Incidental Mutation 'R4090:Pcdha3'
ID 317584
Institutional Source Beutler Lab
Gene Symbol Pcdha3
Ensembl Gene ENSMUSG00000102312
Gene Name protocadherin alpha 3
Synonyms
MMRRC Submission 040983-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.111) question?
Stock # R4090 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 37079158-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 37081504 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glycine at position 749 (R749G)
Ref Sequence ENSEMBL: ENSMUSP00000141989 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000193839] [ENSMUST00000195590]
AlphaFold Q91Y16
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: 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
AA Change: R749G

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: R749G

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 noncoding transcript
Transcript: ENSMUST00000194001
Predicted Effect noncoding transcript
Transcript: ENSMUST00000194235
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
Meta Mutation Damage Score 0.3701 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.7%
Validation Efficiency 96% (53/55)
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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acss3 T G 10: 106,889,313 (GRCm39) Y169S probably damaging Het
Apc2 A G 10: 80,141,378 (GRCm39) K268E probably damaging Het
Arhgef2 G C 3: 88,551,185 (GRCm39) R765P probably benign Het
Bptf T C 11: 106,972,349 (GRCm39) K840E probably damaging Het
Carf A G 1: 60,175,506 (GRCm39) R245G possibly damaging Het
Cd36 A G 5: 17,990,718 (GRCm39) probably null Het
Cep250 G A 2: 155,834,552 (GRCm39) R2159K probably damaging Het
Cldn34c4 A T X: 126,629,011 (GRCm39) V153E probably damaging Het
Col4a4 T A 1: 82,501,643 (GRCm39) Y370F unknown Het
Cplane1 T A 15: 8,241,842 (GRCm39) probably null Het
Ddx4 A G 13: 112,750,295 (GRCm39) V386A probably benign Het
Exoc6 A G 19: 37,560,360 (GRCm39) T126A probably benign Het
Fam83f A T 15: 80,576,393 (GRCm39) N348I possibly damaging Het
Gja8 A G 3: 96,826,468 (GRCm39) V398A probably benign Het
Gkn3 C T 6: 87,360,507 (GRCm39) A163T probably damaging Het
Gm12789 A T 4: 101,845,526 (GRCm39) T72S possibly damaging Het
Gm1988 A G 7: 38,820,292 (GRCm39) noncoding transcript Het
Gm21370 A G 13: 120,488,489 (GRCm39) V20A probably benign Het
Hjurp G C 1: 88,204,937 (GRCm39) probably benign Het
Hsd17b13 T A 5: 104,113,720 (GRCm39) S245C probably benign Het
Htr1f T C 16: 64,746,324 (GRCm39) K323E probably benign Het
Igkc T C 6: 70,703,442 (GRCm39) probably benign Het
Ksr1 T C 11: 78,918,303 (GRCm39) E535G probably damaging Het
Mlxipl A T 5: 135,161,381 (GRCm39) E433D probably benign Het
Npc1 T C 18: 12,331,219 (GRCm39) probably null Het
Or10ak7 C T 4: 118,791,230 (GRCm39) E272K probably benign Het
Or1e29 A G 11: 73,667,667 (GRCm39) L162P probably damaging Het
Or6y1 A G 1: 174,276,500 (GRCm39) T104A probably benign Het
Or7g17 T C 9: 18,768,398 (GRCm39) I159T probably benign Het
Ppme1 A T 7: 99,997,044 (GRCm39) N122K possibly damaging Het
Rasal1 G A 5: 120,813,674 (GRCm39) V657M possibly damaging Het
Rbm47 A G 5: 66,180,080 (GRCm39) M409T probably benign Het
Rragd C T 4: 33,007,155 (GRCm39) T161M probably damaging Het
Slurp1 T C 15: 74,598,724 (GRCm39) H89R possibly damaging Het
Snap23 A G 2: 120,416,061 (GRCm39) I42V probably benign Het
Sypl2 A G 3: 108,124,992 (GRCm39) I123T possibly damaging Het
Taar8a T A 10: 23,953,062 (GRCm39) V222E probably damaging Het
Tmem171 A T 13: 98,829,096 (GRCm39) V18D probably damaging Het
Topors T C 4: 40,260,794 (GRCm39) D830G unknown Het
Traf3ip3 A G 1: 192,863,628 (GRCm39) V414A probably damaging Het
Tubg1 T A 11: 101,015,364 (GRCm39) M270K possibly damaging Het
Vmn1r188 T C 13: 22,272,772 (GRCm39) V242A probably benign Het
Vmn1r19 T A 6: 57,381,720 (GRCm39) I91N probably damaging Het
Vmn2r12 T A 5: 109,239,412 (GRCm39) M384L probably benign Het
Wdr26 T C 1: 181,030,679 (GRCm39) E205G probably damaging Het
Zfp281 T A 1: 136,553,859 (GRCm39) I279N probably damaging Het
Zfp398 T A 6: 47,843,159 (GRCm39) C272S probably damaging Het
Zfp975 A G 7: 42,312,298 (GRCm39) V105A probably benign Het
Other mutations in Pcdha3
AlleleSourceChrCoordTypePredicted EffectPPH Score
R2497:Pcdha3 UTSW 18 37,080,556 (GRCm39) missense probably benign
R3702:Pcdha3 UTSW 18 37,080,401 (GRCm39) missense probably benign 0.16
R4273:Pcdha3 UTSW 18 37,081,144 (GRCm39) missense probably damaging 1.00
R4486:Pcdha3 UTSW 18 37,080,404 (GRCm39) missense probably damaging 1.00
R4535:Pcdha3 UTSW 18 37,081,013 (GRCm39) missense probably damaging 1.00
R4582:Pcdha3 UTSW 18 37,080,485 (GRCm39) missense probably benign
R4712:Pcdha3 UTSW 18 37,079,560 (GRCm39) missense probably damaging 1.00
R5160:Pcdha3 UTSW 18 37,079,480 (GRCm39) missense probably damaging 1.00
R5302:Pcdha3 UTSW 18 37,081,208 (GRCm39) missense probably damaging 0.96
R5361:Pcdha3 UTSW 18 37,079,752 (GRCm39) missense possibly damaging 0.80
R5535:Pcdha3 UTSW 18 37,080,989 (GRCm39) missense probably benign 0.02
R5682:Pcdha3 UTSW 18 37,081,040 (GRCm39) missense probably damaging 0.99
R6656:Pcdha3 UTSW 18 37,080,875 (GRCm39) missense probably benign 0.24
R6878:Pcdha3 UTSW 18 37,080,416 (GRCm39) nonsense probably null
R7150:Pcdha3 UTSW 18 37,080,165 (GRCm39) missense probably benign 0.01
R7167:Pcdha3 UTSW 18 37,080,046 (GRCm39) missense probably damaging 1.00
R7299:Pcdha3 UTSW 18 37,079,977 (GRCm39) missense possibly damaging 0.56
R7301:Pcdha3 UTSW 18 37,079,977 (GRCm39) missense possibly damaging 0.56
R7448:Pcdha3 UTSW 18 37,079,266 (GRCm39) missense probably benign 0.00
R7467:Pcdha3 UTSW 18 37,080,584 (GRCm39) missense probably damaging 1.00
R7542:Pcdha3 UTSW 18 37,080,784 (GRCm39) missense possibly damaging 0.86
R7659:Pcdha3 UTSW 18 37,081,219 (GRCm39) missense probably benign 0.14
R7761:Pcdha3 UTSW 18 37,079,347 (GRCm39) missense probably damaging 1.00
R7782:Pcdha3 UTSW 18 37,081,193 (GRCm39) missense probably damaging 0.98
R7939:Pcdha3 UTSW 18 37,080,933 (GRCm39) missense probably damaging 1.00
R8217:Pcdha3 UTSW 18 37,079,974 (GRCm39) missense probably damaging 0.99
R8440:Pcdha3 UTSW 18 37,080,914 (GRCm39) missense probably damaging 1.00
R8938:Pcdha3 UTSW 18 37,080,154 (GRCm39) missense probably benign 0.43
R9375:Pcdha3 UTSW 18 37,079,353 (GRCm39) missense probably benign 0.29
R9378:Pcdha3 UTSW 18 37,080,284 (GRCm39) missense probably damaging 1.00
R9546:Pcdha3 UTSW 18 37,079,389 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TACCTGATCATCGCCATCTGTG -3'
(R):5'- TAGCGAGTGTAAAGTTCTCTACAG -3'

Sequencing Primer
(F):5'- GCCATCTGTGCCGTGTCTAG -3'
(R):5'- GAATAGTTCATTTTAACGCCATCTCC -3'
Posted On 2015-05-15