Incidental Mutation 'R5165:Pcdhga3'
ID 395678
Institutional Source Beutler Lab
Gene Symbol Pcdhga3
Ensembl Gene ENSMUSG00000104346
Gene Name protocadherin gamma subfamily A, 3
Synonyms
MMRRC Submission 042746-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.121) question?
Stock # R5165 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 37807388-37974926 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 37808723 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 392 (E392G)
Ref Sequence ENSEMBL: ENSMUSP00000073150 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000192931] [ENSMUST00000193869] [ENSMUST00000194190] [ENSMUST00000194544]
AlphaFold Q91XY5
Predicted Effect possibly damaging
Transcript: ENSMUST00000073447
AA Change: E392G

PolyPhen 2 Score 0.595 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346
AA Change: E392G

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
CA 42 128 2.15e-2 SMART
CA 152 237 4.8e-13 SMART
CA 261 342 9.36e-25 SMART
CA 366 447 6.62e-25 SMART
CA 471 557 6.72e-26 SMART
CA 588 666 2.15e-15 SMART
Pfam:Cadherin_C_2 685 768 4.8e-24 PFAM
Pfam:Cadherin_tail 805 928 8.1e-38 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: ENSMUST00000192931
SMART Domains Protein: ENSMUSP00000141348
Gene: ENSMUSG00000103037

DomainStartEndE-ValueType
CA 36 119 8e-3 SMART
CA 143 228 1.34e-20 SMART
CA 252 333 1.52e-24 SMART
CA 357 438 9.22e-24 SMART
CA 462 548 1.24e-24 SMART
CA 579 660 1.3e-9 SMART
transmembrane domain 679 701 N/A INTRINSIC
low complexity region 899 918 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193869
SMART Domains Protein: ENSMUSP00000141482
Gene: ENSMUSG00000103332

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
CA 45 131 1.64e-2 SMART
CA 155 240 6.42e-23 SMART
CA 264 345 1.76e-20 SMART
CA 369 450 2.27e-23 SMART
CA 474 560 1.5e-23 SMART
CA 591 669 1.17e-16 SMART
transmembrane domain 692 714 N/A INTRINSIC
low complexity region 912 931 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193984
Predicted Effect probably benign
Transcript: ENSMUST00000194190
SMART Domains Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
CA 31 131 3.16e-2 SMART
CA 155 240 5.39e-16 SMART
CA 264 345 6.72e-26 SMART
CA 369 450 1.32e-24 SMART
CA 474 560 4.17e-22 SMART
CA 591 669 4.48e-13 SMART
transmembrane domain 692 714 N/A INTRINSIC
low complexity region 912 931 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000195624
Predicted Effect probably benign
Transcript: ENSMUST00000194544
SMART Domains Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

DomainStartEndE-ValueType
Blast:CA 18 66 5e-20 BLAST
Meta Mutation Damage Score 0.3222 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.3%
Validation Efficiency 98% (58/59)
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 gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actg2 T A 6: 83,503,814 (GRCm39) I77F probably benign Het
Actl6a G A 3: 32,774,357 (GRCm39) V285I probably benign Het
Adam9 A T 8: 25,457,190 (GRCm39) I646N possibly damaging Het
Ahnak T C 19: 8,993,029 (GRCm39) I4771T possibly damaging Het
Alas1 T C 9: 106,118,454 (GRCm39) T223A probably damaging Het
Apc2 A G 10: 80,151,684 (GRCm39) E2246G probably damaging Het
Atp1a1 A G 3: 101,489,105 (GRCm39) I795T probably benign Het
Ccn3 A G 15: 54,612,585 (GRCm39) D198G probably damaging Het
Cdhr4 T C 9: 107,874,829 (GRCm39) L633P probably damaging Het
Cep350 A G 1: 155,804,114 (GRCm39) S990P probably damaging Het
Cplx2 A G 13: 54,526,789 (GRCm39) I66V possibly damaging Het
Cx3cl1 T C 8: 95,506,504 (GRCm39) S170P probably benign Het
Cyth1 T C 11: 118,059,908 (GRCm39) N353S possibly damaging Het
Dapp1 T C 3: 137,644,976 (GRCm39) probably null Het
Dmwd G A 7: 18,811,960 (GRCm39) probably benign Het
Dsg1c A G 18: 20,410,080 (GRCm39) H516R probably damaging Het
Efemp2 T C 19: 5,525,439 (GRCm39) C39R probably damaging Het
Fnbp4 C G 2: 90,608,001 (GRCm39) Q908E possibly damaging Het
Foxred2 A G 15: 77,840,212 (GRCm39) V26A probably damaging Het
Gkap1 A G 13: 58,411,010 (GRCm39) probably null Het
Gstcd A C 3: 132,790,440 (GRCm39) V109G probably damaging Het
Hoxc9 T A 15: 102,892,432 (GRCm39) M215K probably damaging Het
Igkv4-80 A C 6: 68,993,649 (GRCm39) S81A probably benign Het
Kcnj9 A T 1: 172,150,724 (GRCm39) D296E probably benign Het
Kctd18 T C 1: 57,998,395 (GRCm39) Y68C probably damaging Het
Kif21a A T 15: 90,840,579 (GRCm39) M1179K probably benign Het
Lrfn5 T C 12: 61,886,410 (GRCm39) I66T possibly damaging Het
Lrp12 A G 15: 39,735,857 (GRCm39) S692P probably benign Het
Lrrc10 A T 10: 116,881,965 (GRCm39) N213I probably benign Het
Nceh1 G A 3: 27,295,677 (GRCm39) V313I probably benign Het
Nkx6-3 T A 8: 23,643,759 (GRCm39) H53Q probably damaging Het
Ntmt2 A G 1: 163,550,092 (GRCm39) I53T probably benign Het
Or14j7 A G 17: 38,235,252 (GRCm39) D265G probably benign Het
Or2y16 A G 11: 49,335,203 (GRCm39) H175R probably damaging Het
Or4f53 T A 2: 111,087,568 (GRCm39) V36E possibly damaging Het
Or5b97 A T 19: 12,878,564 (GRCm39) N193K probably benign Het
Oxct1 A T 15: 4,083,251 (GRCm39) T157S possibly damaging Het
Polr1a T G 6: 71,944,909 (GRCm39) Y1322D probably damaging Het
Prkdc T A 16: 15,496,136 (GRCm39) S776T probably damaging Het
Ralgapb A G 2: 158,307,832 (GRCm39) I1047V possibly damaging Het
Sertad4 A T 1: 192,529,130 (GRCm39) S229T possibly damaging Het
Shank2 T A 7: 143,963,373 (GRCm39) V327D possibly damaging Het
Skint6 A T 4: 112,722,865 (GRCm39) V904E possibly damaging Het
Slfn8 A T 11: 82,907,953 (GRCm39) Y197N probably damaging Het
Smo T A 6: 29,736,077 (GRCm39) L23Q unknown Het
Snx29 T A 16: 11,238,639 (GRCm39) M23K probably damaging Het
Synrg T C 11: 83,881,761 (GRCm39) S366P probably benign Het
Tomm40 A G 7: 19,447,592 (GRCm39) probably null Het
Tpcn1 T C 5: 120,696,010 (GRCm39) E81G probably damaging Het
Trappc1 A G 11: 69,215,060 (GRCm39) Q26R probably benign Het
Ttn T A 2: 76,606,900 (GRCm39) probably null Het
Usp25 T A 16: 76,873,293 (GRCm39) D450E possibly damaging Het
Zmynd19 T A 2: 24,848,201 (GRCm39) Y132* probably null Het
Other mutations in Pcdhga3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00934:Pcdhga3 APN 18 37,808,486 (GRCm39) missense possibly damaging 0.92
R2863:Pcdhga3 UTSW 18 37,807,643 (GRCm39) missense probably damaging 0.99
R4446:Pcdhga3 UTSW 18 37,808,938 (GRCm39) missense probably damaging 0.99
R4581:Pcdhga3 UTSW 18 37,809,934 (GRCm39) missense probably benign 0.00
R4747:Pcdhga3 UTSW 18 37,809,799 (GRCm39) missense probably benign 0.29
R4964:Pcdhga3 UTSW 18 37,809,154 (GRCm39) missense probably benign 0.05
R5210:Pcdhga3 UTSW 18 37,808,963 (GRCm39) missense probably benign 0.03
R5370:Pcdhga3 UTSW 18 37,808,343 (GRCm39) missense probably damaging 1.00
R5402:Pcdhga3 UTSW 18 37,808,747 (GRCm39) missense probably benign 0.33
R5610:Pcdhga3 UTSW 18 37,808,276 (GRCm39) missense possibly damaging 0.83
R5782:Pcdhga3 UTSW 18 37,809,353 (GRCm39) missense possibly damaging 0.91
R5889:Pcdhga3 UTSW 18 37,809,662 (GRCm39) missense probably damaging 1.00
R6058:Pcdhga3 UTSW 18 37,808,141 (GRCm39) missense probably damaging 1.00
R6127:Pcdhga3 UTSW 18 37,807,757 (GRCm39) missense probably damaging 0.98
R6307:Pcdhga3 UTSW 18 37,809,674 (GRCm39) unclassified probably benign
R6893:Pcdhga3 UTSW 18 37,809,598 (GRCm39) missense probably benign 0.37
R7013:Pcdhga3 UTSW 18 37,808,674 (GRCm39) missense probably damaging 1.00
R7174:Pcdhga3 UTSW 18 37,808,980 (GRCm39) missense probably benign 0.02
R7448:Pcdhga3 UTSW 18 37,808,917 (GRCm39) missense possibly damaging 0.94
R7492:Pcdhga3 UTSW 18 37,809,178 (GRCm39) missense probably benign 0.01
R7509:Pcdhga3 UTSW 18 37,808,910 (GRCm39) nonsense probably null
R7914:Pcdhga3 UTSW 18 37,808,013 (GRCm39) missense probably benign 0.00
R7984:Pcdhga3 UTSW 18 37,809,549 (GRCm39) missense probably benign 0.00
R8782:Pcdhga3 UTSW 18 37,807,865 (GRCm39) missense probably damaging 1.00
R9157:Pcdhga3 UTSW 18 37,809,229 (GRCm39) missense probably benign 0.40
R9169:Pcdhga3 UTSW 18 37,809,088 (GRCm39) missense probably damaging 1.00
R9436:Pcdhga3 UTSW 18 37,808,144 (GRCm39) missense probably damaging 1.00
R9437:Pcdhga3 UTSW 18 37,808,144 (GRCm39) missense probably damaging 1.00
R9588:Pcdhga3 UTSW 18 37,808,564 (GRCm39) missense probably damaging 1.00
R9767:Pcdhga3 UTSW 18 37,808,096 (GRCm39) missense probably benign 0.00
R9778:Pcdhga3 UTSW 18 37,807,786 (GRCm39) missense probably benign 0.42
Z1177:Pcdhga3 UTSW 18 37,809,674 (GRCm39) unclassified probably benign
Predicted Primers PCR Primer
(F):5'- TGGATGTGAATGACAACGCC -3'
(R):5'- TGGGTCCTGTGCTGTAACAG -3'

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