Incidental Mutation 'R5302:Pcdha3'
ID 404321
Institutional Source Beutler Lab
Gene Symbol Pcdha3
Ensembl Gene ENSMUSG00000102312
Gene Name protocadherin alpha 3
Synonyms
MMRRC Submission 042885-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.111) question?
Stock # R5302 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37079158-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 37081208 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 650 (E650G)
Ref Sequence ENSEMBL: ENSMUSP00000141989 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000195590] [ENSMUST00000193839]
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 damaging
Transcript: ENSMUST00000192503
AA Change: E650G

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: E650G

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: 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
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.6%
  • 20x: 96.0%
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 A G 1: 71,323,111 (GRCm39) V1657A possibly damaging Het
Abca8b C A 11: 109,868,639 (GRCm39) G175V probably damaging Het
Acot5 A G 12: 84,120,215 (GRCm39) Y190C probably damaging Het
Ascc3 T A 10: 50,583,873 (GRCm39) Y941N probably benign Het
BC035947 A T 1: 78,488,599 (GRCm39) M1K probably null Het
C2cd5 A G 6: 143,019,482 (GRCm39) C278R probably benign Het
Cd200r1 G T 16: 44,613,172 (GRCm39) L259F possibly damaging Het
Clcn4 A G 7: 7,297,050 (GRCm39) V136A possibly damaging Het
Cntnap5a T C 1: 116,085,300 (GRCm39) S413P probably benign Het
Corin T A 5: 72,473,441 (GRCm39) E748D probably benign Het
Crtc2 G T 3: 90,168,325 (GRCm39) G356V probably damaging Het
D1Pas1 T A 1: 186,701,642 (GRCm39) Y524N probably damaging Het
Dlgap4 T C 2: 156,602,818 (GRCm39) S147P probably damaging Het
Eif1ad16 T A 12: 87,985,316 (GRCm39) I76F probably damaging Het
Enpp1 A T 10: 24,527,288 (GRCm39) I633N probably benign Het
Gm3095 A G 14: 15,170,367 (GRCm39) D72G probably null Het
Gm5449 C T 13: 53,679,787 (GRCm39) noncoding transcript Het
Gpx7 T C 4: 108,258,111 (GRCm39) T161A probably benign Het
Grip1 T C 10: 119,855,982 (GRCm39) L236P probably damaging Het
H2-Q2 G T 17: 35,563,885 (GRCm39) R255S probably damaging Het
Il17rc G T 6: 113,459,997 (GRCm39) A648S possibly damaging Het
Klhl12 A G 1: 134,417,189 (GRCm39) E540G possibly damaging Het
Mcm10 T C 2: 5,012,181 (GRCm39) I135V probably benign Het
Mrps26 C A 2: 130,406,087 (GRCm39) T100K probably benign Het
Nid2 A G 14: 19,829,769 (GRCm39) T687A probably benign Het
Npas3 A T 12: 54,115,619 (GRCm39) D829V probably damaging Het
Ocln T C 13: 100,642,807 (GRCm39) D176G probably damaging Het
Or11h6 A G 14: 50,879,776 (GRCm39) probably null Het
Pax3 A C 1: 78,098,249 (GRCm39) M380R possibly damaging Het
Pdcd11 C A 19: 47,096,083 (GRCm39) H668N probably damaging Het
Polr3b T C 10: 84,535,264 (GRCm39) Y858H possibly damaging Het
Pus10 T C 11: 23,617,416 (GRCm39) probably null Het
Raver1 T C 9: 20,986,677 (GRCm39) D739G probably damaging Het
Skic3 G A 13: 76,295,886 (GRCm39) E1050K possibly damaging Het
Slc26a11 T C 11: 119,254,276 (GRCm39) L198P probably damaging Het
Slc44a3 A G 3: 121,303,962 (GRCm39) V258A probably damaging Het
Socs7 T A 11: 97,280,025 (GRCm39) I524N probably damaging Het
Steap4 T A 5: 8,025,547 (GRCm39) L36* probably null Het
Svep1 G C 4: 58,096,183 (GRCm39) T1479S possibly damaging Het
Ttn C A 2: 76,547,619 (GRCm39) V32184F probably damaging Het
Vmn1r22 T C 6: 57,877,960 (GRCm39) N6D 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
R5160:Pcdha3 UTSW 18 37,079,480 (GRCm39) missense probably damaging 1.00
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'- TTTGTGCTGGATGAGAACGAC -3'
(R):5'- TGAGCACCAACAGGCTAGAC -3'

Sequencing Primer
(F):5'- TGAGCGAACTGGTGTCAC -3'
(R):5'- CAGGCTAGACACGGCACAG -3'
Posted On 2016-07-22