Incidental Mutation 'R4493:Pcdha4'
ID 330850
Institutional Source Beutler Lab
Gene Symbol Pcdha4
Ensembl Gene ENSMUSG00000104252
Gene Name protocadherin alpha 4
Synonyms Crnr1, Cnr1
MMRRC Submission 041748-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.161) question?
Stock # R4493 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 37085742-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 37087644 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 609 (Y609F)
Ref Sequence ENSEMBL: ENSMUSP00000141408 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000195590] [ENSMUST00000193839]
AlphaFold no structure available at present
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 possibly damaging
Transcript: ENSMUST00000115661
AA Change: Y609F

PolyPhen 2 Score 0.803 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: Y609F

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
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 possibly damaging
Transcript: ENSMUST00000192512
AA Change: Y609F

PolyPhen 2 Score 0.803 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: Y609F

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: ENSMUST00000194235
Predicted Effect noncoding transcript
Transcript: ENSMUST00000194001
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: 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
Meta Mutation Damage Score 0.4197 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.7%
Validation Efficiency 94% (45/48)
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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Cacna1b T C 2: 24,542,950 (GRCm39) T1301A probably damaging Het
Ccdc141 A G 2: 76,962,641 (GRCm39) V101A probably damaging Het
Ccdc146 T C 5: 21,508,191 (GRCm39) E619G possibly damaging Het
Cfap91 T C 16: 38,162,130 (GRCm39) T4A probably benign Het
Cmya5 T C 13: 93,230,573 (GRCm39) E1505G probably benign Het
Cngb3 C A 4: 19,367,778 (GRCm39) P229Q probably damaging Het
Ctnna2 A G 6: 76,958,831 (GRCm39) V461A probably damaging Het
D430041D05Rik T C 2: 104,086,684 (GRCm39) D764G probably benign Het
Dgki T C 6: 36,951,796 (GRCm39) probably benign Het
Dhx36 A T 3: 62,395,925 (GRCm39) probably benign Het
Gcn1 T C 5: 115,732,203 (GRCm39) I1006T probably benign Het
Glt8d2 T A 10: 82,500,547 (GRCm39) M20L possibly damaging Het
Greb1 C A 12: 16,748,611 (GRCm39) G1122V probably benign Het
Hmcn1 A T 1: 150,577,650 (GRCm39) I2037N probably damaging Het
Hspa4l A G 3: 40,722,434 (GRCm39) I340V possibly damaging Het
Itpr3 A G 17: 27,323,586 (GRCm39) K1204E probably damaging Het
Kcnh8 GAGACCAACGAGCAGCTGATGCTTCAGA GAGA 17: 53,032,934 (GRCm39) 74 probably benign Het
Lyst G A 13: 13,809,968 (GRCm39) R546H probably damaging Het
Mcph1 T A 8: 18,681,752 (GRCm39) C296* probably null Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Naga A G 15: 82,216,715 (GRCm39) F259S probably damaging Het
Nes A G 3: 87,884,120 (GRCm39) E793G probably damaging Het
Nfkb2 A G 19: 46,296,878 (GRCm39) D316G probably damaging Het
Pgam1 C T 19: 41,904,215 (GRCm39) A104V possibly damaging Het
Piezo2 T C 18: 63,247,134 (GRCm39) I525V probably damaging Het
Pold1 A G 7: 44,187,132 (GRCm39) V683A probably damaging Het
Poteg T C 8: 27,970,125 (GRCm39) V316A possibly damaging Het
Ppih A T 4: 119,168,042 (GRCm39) N156K probably damaging Het
Prep T C 10: 44,996,915 (GRCm39) F398L probably benign Het
Prlhr A T 19: 60,455,519 (GRCm39) M349K probably benign Het
Rtp4 A T 16: 23,428,827 (GRCm39) H30L probably benign Het
Stkld1 A G 2: 26,836,638 (GRCm39) N268S probably benign Het
Syt6 A G 3: 103,492,946 (GRCm39) E66G probably damaging Het
Tas2r129 A G 6: 132,928,317 (GRCm39) I85V probably benign Het
Tma16 C T 8: 66,936,823 (GRCm39) probably null Het
Tprn T C 2: 25,158,904 (GRCm39) S643P probably damaging Het
Trrap T C 5: 144,767,858 (GRCm39) V2605A probably benign Het
Vmn1r230 T A 17: 21,066,863 (GRCm39) N17K probably benign Het
Xkrx T C X: 133,051,745 (GRCm39) N302S possibly damaging Het
Zfp946 T A 17: 22,670,067 (GRCm39) probably null Het
Other mutations in Pcdha4
AlleleSourceChrCoordTypePredicted EffectPPH Score
R2570:Pcdha4 UTSW 18 37,086,665 (GRCm39) missense probably benign 0.00
R3114:Pcdha4 UTSW 18 37,086,603 (GRCm39) missense probably benign 0.02
R3115:Pcdha4 UTSW 18 37,086,603 (GRCm39) missense probably benign 0.02
R4154:Pcdha4 UTSW 18 37,086,639 (GRCm39) splice site probably null
R4381:Pcdha4 UTSW 18 37,085,928 (GRCm39) missense probably damaging 1.00
R4389:Pcdha4 UTSW 18 37,087,842 (GRCm39) missense probably benign
R4801:Pcdha4 UTSW 18 37,087,008 (GRCm39) nonsense probably null
R4802:Pcdha4 UTSW 18 37,087,008 (GRCm39) nonsense probably null
R4827:Pcdha4 UTSW 18 37,086,251 (GRCm39) missense probably damaging 1.00
R4928:Pcdha4 UTSW 18 37,087,869 (GRCm39) missense probably benign 0.01
R5001:Pcdha4 UTSW 18 37,088,001 (GRCm39) missense probably benign
R5330:Pcdha4 UTSW 18 37,087,755 (GRCm39) missense probably benign 0.01
R5331:Pcdha4 UTSW 18 37,087,755 (GRCm39) missense probably benign 0.01
R5540:Pcdha4 UTSW 18 37,087,890 (GRCm39) missense probably benign 0.01
R5587:Pcdha4 UTSW 18 37,087,875 (GRCm39) missense probably benign
R5931:Pcdha4 UTSW 18 37,087,808 (GRCm39) missense probably damaging 1.00
R6249:Pcdha4 UTSW 18 37,086,729 (GRCm39) missense probably damaging 0.99
R6427:Pcdha4 UTSW 18 37,086,786 (GRCm39) missense probably benign 0.00
R6612:Pcdha4 UTSW 18 37,088,031 (GRCm39) missense probably benign 0.00
R6616:Pcdha4 UTSW 18 37,086,953 (GRCm39) missense probably benign
R7030:Pcdha4 UTSW 18 37,087,080 (GRCm39) missense probably damaging 1.00
R7198:Pcdha4 UTSW 18 37,086,613 (GRCm39) missense probably damaging 0.99
R7411:Pcdha4 UTSW 18 37,086,111 (GRCm39) missense probably benign 0.01
R7491:Pcdha4 UTSW 18 37,087,689 (GRCm39) missense probably damaging 1.00
R7513:Pcdha4 UTSW 18 37,086,392 (GRCm39) missense probably damaging 1.00
R7544:Pcdha4 UTSW 18 37,086,776 (GRCm39) missense probably benign 0.05
R7735:Pcdha4 UTSW 18 37,085,961 (GRCm39) missense probably damaging 1.00
R7753:Pcdha4 UTSW 18 37,086,354 (GRCm39) missense possibly damaging 0.49
R8104:Pcdha4 UTSW 18 37,087,106 (GRCm39) missense probably damaging 1.00
R8239:Pcdha4 UTSW 18 37,086,128 (GRCm39) missense probably damaging 1.00
R8767:Pcdha4 UTSW 18 37,086,905 (GRCm39) missense possibly damaging 0.73
R8802:Pcdha4 UTSW 18 37,087,211 (GRCm39) missense possibly damaging 0.91
R8869:Pcdha4 UTSW 18 37,086,011 (GRCm39) nonsense probably null
R9102:Pcdha4 UTSW 18 37,087,630 (GRCm39) missense probably damaging 1.00
R9365:Pcdha4 UTSW 18 37,087,112 (GRCm39) missense possibly damaging 0.92
R9593:Pcdha4 UTSW 18 37,086,740 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GCAATGTGACTCTGCAGGTG -3'
(R):5'- TACTCGCGATGGAGCCTTTG -3'

Sequencing Primer
(F):5'- GTTTGTGCTGGACGAGAATGACAAC -3'
(R):5'- CGATGGAGCCTTTGGTACC -3'
Posted On 2015-07-21