Incidental Mutation 'R4049:Pcdha9'
ID 475380
Institutional Source Beutler Lab
Gene Symbol Pcdha9
Ensembl Gene ENSMUSG00000103770
Gene Name protocadherin alpha 9
Synonyms
MMRRC Submission 041616-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.684) question?
Stock # R4049 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37130933-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 37130995 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 21 (H21Q)
Ref Sequence ENSEMBL: ENSMUSP00000111323 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115659] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000194544] [ENSMUST00000194751] [ENSMUST00000193777] [ENSMUST00000192512] [ENSMUST00000192631] [ENSMUST00000193839] [ENSMUST00000195590] [ENSMUST00000194038] [ENSMUST00000192503] [ENSMUST00000193389]
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 benign
Transcript: ENSMUST00000115659
AA Change: H21Q

PolyPhen 2 Score 0.161 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000111323
Gene: ENSMUSG00000103770
AA Change: H21Q

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: 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: 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
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: ENSMUST00000193984
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: 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: 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
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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.6%
Validation Efficiency 100% (65/65)
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
Abcb5 T A 12: 118,832,404 (GRCm39) E1190V probably damaging Het
Arhgef10 A G 8: 15,029,998 (GRCm39) T928A probably benign Het
Arhgef10l T A 4: 140,242,762 (GRCm39) I836F probably benign Het
Blm T A 7: 80,152,610 (GRCm39) T446S probably benign Het
Ccdc63 T A 5: 122,260,813 (GRCm39) Q237L probably damaging Het
Ccn5 A G 2: 163,670,904 (GRCm39) D137G probably damaging Het
Cep57l1 G T 10: 41,605,356 (GRCm39) R130S probably damaging Het
Clstn2 T G 9: 97,339,613 (GRCm39) E786A possibly damaging Het
Col16a1 C T 4: 129,962,545 (GRCm39) P540L probably damaging Het
Csf2 A G 11: 54,140,159 (GRCm39) F61L probably damaging Het
Ctr9 C T 7: 110,654,750 (GRCm39) R1094C unknown Het
Cyp3a41a A G 5: 145,650,350 (GRCm39) C98R probably damaging Het
Dthd1 T A 5: 62,984,508 (GRCm39) C404* probably null Het
Egfem1 A C 3: 29,740,880 (GRCm39) H518P probably benign Het
Elf3 T C 1: 135,182,015 (GRCm39) S369G probably benign Het
Eml6 C T 11: 29,788,577 (GRCm39) V503M probably damaging Het
Enthd1 T C 15: 80,444,240 (GRCm39) D105G probably damaging Het
Eral1 A G 11: 77,966,428 (GRCm39) L250P probably damaging Het
Gdf15 A T 8: 71,082,605 (GRCm39) M167K probably benign Het
Ggps1 T C 13: 14,228,284 (GRCm39) K300E probably benign Het
Gm8074 G A 9: 78,229,618 (GRCm39) noncoding transcript Het
Herc3 A G 6: 58,853,822 (GRCm39) I623V probably damaging Het
Mad1l1 A G 5: 140,118,571 (GRCm39) S457P probably damaging Het
Map1lc3a G T 2: 155,119,462 (GRCm39) V91F possibly damaging Het
Map4k3 A G 17: 80,913,394 (GRCm39) V617A probably benign Het
Mov10l1 T A 15: 88,879,235 (GRCm39) probably benign Het
Mroh2a A G 1: 88,186,386 (GRCm39) S64G probably benign Het
Ncor1 G T 11: 62,220,494 (GRCm39) probably null Het
Nfe2 C T 15: 103,159,364 (GRCm39) E36K possibly damaging Het
Oprm1 G A 10: 6,779,087 (GRCm39) V95I probably benign Het
Or4a78 T C 2: 89,498,006 (GRCm39) I75V probably benign Het
Or4c107 A G 2: 88,789,617 (GRCm39) K269R probably benign Het
Or52d3 T C 7: 104,229,575 (GRCm39) F241L probably benign Het
Or5d46 T C 2: 88,174,144 (GRCm39) probably null Het
Pcolce2 A T 9: 95,520,808 (GRCm39) I62F probably damaging Het
Pfpl T A 19: 12,407,053 (GRCm39) C435S probably damaging Het
Pkhd1l1 G A 15: 44,361,953 (GRCm39) C542Y probably damaging Het
Plekha5 T C 6: 140,529,597 (GRCm39) S75P probably damaging Het
Pphln1 C A 15: 93,362,987 (GRCm39) A202E probably damaging Het
Ppp1r1a A G 15: 103,440,881 (GRCm39) L92P probably damaging Het
Prokr2 T C 2: 132,223,414 (GRCm39) T43A probably benign Het
Rai14 T C 15: 10,592,298 (GRCm39) N199S probably benign Het
Rasgrp2 T C 19: 6,454,757 (GRCm39) L199P probably damaging Het
Rnf213 A C 11: 119,373,274 (GRCm39) M4939L possibly damaging Het
Slc23a2 C T 2: 131,902,603 (GRCm39) R533Q probably benign Het
Slc7a7 T C 14: 54,610,548 (GRCm39) probably null Het
Snrpd2 T A 7: 18,885,232 (GRCm39) V31E probably damaging Het
Spire1 G T 18: 67,662,101 (GRCm39) probably null Het
Srsf4 T C 4: 131,627,854 (GRCm39) probably benign Het
Tcf20 A G 15: 82,737,630 (GRCm39) S1274P probably damaging Het
Tcof1 C A 18: 60,965,975 (GRCm39) A376S possibly damaging Het
Thsd1 T A 8: 22,733,180 (GRCm39) Y76N possibly damaging Het
Timm44 A G 8: 4,310,561 (GRCm39) V397A probably benign Het
Tmc6 G A 11: 117,669,087 (GRCm39) T89I possibly damaging Het
Trbv31 C A 6: 41,534,639 (GRCm39) C107F probably damaging Het
Trim37 T A 11: 87,031,429 (GRCm39) probably null Het
Ttll5 T C 12: 86,059,573 (GRCm39) V1226A probably benign Het
Ube3b T C 5: 114,550,931 (GRCm39) V865A probably benign Het
Vmn2r86 A T 10: 130,282,966 (GRCm39) M550K probably damaging Het
Vps54 C A 11: 21,250,183 (GRCm39) T373N probably benign Het
Wdr64 T G 1: 175,633,422 (GRCm39) I891S probably benign Het
Zfhx4 C T 3: 5,463,919 (GRCm39) S1384L probably damaging Het
Zfp703 A G 8: 27,469,113 (GRCm39) E259G possibly damaging Het
Zfp933 T C 4: 147,910,969 (GRCm39) H209R probably damaging Het
Zfp980 A G 4: 145,429,170 (GRCm39) H633R probably damaging 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
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
R5487:Pcdha9 UTSW 18 37,132,703 (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
Posted On 2017-04-14