Incidental Mutation 'R5160:Pcdha3'
ID 396968
Institutional Source Beutler Lab
Gene Symbol Pcdha3
Ensembl Gene ENSMUSG00000102312
Gene Name protocadherin alpha 3
Synonyms
MMRRC Submission 042742-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.111) question?
Stock # R5160 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37079158-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 37079480 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 74 (V74A)
Ref Sequence ENSEMBL: ENSMUSP00000141989 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115662] [ENSMUST00000192503] [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: 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 damaging
Transcript: ENSMUST00000192503
AA Change: V74A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: V74A

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: 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: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.7%
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aftph G A 11: 20,662,197 (GRCm39) P681L probably benign Het
Akap9 A G 5: 4,080,007 (GRCm39) R1920G probably damaging Het
Ano9 G A 7: 140,684,278 (GRCm39) R495C probably damaging Het
Apoa5 A G 9: 46,181,794 (GRCm39) Y290C probably damaging Het
Apob T C 12: 8,062,126 (GRCm39) I3536T possibly damaging Het
Arhgap42 T G 9: 8,997,656 (GRCm39) K823T probably damaging Het
Bicc1 T C 10: 70,768,066 (GRCm39) Y850C probably damaging Het
Cdh2 A T 18: 16,762,644 (GRCm39) D433E probably damaging Het
Cfap100 A G 6: 90,390,692 (GRCm39) probably null Het
Col6a5 T C 9: 105,808,208 (GRCm39) N947D unknown Het
Col8a2 A G 4: 126,204,205 (GRCm39) K72E possibly damaging Het
Ddx18 A G 1: 121,493,608 (GRCm39) probably null Het
Dna2 T C 10: 62,782,933 (GRCm39) V21A probably benign Het
Dnaja3 T A 16: 4,502,152 (GRCm39) M52K probably benign Het
Fnip2 G A 3: 79,396,298 (GRCm39) T504I probably damaging Het
Il18 G A 9: 50,489,193 (GRCm39) probably null Het
Ina T A 19: 47,003,519 (GRCm39) I109N probably damaging Het
Katnb1 G T 8: 95,822,098 (GRCm39) V275L probably benign Het
Kdm6b C A 11: 69,291,594 (GRCm39) probably benign Het
Kifc2 T A 15: 76,547,177 (GRCm39) L251Q probably damaging Het
Kmt2d A G 15: 98,738,105 (GRCm39) probably benign Het
Lcor T A 19: 41,544,053 (GRCm39) V82E probably damaging Het
Limk2 A C 11: 3,300,772 (GRCm39) V190G probably damaging Het
Luc7l A G 17: 26,486,271 (GRCm39) D150G probably benign Het
Magi3 T A 3: 103,935,224 (GRCm39) H903L possibly damaging Het
Mdh1b C T 1: 63,764,804 (GRCm39) R33Q probably null Het
Myo9a T C 9: 59,779,085 (GRCm39) F1614L probably benign Het
Ngly1 A G 14: 16,281,751 (GRCm38) T210A probably damaging Het
Oas1h A G 5: 121,009,145 (GRCm39) Y285C probably damaging Het
Or1l4b T A 2: 37,036,815 (GRCm39) M197K probably benign Het
Or2h1 T C 17: 37,404,616 (GRCm39) D50G possibly damaging Het
Or2y12 T C 11: 49,426,516 (GRCm39) L168P probably damaging Het
Or4a79 T C 2: 89,551,763 (GRCm39) R231G probably damaging Het
Or5ac25 C T 16: 59,182,129 (GRCm39) G151R probably damaging Het
Or9s23 C T 1: 92,501,544 (GRCm39) T217I probably benign Het
Osbpl7 T C 11: 96,945,382 (GRCm39) S81P probably damaging Het
Pi4ka T C 16: 17,140,917 (GRCm39) D68G probably benign Het
Prkcz A T 4: 155,377,689 (GRCm39) V79D probably benign Het
Ptpn12 T A 5: 21,202,829 (GRCm39) I650F probably damaging Het
Rb1 A G 14: 73,501,895 (GRCm39) silent Het
Rnaseh2b T G 14: 62,590,980 (GRCm39) Y56* probably null Het
Ryr3 A T 2: 112,477,272 (GRCm39) C4495S probably damaging Het
Tk1 A G 11: 117,715,572 (GRCm39) I45T possibly damaging Het
Ttc23l G T 15: 10,551,636 (GRCm39) T30K possibly damaging Het
Upp1 T C 11: 9,085,193 (GRCm39) S227P possibly damaging Het
Vmn1r30 T A 6: 58,412,368 (GRCm39) N155Y probably benign Het
Wdr35 C T 12: 9,058,487 (GRCm39) A548V probably damaging Het
Zc3h3 A T 15: 75,681,512 (GRCm39) M523K probably benign Het
Zc3h4 T C 7: 16,168,573 (GRCm39) L894P unknown Het
Zfp790 C T 7: 29,529,192 (GRCm39) H626Y probably benign Het
Zfp873 C T 10: 81,896,876 (GRCm39) H536Y possibly damaging Het
Zmym4 A T 4: 126,763,977 (GRCm39) N1354K probably damaging Het
Zscan20 A G 4: 128,486,275 (GRCm39) S142P possibly damaging 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
R4090:Pcdha3 UTSW 18 37,081,504 (GRCm39) missense probably benign 0.04
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
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'- GAGAGCAACCAAACATTCGG -3'
(R):5'- CTGGAAATACTGGAGGGTTGTC -3'

Sequencing Primer
(F):5'- TTCTCAGAGAGAAGATCGGCATCTG -3'
(R):5'- AGGGTTGTCGTTAATGTCCCTCAC -3'
Posted On 2016-06-21