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000111323
Gene: ENSMUSG00000103770
AA Change: N591Y

DomainStartEndE-ValueType
low complexity region 44 51 N/A INTRINSIC
CA 75 161 2.46e-2 SMART
CA 185 270 8.1e-20 SMART
CA 294 378 1.69e-22 SMART
CA 402 483 1.52e-24 SMART
CA 507 593 5.68e-24 SMART
CA 624 705 6.69e-12 SMART
transmembrane domain 727 749 N/A INTRINSIC
Pfam:Cadherin_tail 828 962 5.6e-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: 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: ENSMUST00000193984
Predicted Effect probably benign
Transcript: ENSMUST00000193389
SMART Domains Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707

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: 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 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: 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: 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: ENSMUST00000194038
SMART Domains Protein: ENSMUSP00000142159
Gene: ENSMUSG00000103800

DomainStartEndE-ValueType
CA 20 131 6.34e-2 SMART
CA 155 240 4.27e-19 SMART
CA 264 348 2.04e-25 SMART
CA 372 453 2.84e-24 SMART
CA 477 563 9.88e-24 SMART
CA 594 676 8.62e-15 SMART
transmembrane domain 699 721 N/A INTRINSIC
low complexity region 914 938 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193777
SMART Domains Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707

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
Coding Region Coverage
  • 1x: 98.2%
  • 3x: 97.1%
  • 10x: 94.6%
  • 20x: 89.0%
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8b A G 11: 109,844,340 (GRCm39) V959A probably damaging Het
Alg3 A T 16: 20,426,530 (GRCm39) I115N probably damaging Het
Ash1l A G 3: 88,888,733 (GRCm39) D204G probably benign Het
Camta1 C A 4: 151,229,211 (GRCm39) E540D possibly damaging Het
Cblc T C 7: 19,518,733 (GRCm39) T413A probably benign Het
Ccdc122 T A 14: 77,329,119 (GRCm39) H57Q probably benign Het
Ccdc85a A T 11: 28,526,768 (GRCm39) L280* probably null Het
Cd46 T G 1: 194,750,478 (GRCm39) probably null Het
Cmklr1 C G 5: 113,752,990 (GRCm39) D4H possibly damaging Het
Dnaaf3 T C 7: 4,526,864 (GRCm39) probably null Het
Dnajb12 GC G 10: 59,728,574 (GRCm39) probably null Het
Ecpas T C 4: 58,809,421 (GRCm39) D1651G probably benign Het
Eif2ak1 A G 5: 143,833,981 (GRCm39) probably null Het
Erich4 A G 7: 25,314,664 (GRCm39) M83T probably benign Het
Fbxo24 C T 5: 137,617,094 (GRCm39) G331E possibly damaging Het
Fzd4 A G 7: 89,056,615 (GRCm39) I221V probably benign Het
G6pc2 T C 2: 69,056,921 (GRCm39) V189A probably damaging Het
Gm10663 A C 8: 65,527,686 (GRCm39) E1A probably null Het
Gm4871 C A 5: 144,967,199 (GRCm39) E178D probably damaging Het
Igdcc3 A G 9: 65,088,866 (GRCm39) E415G probably damaging Het
Kmt2a A T 9: 44,733,272 (GRCm39) probably benign Het
Krba1 T C 6: 48,380,973 (GRCm39) V103A probably damaging Het
Lcat T C 8: 106,666,296 (GRCm39) K409E probably benign Het
Lrriq4 C A 3: 30,714,144 (GRCm39) N497K probably benign Het
Mical2 A G 7: 111,919,842 (GRCm39) T451A probably damaging Het
Noxo1 C T 17: 24,917,291 (GRCm39) probably benign Het
Oas1a A G 5: 121,045,490 (GRCm39) I17T probably damaging Het
Otog A T 7: 45,938,192 (GRCm39) Y1967F probably benign Het
Plxna4 A G 6: 32,494,218 (GRCm39) Y133H probably damaging Het
Pou5f2 T C 13: 78,173,118 (GRCm39) L20P probably benign Het
Prkcb T A 7: 122,199,948 (GRCm39) C586* probably null Het
Sema3b A T 9: 107,478,161 (GRCm39) M408K probably damaging Het
Serpinf2 G A 11: 75,324,031 (GRCm39) T332I probably damaging Het
Tmbim1 A G 1: 74,332,164 (GRCm39) V121A probably benign Het
Tph2 C T 10: 114,955,779 (GRCm39) G338D probably damaging Het
Trpc2 GTGTCCTA GTGTCCTATGTCCTA 7: 101,744,420 (GRCm39) probably null Het
Ttn C T 2: 76,642,896 (GRCm39) V13247M probably damaging Het
Uty C T Y: 1,174,825 (GRCm39) G192R probably damaging Het
Vmn2r65 G T 7: 84,595,529 (GRCm39) P385Q possibly damaging Het
Wdfy3 G A 5: 101,984,140 (GRCm39) R3489W probably damaging Het
Zfp750 A G 11: 121,404,558 (GRCm39) S106P probably benign Het
Other mutations in Pcdha9
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0761:Pcdha9 UTSW 18 37,133,016 (GRCm39) nonsense probably null
R2985:Pcdha9 UTSW 18 37,131,255 (GRCm39) missense possibly damaging 0.88
R3926:Pcdha9 UTSW 18 37,132,465 (GRCm39) missense probably damaging 1.00
R4049:Pcdha9 UTSW 18 37,130,995 (GRCm39) missense probably benign 0.16
R4409:Pcdha9 UTSW 18 37,132,198 (GRCm39) missense probably benign 0.12
R4816:Pcdha9 UTSW 18 37,132,511 (GRCm39) missense probably damaging 1.00
R4905:Pcdha9 UTSW 18 37,131,945 (GRCm39) missense probably damaging 0.96
R4991:Pcdha9 UTSW 18 37,131,398 (GRCm39) missense probably damaging 0.99
R5484:Pcdha9 UTSW 18 37,131,156 (GRCm39) missense probably damaging 1.00
R5617:Pcdha9 UTSW 18 37,131,869 (GRCm39) missense probably benign 0.03
R5637:Pcdha9 UTSW 18 37,131,426 (GRCm39) missense probably benign 0.00
R5694:Pcdha9 UTSW 18 37,131,425 (GRCm39) missense probably benign 0.00
R5975:Pcdha9 UTSW 18 37,132,164 (GRCm39) missense probably benign 0.00
R6089:Pcdha9 UTSW 18 37,131,551 (GRCm39) missense probably benign 0.00
R6176:Pcdha9 UTSW 18 37,131,984 (GRCm39) missense probably benign 0.24
R6220:Pcdha9 UTSW 18 37,131,531 (GRCm39) missense probably damaging 1.00
R6238:Pcdha9 UTSW 18 37,132,028 (GRCm39) missense probably benign 0.43
R6391:Pcdha9 UTSW 18 37,130,972 (GRCm39) missense probably benign 0.12
R6622:Pcdha9 UTSW 18 37,131,707 (GRCm39) missense possibly damaging 0.84
R6720:Pcdha9 UTSW 18 37,131,122 (GRCm39) missense probably damaging 0.99
R7239:Pcdha9 UTSW 18 37,131,551 (GRCm39) missense probably benign 0.06
R7624:Pcdha9 UTSW 18 37,132,849 (GRCm39) nonsense probably null
R7721:Pcdha9 UTSW 18 37,132,689 (GRCm39) missense probably benign
R8211:Pcdha9 UTSW 18 37,131,912 (GRCm39) missense possibly damaging 0.56
R8483:Pcdha9 UTSW 18 37,131,636 (GRCm39) missense probably benign 0.01
R8778:Pcdha9 UTSW 18 37,132,244 (GRCm39) missense possibly damaging 0.65
R8946:Pcdha9 UTSW 18 37,131,546 (GRCm39) missense possibly damaging 0.92
R8963:Pcdha9 UTSW 18 37,131,750 (GRCm39) missense probably benign 0.43
R8987:Pcdha9 UTSW 18 37,132,998 (GRCm39) missense probably benign 0.22
R9227:Pcdha9 UTSW 18 37,131,954 (GRCm39) missense probably damaging 1.00
R9287:Pcdha9 UTSW 18 37,132,281 (GRCm39) missense probably benign 0.00
R9439:Pcdha9 UTSW 18 37,131,527 (GRCm39) missense probably benign 0.07
Z1177:Pcdha9 UTSW 18 37,131,267 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGCTATGTGTCTGTGCACG -3'
(R):5'- TCAGATTCATCCAGGGCTCG -3'

Sequencing Primer
(F):5'- TGTCTGTGCACGCGGAGAG -3'
(R):5'- ATGCTGATCTCACCCGTGTAGAG -3'
Posted On 2016-10-05