Incidental Mutation 'R5889:Pcdhga3'
ID 456249
Institutional Source Beutler Lab
Gene Symbol Pcdhga3
Ensembl Gene ENSMUSG00000104346
Gene Name protocadherin gamma subfamily A, 3
Synonyms
MMRRC Submission 044090-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.121) question?
Stock # R5889 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 37807388-37974926 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 37809662 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 705 (V705D)
Ref Sequence ENSEMBL: ENSMUSP00000073150 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000192931] [ENSMUST00000193869] [ENSMUST00000194190] [ENSMUST00000194544]
AlphaFold Q91XY5
Predicted Effect probably damaging
Transcript: ENSMUST00000073447
AA Change: V705D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346
AA Change: V705D

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 0.5696 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.6%
  • 20x: 92.3%
Validation Efficiency 100% (63/63)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930568D16Rik T C 2: 35,244,461 (GRCm39) E297G probably damaging Het
Astn1 C T 1: 158,427,950 (GRCm39) P707L possibly damaging Het
Cep290 T C 10: 100,334,936 (GRCm39) S319P possibly damaging Het
Chrna4 A C 2: 180,670,451 (GRCm39) L435W probably damaging Het
Cilp C A 9: 65,187,625 (GRCm39) A1240D possibly damaging Het
Col17a1 A G 19: 47,637,511 (GRCm39) F1249S possibly damaging Het
Creb3l3 T C 10: 80,928,367 (GRCm39) probably benign Het
Cyp4f40 C A 17: 32,894,731 (GRCm39) T432N probably benign Het
Dsg1c T G 18: 20,416,658 (GRCm39) I853R possibly damaging Het
Ebna1bp2 T A 4: 118,478,620 (GRCm39) D34E probably damaging Het
Edc4 C T 8: 106,614,654 (GRCm39) T112I possibly damaging Het
Enpep T A 3: 129,106,227 (GRCm39) Y333F probably damaging Het
Exoc6 A G 19: 37,570,693 (GRCm39) H291R probably damaging Het
Fbln5 G T 12: 101,731,485 (GRCm39) N236K probably damaging Het
Fndc8 A T 11: 82,789,555 (GRCm39) T238S probably damaging Het
Frem3 T C 8: 81,340,917 (GRCm39) V1070A probably damaging Het
Gabra4 A T 5: 71,729,234 (GRCm39) N515K possibly damaging Het
Gemin5 A G 11: 58,013,181 (GRCm39) V1422A possibly damaging Het
Gm10118 A G 10: 63,762,890 (GRCm39) probably benign Het
Grm5 A G 7: 87,252,281 (GRCm39) D177G probably damaging Het
Gtf2h4 G A 17: 35,981,792 (GRCm39) P147L possibly damaging Het
Hgsnat T C 8: 26,453,395 (GRCm39) D265G probably damaging Het
Hsd17b4 T A 18: 50,310,276 (GRCm39) L513Q probably damaging Het
Hsd17b7 A T 1: 169,783,487 (GRCm39) M307K probably benign Het
Hspa5 T C 2: 34,664,629 (GRCm39) V361A probably damaging Het
Iqgap2 A G 13: 95,768,550 (GRCm39) V1450A probably benign Het
Itpr3 A G 17: 27,334,039 (GRCm39) E2037G probably damaging Het
Itprid2 T A 2: 79,488,072 (GRCm39) D718E probably damaging Het
Lama5 T C 2: 179,835,467 (GRCm39) probably benign Het
Manba G T 3: 135,230,359 (GRCm39) G311* probably null Het
Mettl24 T A 10: 40,622,486 (GRCm39) V236E probably benign Het
Myh3 A G 11: 66,977,201 (GRCm39) D310G probably damaging Het
Ncoa4 A T 14: 31,888,616 (GRCm39) probably benign Het
Nop56 G T 2: 130,117,902 (GRCm39) R126L probably damaging Het
Nos3 C A 5: 24,573,775 (GRCm39) probably benign Het
Or13c7b T C 4: 43,820,492 (GRCm39) M290V possibly damaging Het
Prom2 C T 2: 127,371,331 (GRCm39) A776T possibly damaging Het
Prss48 A G 3: 85,905,492 (GRCm39) I127T probably damaging Het
Rtca T C 3: 116,293,232 (GRCm39) Y193C possibly damaging Het
Samd9l T C 6: 3,376,460 (GRCm39) Y267C probably damaging Het
Scube3 A G 17: 28,379,887 (GRCm39) R272G possibly damaging Het
Sprr1a G T 3: 92,391,951 (GRCm39) H17N probably benign Het
Stard3 G C 11: 98,266,361 (GRCm39) Q120H probably benign Het
Supt6 A G 11: 78,103,574 (GRCm39) I1377T probably damaging Het
Svop A T 5: 114,203,692 (GRCm39) S30T probably benign Het
Syne2 T A 12: 76,119,026 (GRCm39) L5882* probably null Het
Tanc2 G T 11: 105,812,633 (GRCm39) R1359L probably benign Het
Tmc7 A C 7: 118,165,549 (GRCm39) L55R probably benign Het
Trappc11 G A 8: 47,972,613 (GRCm39) A320V probably benign Het
Ttll8 G C 15: 88,818,142 (GRCm39) P178A probably damaging Het
Ttn T C 2: 76,560,993 (GRCm39) E20809G probably damaging Het
Tubb2a A T 13: 34,259,451 (GRCm39) V113E possibly damaging Het
Ube2d1 A T 10: 71,095,699 (GRCm39) probably benign Het
Usp48 T C 4: 137,343,723 (GRCm39) V452A probably benign Het
Vldlr T A 19: 27,217,064 (GRCm39) I39N probably damaging Het
Wbp1l C T 19: 46,642,619 (GRCm39) R191* probably null Het
Zyg11b C T 4: 108,094,577 (GRCm39) W669* 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
R5165:Pcdhga3 UTSW 18 37,808,723 (GRCm39) missense possibly damaging 0.60
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
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'- TTCTCAGTAGGGCTGCACAC -3'
(R):5'- AGATCAGGTGACTCTTCCGAG -3'

Sequencing Primer
(F):5'- TGCTGGACAGAGATGCTCTC -3'
(R):5'- GAGCCTGCGGTAAGTGAAACTTC -3'
Posted On 2017-02-15