Incidental Mutation 'R6211:Pcdha12'
ID 503481
Institutional Source Beutler Lab
Gene Symbol Pcdha12
Ensembl Gene ENSMUSG00000103310
Gene Name protocadherin alpha 12
Synonyms Cnr5, Pcdha13, Crnr5
Accession Numbers
Essential gene? Probably non essential (E-score: 0.198) question?
Stock # R6211 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 37153283-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 37153374 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 31 (L31P)
Ref Sequence ENSEMBL: ENSMUSP00000047609 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047614] [ENSMUST00000070797] [ENSMUST00000115657] [ENSMUST00000115658] [ENSMUST00000115659] [ENSMUST00000193777] [ENSMUST00000192447] [ENSMUST00000193839] [ENSMUST00000192503] [ENSMUST00000115661] [ENSMUST00000192512] [ENSMUST00000192295] [ENSMUST00000193389] [ENSMUST00000192631] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000194751] [ENSMUST00000194544] [ENSMUST00000194038] [ENSMUST00000195590]
AlphaFold Q91Y18
Predicted Effect probably damaging
Transcript: ENSMUST00000047614
AA Change: L31P

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000047609
Gene: ENSMUSG00000103310
AA Change: L31P

DomainStartEndE-ValueType
CA 19 131 3.78e-2 SMART
CA 155 240 3.26e-24 SMART
CA 264 348 6.37e-27 SMART
CA 372 453 3.31e-25 SMART
CA 477 563 6.18e-25 SMART
CA 594 676 5.6e-14 SMART
low complexity region 679 696 N/A INTRINSIC
transmembrane domain 699 721 N/A INTRINSIC
Pfam:Cadherin_tail 799 933 5.3e-58 PFAM
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 noncoding transcript
Transcript: ENSMUST00000097612
Predicted Effect probably benign
Transcript: ENSMUST00000115657
SMART Domains Protein: ENSMUSP00000111321
Gene: ENSMUSG00000102206

DomainStartEndE-ValueType
CA 21 131 2.95e-2 SMART
CA 155 240 7.44e-19 SMART
CA 264 347 5.63e-28 SMART
CA 371 452 3.14e-26 SMART
CA 476 562 1.42e-24 SMART
CA 593 675 1.03e-12 SMART
transmembrane domain 697 719 N/A INTRINSIC
low complexity region 783 794 N/A INTRINSIC
low complexity region 918 942 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000115658
SMART Domains Protein: ENSMUSP00000111322
Gene: ENSMUSG00000007440

DomainStartEndE-ValueType
low complexity region 15 21 N/A INTRINSIC
CA 46 132 6.34e-2 SMART
CA 156 241 4.65e-20 SMART
CA 265 349 1.25e-25 SMART
CA 373 454 9.22e-24 SMART
CA 478 564 4.3e-24 SMART
CA 595 678 5.07e-12 SMART
low complexity region 706 721 N/A INTRINSIC
Pfam:Cadherin_tail 795 929 5.3e-58 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000115659
SMART Domains Protein: ENSMUSP00000111323
Gene: ENSMUSG00000103770

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: 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: ENSMUST00000193856
Predicted Effect probably benign
Transcript: ENSMUST00000192447
SMART Domains Protein: ENSMUSP00000142270
Gene: ENSMUSG00000102206

DomainStartEndE-ValueType
CA 21 131 1.5e-4 SMART
CA 155 240 3.6e-21 SMART
CA 264 347 2.8e-30 SMART
CA 371 452 1.5e-28 SMART
CA 476 562 6.8e-27 SMART
CA 593 675 4.9e-15 SMART
transmembrane domain 697 719 N/A INTRINSIC
low complexity region 783 794 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: 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: 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: 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: 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: 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: 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: 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: ENSMUST00000194544
SMART Domains Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

DomainStartEndE-ValueType
Blast:CA 18 66 5e-20 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000193984
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: 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 noncoding transcript
Transcript: ENSMUST00000194691
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.2%
  • 20x: 97.6%
Validation Efficiency 100% (54/54)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acin1 A T 14: 54,881,503 (GRCm39) W391R probably damaging Het
Arl6ip1 A T 7: 117,726,473 (GRCm39) S18R probably benign Het
Armc3 G A 2: 19,301,614 (GRCm39) probably null Het
Ccdc162 G T 10: 41,506,141 (GRCm39) S883* probably null Het
Cd300lg A G 11: 101,944,995 (GRCm39) M358V possibly damaging Het
Cdh23 A G 10: 60,246,600 (GRCm39) V949A possibly damaging Het
Cenpo C T 12: 4,266,733 (GRCm39) S126N probably benign Het
Chd3 A T 11: 69,243,503 (GRCm39) D1366E probably damaging Het
Chd4 A G 6: 125,078,248 (GRCm39) E169G possibly damaging Het
Clec1b A G 6: 129,378,440 (GRCm39) T24A possibly damaging Het
Clhc1 A G 11: 29,528,145 (GRCm39) I558V probably damaging Het
Col5a2 T A 1: 45,415,826 (GRCm39) R1440S probably damaging Het
Cops3 A G 11: 59,708,727 (GRCm39) probably benign Het
Cxcr4 A G 1: 128,517,187 (GRCm39) V158A probably damaging Het
Dnah7a A G 1: 53,458,795 (GRCm39) M3781T probably damaging Het
Dnai7 C T 6: 145,146,217 (GRCm39) R95Q probably damaging Het
Elovl5 C A 9: 77,888,784 (GRCm39) T217K probably damaging Het
Fbln7 G T 2: 128,737,260 (GRCm39) M358I probably damaging Het
Fbxl13 C T 5: 21,689,019 (GRCm39) R763Q possibly damaging Het
Gabrr3 C A 16: 59,268,471 (GRCm39) N361K probably benign Het
Garre1 A T 7: 33,938,429 (GRCm39) H1035Q possibly damaging Het
Gbp7 A G 3: 142,251,754 (GRCm39) M534V probably benign Het
Hcar2 G A 5: 124,003,017 (GRCm39) T162I probably benign Het
Hdc A T 2: 126,435,897 (GRCm39) L658Q probably damaging Het
Hivep3 A G 4: 119,955,602 (GRCm39) Y1306C probably damaging Het
Homer3 C T 8: 70,738,174 (GRCm39) R49C probably damaging Het
Hspa4 C T 11: 53,153,766 (GRCm39) E702K probably benign Het
Iqgap3 A G 3: 87,998,822 (GRCm39) N308D probably benign Het
Itga8 G A 2: 12,198,320 (GRCm39) T555M probably damaging Het
Lrfn5 G T 12: 61,886,256 (GRCm39) V15L probably benign Het
Lrrk1 T C 7: 65,952,458 (GRCm39) K493E possibly damaging Het
Lyzl6 A G 11: 103,525,889 (GRCm39) I77T probably damaging Het
Mavs G T 2: 131,082,311 (GRCm39) R65L probably damaging Het
Mdn1 T G 4: 32,696,269 (GRCm39) D1217E probably benign Het
Or12d13 A T 17: 37,647,599 (GRCm39) F175I possibly damaging Het
Or52h1 A T 7: 103,828,954 (GRCm39) Y220* probably null Het
Or9i1 A G 19: 13,839,938 (GRCm39) I260M probably benign Het
Otof C A 5: 30,529,244 (GRCm39) V1762L probably damaging Het
Pxk C A 14: 8,163,952 (GRCm38) P515T probably damaging Het
Qrich2 A T 11: 116,344,368 (GRCm39) D1759E probably benign Het
Rps6ka1 A T 4: 133,596,617 (GRCm39) F33Y probably damaging Het
Rxfp2 G A 5: 149,967,591 (GRCm39) probably null Het
Slc23a4 A T 6: 34,933,896 (GRCm39) I202N probably damaging Het
Slc24a5 A T 2: 124,930,171 (GRCm39) I491F probably benign Het
Slco1a1 T A 6: 141,854,775 (GRCm39) K625N probably benign Het
Snx31 A G 15: 36,547,030 (GRCm39) V51A probably damaging Het
Sox6 G T 7: 115,400,697 (GRCm39) H48Q probably damaging Het
Tas2r109 A T 6: 132,957,587 (GRCm39) Y114* probably null Het
Tbc1d2 C T 4: 46,629,912 (GRCm39) G252R probably benign Het
Timm13 A C 10: 80,736,314 (GRCm39) probably null Het
Tpsb2 G A 17: 25,586,737 (GRCm39) A250T possibly damaging Het
Trpm6 T C 19: 18,760,492 (GRCm39) I131T probably damaging Het
Vars2 A T 17: 35,976,554 (GRCm39) probably null Het
Vmn2r35 T A 7: 7,789,527 (GRCm39) I737F probably damaging Het
Wdr46 C A 17: 34,163,459 (GRCm39) T339K probably damaging Het
Other mutations in Pcdha12
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00817:Pcdha12 APN 18 37,154,986 (GRCm39) missense probably benign 0.00
R2884:Pcdha12 UTSW 18 37,153,757 (GRCm39) missense probably damaging 1.00
R3111:Pcdha12 UTSW 18 37,155,243 (GRCm39) missense probably damaging 0.98
R3619:Pcdha12 UTSW 18 37,153,757 (GRCm39) missense probably damaging 1.00
R4605:Pcdha12 UTSW 18 37,154,576 (GRCm39) missense probably damaging 1.00
R4629:Pcdha12 UTSW 18 37,154,926 (GRCm39) missense probably damaging 0.99
R4711:Pcdha12 UTSW 18 37,153,976 (GRCm39) missense probably benign 0.00
R4987:Pcdha12 UTSW 18 37,154,604 (GRCm39) missense probably damaging 1.00
R5489:Pcdha12 UTSW 18 37,155,260 (GRCm39) missense probably benign 0.01
R5568:Pcdha12 UTSW 18 37,153,443 (GRCm39) missense probably damaging 1.00
R5649:Pcdha12 UTSW 18 37,155,468 (GRCm39) missense probably benign 0.01
R6268:Pcdha12 UTSW 18 37,155,477 (GRCm39) missense possibly damaging 0.94
R6793:Pcdha12 UTSW 18 37,155,234 (GRCm39) missense probably damaging 1.00
R6999:Pcdha12 UTSW 18 37,153,329 (GRCm39) missense probably benign 0.00
R7065:Pcdha12 UTSW 18 37,154,679 (GRCm39) missense probably damaging 1.00
R7192:Pcdha12 UTSW 18 37,153,316 (GRCm39) missense probably benign 0.00
R7411:Pcdha12 UTSW 18 37,154,661 (GRCm39) missense probably damaging 1.00
R7486:Pcdha12 UTSW 18 37,154,610 (GRCm39) missense probably damaging 1.00
R7768:Pcdha12 UTSW 18 37,155,404 (GRCm39) missense probably damaging 1.00
R7857:Pcdha12 UTSW 18 37,155,468 (GRCm39) missense probably benign 0.01
R7940:Pcdha12 UTSW 18 37,153,409 (GRCm39) missense probably damaging 0.99
R8271:Pcdha12 UTSW 18 37,154,953 (GRCm39) missense probably damaging 0.99
R8306:Pcdha12 UTSW 18 37,155,638 (GRCm39) missense probably benign 0.06
R8405:Pcdha12 UTSW 18 37,154,250 (GRCm39) missense possibly damaging 0.94
R8475:Pcdha12 UTSW 18 37,154,136 (GRCm39) missense possibly damaging 0.95
R8715:Pcdha12 UTSW 18 37,153,523 (GRCm39) missense probably damaging 1.00
R8725:Pcdha12 UTSW 18 37,154,736 (GRCm39) missense probably benign 0.01
R9307:Pcdha12 UTSW 18 37,153,874 (GRCm39) missense probably damaging 1.00
R9407:Pcdha12 UTSW 18 37,153,614 (GRCm39) missense probably damaging 0.99
R9450:Pcdha12 UTSW 18 37,153,992 (GRCm39) missense probably damaging 1.00
R9460:Pcdha12 UTSW 18 37,153,574 (GRCm39) missense probably damaging 1.00
R9495:Pcdha12 UTSW 18 37,155,526 (GRCm39) missense probably damaging 1.00
R9514:Pcdha12 UTSW 18 37,155,526 (GRCm39) missense probably damaging 1.00
R9562:Pcdha12 UTSW 18 37,155,284 (GRCm39) missense probably damaging 1.00
R9577:Pcdha12 UTSW 18 37,155,126 (GRCm39) missense probably benign 0.17
R9596:Pcdha12 UTSW 18 37,154,302 (GRCm39) missense probably benign 0.32
R9673:Pcdha12 UTSW 18 37,155,234 (GRCm39) missense possibly damaging 0.72
Predicted Primers PCR Primer
(F):5'- TCTTCAAAACAGCGTTTGAGAGG -3'
(R):5'- GTGGATGCTACACTCCAAGC -3'

Sequencing Primer
(F):5'- AACAGCGTTTGAGAGGCAGTTTC -3'
(R):5'- GGTCGATCCGAGAATTCACAAAC -3'
Posted On 2018-02-27