Incidental Mutation 'R5326:Pcdhga4'
ID 421999
Institutional Source Beutler Lab
Gene Symbol Pcdhga4
Ensembl Gene ENSMUSG00000103677
Gene Name protocadherin gamma subfamily A, 4
Synonyms
MMRRC Submission 042909-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.132) question?
Stock # R5326 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37818290-37974923 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 37819651 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 400 (Y400F)
Ref Sequence ENSEMBL: ENSMUSP00000142140 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000192931] [ENSMUST00000193869] [ENSMUST00000194418] [ENSMUST00000194544] [ENSMUST00000194190] [ENSMUST00000195112]
AlphaFold Q91XY4
Predicted Effect probably benign
Transcript: ENSMUST00000073447
SMART Domains Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346

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 noncoding transcript
Transcript: ENSMUST00000193631
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 damaging
Transcript: ENSMUST00000194418
AA Change: Y400F

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: Y400F

DomainStartEndE-ValueType
CA 44 130 1.64e-2 SMART
CA 154 239 3.93e-18 SMART
CA 263 344 5.22e-23 SMART
CA 368 449 5.02e-25 SMART
CA 473 559 2.07e-26 SMART
CA 590 668 6.84e-18 SMART
transmembrane domain 690 712 N/A INTRINSIC
low complexity region 911 930 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
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 probably benign
Transcript: ENSMUST00000195163
Predicted Effect probably benign
Transcript: ENSMUST00000195112
SMART Domains Protein: ENSMUSP00000141449
Gene: ENSMUSG00000102748

DomainStartEndE-ValueType
CA 24 130 8.18e-3 SMART
CA 154 239 1.39e-18 SMART
CA 263 344 7.91e-23 SMART
CA 368 449 2.27e-23 SMART
CA 473 559 1.24e-24 SMART
CA 590 671 1.3e-9 SMART
transmembrane domain 690 712 N/A INTRINSIC
low complexity region 909 928 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.6%
  • 20x: 96.1%
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 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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700003E16Rik A G 6: 83,138,336 (GRCm39) T127A probably damaging Het
Aadacl2 C T 3: 59,932,484 (GRCm39) T333I probably damaging Het
Actl6b T C 5: 137,565,313 (GRCm39) S366P probably damaging Het
Actr10 T C 12: 71,001,430 (GRCm39) probably benign Het
Adgrf5 T A 17: 43,750,965 (GRCm39) I510N probably damaging Het
Adra2a A G 19: 54,035,112 (GRCm39) Y156C probably damaging Het
Angpt4 T C 2: 151,767,464 (GRCm39) probably null Het
Ankdd1a T A 9: 65,411,472 (GRCm39) probably null Het
AW146154 C A 7: 41,130,801 (GRCm39) G105V probably benign Het
Brd3 A G 2: 27,340,556 (GRCm39) L551P probably benign Het
Calb2 C T 8: 110,883,610 (GRCm39) G38D possibly damaging Het
Cand1 G A 10: 119,047,933 (GRCm39) A519V probably benign Het
Cnbd1 T C 4: 18,860,517 (GRCm39) T410A possibly damaging Het
Cndp2 A T 18: 84,690,201 (GRCm39) M247K probably damaging Het
Cog6 T A 3: 52,921,237 (GRCm39) Q123L probably null Het
Crx G A 7: 15,602,262 (GRCm39) R139C probably damaging Het
Ctrc A G 4: 141,571,037 (GRCm39) Y68H probably damaging Het
Ddx4 T C 13: 112,757,779 (GRCm39) D326G probably damaging Het
Depdc1a T C 3: 159,232,286 (GRCm39) V679A probably damaging Het
Dyrk1a A G 16: 94,487,440 (GRCm39) D512G probably damaging Het
Edem1 C T 6: 108,831,290 (GRCm39) R584C possibly damaging Het
Emcn A G 3: 137,085,638 (GRCm39) T79A probably benign Het
Fbrsl1 C T 5: 110,526,307 (GRCm39) G437R probably damaging Het
Fbxo9 T C 9: 78,008,938 (GRCm39) M12V possibly damaging Het
Fcgbpl1 A T 7: 27,854,914 (GRCm39) I1847F probably damaging Het
Flii A G 11: 60,609,688 (GRCm39) S640P probably benign Het
Frs2 T C 10: 116,913,468 (GRCm39) S121G probably benign Het
Fsip2 A T 2: 82,812,207 (GRCm39) N2842I possibly damaging Het
Fst G T 13: 114,592,241 (GRCm39) Q159K probably damaging Het
Ggt1 T C 10: 75,421,540 (GRCm39) probably null Het
Gigyf2 T C 1: 87,352,860 (GRCm39) probably benign Het
Gm10439 T G X: 148,419,159 (GRCm39) *434E probably null Het
Gm9476 T A 10: 100,142,996 (GRCm39) noncoding transcript Het
Gmcl1 A T 6: 86,703,127 (GRCm39) N102K possibly damaging Het
Gml T C 15: 74,688,299 (GRCm39) N56S probably damaging Het
Gpam A C 19: 55,079,597 (GRCm39) S128R probably benign Het
Gucy1b2 C T 14: 62,690,779 (GRCm39) probably null Het
Hhipl2 A G 1: 183,214,055 (GRCm39) D377G probably damaging Het
Hmx3 C T 7: 131,146,146 (GRCm39) Q285* probably null Het
Hspa14 A G 2: 3,503,560 (GRCm39) V116A possibly damaging Het
Ighv5-17 T C 12: 113,822,878 (GRCm39) D81G possibly damaging Het
Ipo5 T C 14: 121,163,683 (GRCm39) V247A probably benign Het
Iqcd A G 5: 120,740,440 (GRCm39) Q257R probably damaging Het
Itpk1 T C 12: 102,540,225 (GRCm39) N286S possibly damaging Het
Knl1 T A 2: 118,898,829 (GRCm39) C177S possibly damaging Het
Knop1 T C 7: 118,452,495 (GRCm39) K23E possibly damaging Het
Ksr2 T A 5: 117,846,305 (GRCm39) V724E probably damaging Het
Lrrc17 G A 5: 21,780,156 (GRCm39) G377S probably damaging Het
Macf1 GCCCCC GCCCCCC 4: 123,244,784 (GRCm39) probably null Het
Morc2b T A 17: 33,355,907 (GRCm39) T622S probably benign Het
Msantd2 G A 9: 37,428,555 (GRCm39) G185R probably damaging Het
Mtmr2 A G 9: 13,699,943 (GRCm39) Y38C probably damaging Het
Mycbpap A T 11: 94,398,572 (GRCm39) probably null Het
Nadsyn1 T A 7: 143,362,567 (GRCm39) R279W probably benign Het
Or1e25 T A 11: 73,494,030 (GRCm39) V208E possibly damaging Het
Or2t48 A C 11: 58,420,710 (GRCm39) V34G probably benign Het
Or56b35 T A 7: 104,963,646 (GRCm39) F145Y probably damaging Het
Or7a38 G A 10: 78,753,420 (GRCm39) V249I possibly damaging Het
Pkd2 A G 5: 104,634,515 (GRCm39) silent Het
Prkar1b T C 5: 139,113,544 (GRCm39) probably null Het
Ric8b T C 10: 84,828,076 (GRCm39) Y467H probably damaging Het
Rin1 A G 19: 5,102,652 (GRCm39) E387G probably damaging Het
Robo2 G A 16: 73,695,853 (GRCm39) T1430I probably benign Het
Seh1l C T 18: 67,908,069 (GRCm39) probably benign Het
Slc37a1 A T 17: 31,559,236 (GRCm39) T439S probably damaging Het
Slc6a6 T C 6: 91,712,170 (GRCm39) F233S probably damaging Het
Smyd3 A T 1: 179,238,024 (GRCm39) D114E probably benign Het
Snrnp70 GCGGTCCCGGTCCCGGTC GCGGTCCCGGTC 7: 45,026,657 (GRCm39) probably benign Het
Speer4a1 T A 5: 26,241,736 (GRCm39) N130I probably damaging Het
Spin1 A G 13: 51,293,563 (GRCm39) Y91C probably damaging Het
Tdrd7 T C 4: 46,029,757 (GRCm39) V1030A probably benign Het
Trim30c T A 7: 104,037,511 (GRCm39) M152L possibly damaging Het
Tsga10 T A 1: 37,800,598 (GRCm39) D542V probably damaging Het
Unc93a2 A T 17: 7,637,187 (GRCm39) C334S probably benign Het
Vmn1r175 A T 7: 23,508,531 (GRCm39) I32N possibly damaging Het
Vmn1r81 A T 7: 11,994,034 (GRCm39) D191E probably damaging Het
Wdr11 T C 7: 129,226,973 (GRCm39) S812P probably damaging Het
Zbtb5 C A 4: 44,995,052 (GRCm39) V111F probably damaging Het
Zdbf2 T G 1: 63,343,570 (GRCm39) C650G possibly damaging Het
Zfp282 T A 6: 47,882,261 (GRCm39) N649K probably benign Het
Other mutations in Pcdhga4
AlleleSourceChrCoordTypePredicted EffectPPH Score
PIT1430001:Pcdhga4 UTSW 18 37,819,267 (GRCm39) missense probably benign 0.00
R3828:Pcdhga4 UTSW 18 37,820,654 (GRCm39) missense possibly damaging 0.62
R3970:Pcdhga4 UTSW 18 37,820,654 (GRCm39) missense possibly damaging 0.62
R4080:Pcdhga4 UTSW 18 37,818,832 (GRCm39) missense probably damaging 1.00
R4356:Pcdhga4 UTSW 18 37,820,664 (GRCm39) missense probably damaging 1.00
R4834:Pcdhga4 UTSW 18 37,818,490 (GRCm39) missense probably benign 0.01
R4983:Pcdhga4 UTSW 18 37,819,572 (GRCm39) missense probably damaging 1.00
R5076:Pcdhga4 UTSW 18 37,818,648 (GRCm39) missense probably benign 0.43
R5186:Pcdhga4 UTSW 18 37,820,479 (GRCm39) missense probably benign 0.07
R5194:Pcdhga4 UTSW 18 37,820,794 (GRCm39) missense probably benign 0.08
R5333:Pcdhga4 UTSW 18 37,818,477 (GRCm39) missense probably benign 0.00
R5373:Pcdhga4 UTSW 18 37,818,649 (GRCm39) missense probably damaging 1.00
R5374:Pcdhga4 UTSW 18 37,818,649 (GRCm39) missense probably damaging 1.00
R5419:Pcdhga4 UTSW 18 37,819,798 (GRCm39) missense probably damaging 1.00
R5542:Pcdhga4 UTSW 18 37,819,651 (GRCm39) missense probably damaging 0.98
R5878:Pcdhga4 UTSW 18 37,820,739 (GRCm39) missense probably benign 0.03
R5996:Pcdhga4 UTSW 18 37,818,991 (GRCm39) missense probably benign 0.03
R6056:Pcdhga4 UTSW 18 37,819,383 (GRCm39) missense probably benign 0.00
R6083:Pcdhga4 UTSW 18 37,820,478 (GRCm39) missense probably damaging 0.98
R6155:Pcdhga4 UTSW 18 37,819,546 (GRCm39) missense probably damaging 0.98
R6208:Pcdhga4 UTSW 18 37,819,762 (GRCm39) missense probably damaging 1.00
R6306:Pcdhga4 UTSW 18 37,818,966 (GRCm39) missense probably damaging 1.00
R6580:Pcdhga4 UTSW 18 37,820,370 (GRCm39) missense possibly damaging 0.93
R6936:Pcdhga4 UTSW 18 37,820,458 (GRCm39) missense possibly damaging 0.84
R7132:Pcdhga4 UTSW 18 37,820,430 (GRCm39) missense probably damaging 1.00
R7159:Pcdhga4 UTSW 18 37,819,972 (GRCm39) missense probably damaging 1.00
R7257:Pcdhga4 UTSW 18 37,820,451 (GRCm39) missense probably damaging 0.99
R7263:Pcdhga4 UTSW 18 37,819,873 (GRCm39) missense probably benign 0.42
R7825:Pcdhga4 UTSW 18 37,820,374 (GRCm39) missense probably damaging 1.00
R7882:Pcdhga4 UTSW 18 37,819,681 (GRCm39) missense probably damaging 1.00
R7916:Pcdhga4 UTSW 18 37,818,502 (GRCm39) missense probably benign 0.22
R8053:Pcdhga4 UTSW 18 37,819,308 (GRCm39) missense probably benign 0.07
R9184:Pcdhga4 UTSW 18 37,820,460 (GRCm39) missense possibly damaging 0.95
R9292:Pcdhga4 UTSW 18 37,819,713 (GRCm39) missense probably benign 0.00
R9417:Pcdhga4 UTSW 18 37,820,560 (GRCm39) missense probably damaging 1.00
R9483:Pcdhga4 UTSW 18 37,819,746 (GRCm39) missense possibly damaging 0.73
R9562:Pcdhga4 UTSW 18 37,819,527 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- GATGTAAATGACAATGCCCCG -3'
(R):5'- AGATGGAAGCTCCTCTAGGG -3'

Sequencing Primer
(F):5'- TGACAATGCCCCGGAAGTC -3'
(R):5'- GTTTTCTGGAATGTAAGCAGAATAGG -3'
Posted On 2016-08-04