Incidental Mutation 'R9700:Pcdha5'
ID 729539
Institutional Source Beutler Lab
Gene Symbol Pcdha5
Ensembl Gene ENSMUSG00000103092
Gene Name protocadherin alpha 5
Synonyms Cnr6, Crnr6
MMRRC Submission
Accession Numbers
Essential gene? Probably non essential (E-score: 0.199) question?
Stock # R9700 (G1)
Quality Score 225.009
Status Not validated
Chromosome 18
Chromosomal Location 37093493-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 37094447 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 319 (N319D)
Ref Sequence ENSEMBL: ENSMUSP00000142293 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000193839] [ENSMUST00000195590]
AlphaFold Q91Y15
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
AA Change: N319D

PolyPhen 2 Score 0.121 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000142293
Gene: ENSMUSG00000103092
AA Change: N319D

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 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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts12 C T 15: 11,311,442 (GRCm39) S1233F probably benign Het
Aldh1a2 G T 9: 71,123,228 (GRCm39) E34* probably null Het
Arhgap39 T C 15: 76,611,617 (GRCm39) T856A probably damaging Het
Arpin A G 7: 79,578,015 (GRCm39) V138A probably damaging Het
Art3 T G 5: 92,562,120 (GRCm39) S373A unknown Het
AU018091 A T 7: 3,208,165 (GRCm39) I514N probably benign Het
BC034090 C T 1: 155,101,982 (GRCm39) R94H probably damaging Het
C2cd6 T G 1: 59,117,089 (GRCm39) M135L probably benign Het
Cdc42ep2 T C 19: 5,968,097 (GRCm39) M203V probably damaging Het
Cftr T C 6: 18,268,359 (GRCm39) Y803H probably damaging Het
Dcaf1 C T 9: 106,735,524 (GRCm39) T824I probably benign Het
Ddr1 A T 17: 35,993,288 (GRCm39) D906E probably damaging Het
Dhx8 G A 11: 101,624,015 (GRCm39) probably null Het
Dpysl5 C T 5: 30,904,417 (GRCm39) Q88* probably null Het
Ercc6l2 A G 13: 63,967,525 (GRCm39) T42A probably benign Het
Faf1 A G 4: 109,748,179 (GRCm39) K495E possibly damaging Het
Hr T C 14: 70,804,616 (GRCm39) V928A probably benign Het
Ints14 C T 9: 64,880,007 (GRCm39) R174* probably null Het
Jam3 T C 9: 27,010,183 (GRCm39) Y267C probably damaging Het
Lpin3 A T 2: 160,740,565 (GRCm39) N370I probably benign Het
Mad2l1 C A 6: 66,512,955 (GRCm39) N29K probably damaging Het
Myt1 A G 2: 181,452,177 (GRCm39) K838R probably damaging Het
Ninj2 T C 6: 120,174,873 (GRCm39) S15P probably benign Het
Or14a256 A T 7: 86,265,618 (GRCm39) N78K probably benign Het
Or1j14 T A 2: 36,418,313 (GRCm39) D296E probably benign Het
Or6b9 A G 7: 106,555,630 (GRCm39) V171A probably benign Het
Or9a2 T A 6: 41,749,076 (GRCm39) K52N probably benign Het
Osgin2 A G 4: 16,006,455 (GRCm39) S80P probably damaging Het
Phkb A G 8: 86,567,696 (GRCm39) K14E probably benign Het
Pip5k1b T C 19: 24,281,460 (GRCm39) Y518C probably benign Het
Polh A T 17: 46,510,414 (GRCm39) M14K probably damaging Het
Prtg A G 9: 72,762,313 (GRCm39) D480G probably benign Het
Ptprk T C 10: 28,456,495 (GRCm39) V1099A probably damaging Het
Pum2 T C 12: 8,779,044 (GRCm39) F539L probably damaging Het
Rac3 A T 11: 120,613,399 (GRCm39) T58S probably damaging Het
Setd1a A T 7: 127,385,752 (GRCm39) I820F possibly damaging Het
Six2 A G 17: 85,994,867 (GRCm39) F172L probably damaging Het
Spic T A 10: 88,515,757 (GRCm39) I22F probably benign Het
Tex30 T C 1: 44,130,374 (GRCm39) probably null Het
Tgfbi T C 13: 56,778,411 (GRCm39) I394T probably benign Het
Tnc A G 4: 63,933,186 (GRCm39) F693L probably damaging Het
Ubr4 T A 4: 139,119,388 (GRCm39) V189E probably damaging Het
Vegfa G A 17: 46,342,713 (GRCm39) P35L probably damaging Het
Zan T C 5: 137,454,836 (GRCm39) H1400R unknown Het
Zfp36l2 A G 17: 84,494,184 (GRCm39) I151T possibly damaging Het
Zfp809 T C 9: 22,154,470 (GRCm39) C396R unknown Het
Zfp93 G A 7: 23,974,894 (GRCm39) G293D probably damaging Het
Other mutations in Pcdha5
AlleleSourceChrCoordTypePredicted EffectPPH Score
tarantula UTSW 18 37,094,474 (GRCm39) missense probably benign 0.00
R2483:Pcdha5 UTSW 18 37,094,834 (GRCm39) missense probably damaging 1.00
R2483:Pcdha5 UTSW 18 37,094,542 (GRCm39) missense probably benign
R2888:Pcdha5 UTSW 18 37,094,940 (GRCm39) missense probably damaging 1.00
R2907:Pcdha5 UTSW 18 37,093,868 (GRCm39) missense possibly damaging 0.59
R2981:Pcdha5 UTSW 18 37,094,529 (GRCm39) missense probably damaging 1.00
R4468:Pcdha5 UTSW 18 37,095,233 (GRCm39) missense probably benign 0.08
R4724:Pcdha5 UTSW 18 37,094,549 (GRCm39) missense possibly damaging 0.61
R5280:Pcdha5 UTSW 18 37,094,755 (GRCm39) nonsense probably null
R5412:Pcdha5 UTSW 18 37,095,510 (GRCm39) missense probably benign 0.29
R5731:Pcdha5 UTSW 18 37,093,820 (GRCm39) missense probably damaging 1.00
R5783:Pcdha5 UTSW 18 37,095,534 (GRCm39) missense probably benign 0.00
R5865:Pcdha5 UTSW 18 37,094,474 (GRCm39) missense probably benign 0.00
R5984:Pcdha5 UTSW 18 37,094,733 (GRCm39) missense probably damaging 1.00
R6498:Pcdha5 UTSW 18 37,095,768 (GRCm39) missense possibly damaging 0.52
R6719:Pcdha5 UTSW 18 37,093,925 (GRCm39) missense probably damaging 1.00
R7084:Pcdha5 UTSW 18 37,094,615 (GRCm39) missense probably benign 0.08
R7113:Pcdha5 UTSW 18 37,094,757 (GRCm39) missense probably benign
R7432:Pcdha5 UTSW 18 37,095,379 (GRCm39) missense probably benign 0.07
R7507:Pcdha5 UTSW 18 37,093,909 (GRCm39) missense probably benign 0.01
R7515:Pcdha5 UTSW 18 37,095,171 (GRCm39) missense probably damaging 1.00
R7642:Pcdha5 UTSW 18 37,093,544 (GRCm39) missense probably benign 0.00
R7815:Pcdha5 UTSW 18 37,094,556 (GRCm39) missense possibly damaging 0.63
R8129:Pcdha5 UTSW 18 37,094,832 (GRCm39) missense probably damaging 1.00
R8132:Pcdha5 UTSW 18 37,093,694 (GRCm39) missense possibly damaging 0.83
R8139:Pcdha5 UTSW 18 37,095,791 (GRCm39) missense possibly damaging 0.69
R8469:Pcdha5 UTSW 18 37,094,798 (GRCm39) missense probably benign 0.02
R9533:Pcdha5 UTSW 18 37,093,986 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TAAACTCAATGCTTCAGATGCG -3'
(R):5'- ACCAGCTTGAAGGGGATGTG -3'

Sequencing Primer
(F):5'- CTCAATGCTTCAGATGCGGATGAG -3'
(R):5'- TGTCAAGGAGCAGGTCACC -3'
Posted On 2022-10-06