Incidental Mutation 'R8088:Pcdhac1'
ID 629816
Institutional Source Beutler Lab
Gene Symbol Pcdhac1
Ensembl Gene ENSMUSG00000103255
Gene Name protocadherin alpha subfamily C, 1
Synonyms CNRc1
MMRRC Submission 067521-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8088 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 37223189-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 37224807 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 540 (V540A)
Ref Sequence ENSEMBL: ENSMUSP00000007584 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000007584] [ENSMUST00000047614] [ENSMUST00000070797] [ENSMUST00000115657] [ENSMUST00000115658] [ENSMUST00000115659] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192447] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000192631] [ENSMUST00000193389] [ENSMUST00000193777] [ENSMUST00000193839] [ENSMUST00000194038] [ENSMUST00000194544] [ENSMUST00000194751] [ENSMUST00000195590]
AlphaFold Q91Y10
Predicted Effect possibly damaging
Transcript: ENSMUST00000007584
AA Change: V540A

PolyPhen 2 Score 0.737 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000007584
Gene: ENSMUSG00000103255
AA Change: V540A

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
CA 45 122 3.59e-1 SMART
CA 146 231 6.32e-22 SMART
CA 255 338 5.18e-18 SMART
CA 362 443 9.73e-23 SMART
CA 467 554 4.24e-23 SMART
CA 584 662 1.11e-8 SMART
Pfam:Cadherin_C_2 682 773 1.1e-12 PFAM
Pfam:Cadherin_tail 813 947 5.4e-58 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000047614
SMART Domains Protein: ENSMUSP00000047609
Gene: ENSMUSG00000103310

DomainStartEndE-ValueType
CA 19 131 3.78e-2 SMART
CA 155 240 3.26e-24 SMART
CA 264 348 6.37e-27 SMART
CA 372 453 3.31e-25 SMART
CA 477 563 6.18e-25 SMART
CA 594 676 5.6e-14 SMART
low complexity region 679 696 N/A INTRINSIC
transmembrane domain 699 721 N/A INTRINSIC
Pfam:Cadherin_tail 799 933 5.3e-58 PFAM
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: ENSMUST00000115657
SMART Domains Protein: ENSMUSP00000111321
Gene: ENSMUSG00000102206

DomainStartEndE-ValueType
CA 21 131 2.95e-2 SMART
CA 155 240 7.44e-19 SMART
CA 264 347 5.63e-28 SMART
CA 371 452 3.14e-26 SMART
CA 476 562 1.42e-24 SMART
CA 593 675 1.03e-12 SMART
transmembrane domain 697 719 N/A INTRINSIC
low complexity region 783 794 N/A INTRINSIC
low complexity region 918 942 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000115658
SMART Domains Protein: ENSMUSP00000111322
Gene: ENSMUSG00000007440

DomainStartEndE-ValueType
low complexity region 15 21 N/A INTRINSIC
CA 46 132 6.34e-2 SMART
CA 156 241 4.65e-20 SMART
CA 265 349 1.25e-25 SMART
CA 373 454 9.22e-24 SMART
CA 478 564 4.3e-24 SMART
CA 595 678 5.07e-12 SMART
low complexity region 706 721 N/A INTRINSIC
Pfam:Cadherin_tail 795 929 5.3e-58 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000115659
SMART Domains Protein: ENSMUSP00000111323
Gene: ENSMUSG00000103770

DomainStartEndE-ValueType
low complexity region 44 51 N/A INTRINSIC
CA 75 161 2.46e-2 SMART
CA 185 270 8.1e-20 SMART
CA 294 378 1.69e-22 SMART
CA 402 483 1.52e-24 SMART
CA 507 593 5.68e-24 SMART
CA 624 705 6.69e-12 SMART
transmembrane domain 727 749 N/A INTRINSIC
Pfam:Cadherin_tail 828 962 5.6e-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: ENSMUST00000192168
SMART Domains Protein: ENSMUSP00000142293
Gene: ENSMUSG00000103092

DomainStartEndE-ValueType
CA 21 131 2.2e-2 SMART
CA 155 240 2.05e-21 SMART
CA 264 348 8.81e-21 SMART
CA 372 453 2.01e-24 SMART
CA 477 563 1.42e-24 SMART
CA 591 673 1.63e-15 SMART
transmembrane domain 693 715 N/A INTRINSIC
low complexity region 902 926 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 benign
Transcript: ENSMUST00000192447
SMART Domains Protein: ENSMUSP00000142270
Gene: ENSMUSG00000102206

DomainStartEndE-ValueType
CA 21 131 1.5e-4 SMART
CA 155 240 3.6e-21 SMART
CA 264 347 2.8e-30 SMART
CA 371 452 1.5e-28 SMART
CA 476 562 6.8e-27 SMART
CA 593 675 4.9e-15 SMART
transmembrane domain 697 719 N/A INTRINSIC
low complexity region 783 794 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192503
SMART Domains Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312

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 probably benign
Transcript: ENSMUST00000192631
SMART Domains Protein: ENSMUSP00000142156
Gene: ENSMUSG00000104318

DomainStartEndE-ValueType
CA 21 131 2.58e-2 SMART
CA 155 240 4.27e-19 SMART
CA 264 348 1.42e-24 SMART
CA 372 453 9.36e-25 SMART
CA 477 563 1.42e-24 SMART
CA 594 671 4.03e-6 SMART
transmembrane domain 696 718 N/A INTRINSIC
low complexity region 905 929 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193389
SMART Domains Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707

DomainStartEndE-ValueType
CA 21 131 5.67e-2 SMART
CA 155 240 4.72e-21 SMART
CA 264 348 1.9e-25 SMART
CA 372 453 3.31e-25 SMART
CA 477 563 1.42e-24 SMART
CA 594 676 5.91e-13 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000193777
SMART Domains Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707

DomainStartEndE-ValueType
CA 21 131 5.67e-2 SMART
CA 155 240 4.72e-21 SMART
CA 264 348 1.9e-25 SMART
CA 372 453 3.31e-25 SMART
CA 477 563 1.42e-24 SMART
CA 594 676 5.91e-13 SMART
low complexity region 914 938 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: ENSMUST00000193856
Predicted Effect probably benign
Transcript: ENSMUST00000193984
Predicted Effect probably benign
Transcript: ENSMUST00000194038
SMART Domains Protein: ENSMUSP00000142159
Gene: ENSMUSG00000103800

DomainStartEndE-ValueType
CA 20 131 6.34e-2 SMART
CA 155 240 4.27e-19 SMART
CA 264 348 2.04e-25 SMART
CA 372 453 2.84e-24 SMART
CA 477 563 9.88e-24 SMART
CA 594 676 8.62e-15 SMART
transmembrane domain 699 721 N/A INTRINSIC
low complexity region 914 938 N/A INTRINSIC
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: ENSMUST00000194751
SMART Domains Protein: ENSMUSP00000142285
Gene: ENSMUSG00000103707

DomainStartEndE-ValueType
low complexity region 15 21 N/A INTRINSIC
Pfam:Cadherin_2 29 112 4.5e-32 PFAM
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: 99.9%
  • 3x: 99.8%
  • 10x: 99.1%
  • 20x: 96.8%
Validation Efficiency 100% (69/69)
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]
PHENOTYPE: Mice homozygous for a reporter allele are viable and fertile with no apparent gross phenotype. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atp2c1 A T 9: 105,329,768 (GRCm39) probably null Het
Ccdc134 T A 15: 82,015,990 (GRCm39) probably benign Het
Ccdc162 G T 10: 41,499,410 (GRCm39) H1066Q possibly damaging Het
Ccna1 A G 3: 54,958,492 (GRCm39) S64P probably benign Het
Cplane1 A G 15: 8,215,802 (GRCm39) M453V probably benign Het
Defb12 T C 8: 19,162,837 (GRCm39) probably null Het
Dhx9 C A 1: 153,338,443 (GRCm39) V738L probably benign Het
Dnah10 A G 5: 124,831,330 (GRCm39) N843S probably benign Het
Dspp A G 5: 104,325,122 (GRCm39) D495G unknown Het
Dus2 A G 8: 106,757,073 (GRCm39) M88V probably benign Het
Dusp13b A G 14: 21,791,305 (GRCm39) V49A probably benign Het
Efcab3 A T 11: 104,889,072 (GRCm39) I4163L probably benign Het
Ehbp1 G A 11: 22,039,572 (GRCm39) H843Y probably null Het
Entpd3 A C 9: 120,383,239 (GRCm39) R91S probably benign Het
Fam83c C A 2: 155,673,559 (GRCm39) V210F probably damaging Het
Flot1 G A 17: 36,140,870 (GRCm39) A287T probably damaging Het
Gm19410 A G 8: 36,273,995 (GRCm39) K1412E probably benign Het
Gsn G A 2: 35,182,659 (GRCm39) V241M possibly damaging Het
Gstcd C T 3: 132,787,868 (GRCm39) V277M probably damaging Het
Heatr5a T C 12: 51,994,779 (GRCm39) D451G possibly damaging Het
Hmcn2 G A 2: 31,316,915 (GRCm39) W3831* probably null Het
Il3 A G 11: 54,156,375 (GRCm39) V119A probably benign Het
Jam3 T C 9: 27,010,156 (GRCm39) K276R probably benign Het
Kcnt1 G A 2: 25,784,326 (GRCm39) G277D possibly damaging Het
Kif28 T A 1: 179,527,919 (GRCm39) D744V probably damaging Het
Ldlrad1 G A 4: 107,066,688 (GRCm39) A8T probably benign Het
Loxhd1 T C 18: 77,429,709 (GRCm39) I535T possibly damaging Het
Lzts1 A C 8: 69,588,474 (GRCm39) L494R probably benign Het
Mettl4 A G 17: 95,042,795 (GRCm39) V347A probably damaging Het
Mff A G 1: 82,729,370 (GRCm39) E270G probably damaging Het
Mroh2b A T 15: 4,929,985 (GRCm39) I24F possibly damaging Het
Muc16 A T 9: 18,430,596 (GRCm39) Y8102* probably null Het
Myh14 A T 7: 44,314,920 (GRCm39) M1K probably null Het
Myo18b T A 5: 113,027,376 (GRCm39) probably benign Het
Neurl1a C A 19: 47,245,873 (GRCm39) P502T probably damaging Het
Nrp1 G A 8: 129,194,997 (GRCm39) W484* probably null Het
Or2y3 T A 17: 38,393,452 (GRCm39) H139L possibly damaging Het
Or4f47 T A 2: 111,972,602 (GRCm39) I104N probably benign Het
Pcdhga9 A G 18: 37,870,007 (GRCm39) probably benign Het
Pm20d1 A C 1: 131,729,501 (GRCm39) N176T probably benign Het
Pnldc1 T C 17: 13,116,189 (GRCm39) D271G probably damaging Het
Pold3 A G 7: 99,761,508 (GRCm39) V63A probably damaging Het
Rbm18 A C 2: 36,017,196 (GRCm39) S61A probably benign Het
Rdh14 T C 12: 10,444,551 (GRCm39) L134P probably damaging Het
Repin1 G T 6: 48,574,279 (GRCm39) E403* probably null Het
Rtel1 A G 2: 180,964,138 (GRCm39) T46A probably damaging Het
Rtn3 T C 19: 7,412,363 (GRCm39) I823V probably damaging Het
S1pr1 A G 3: 115,505,683 (GRCm39) S304P probably damaging Het
Scfd2 A G 5: 74,692,024 (GRCm39) V86A probably benign Het
Scgb1a1 C T 19: 9,062,599 (GRCm39) V66M probably damaging Het
Sec31a A T 5: 100,526,721 (GRCm39) M46K Het
Sgsm1 A G 5: 113,403,134 (GRCm39) M971T probably damaging Het
Slc5a11 T C 7: 122,864,951 (GRCm39) I419T probably benign Het
Slco6d1 A T 1: 98,394,431 (GRCm39) T372S possibly damaging Het
Slx9 T C 10: 77,350,229 (GRCm39) N53S probably benign Het
Spata31 T A 13: 65,068,679 (GRCm39) Y276N probably benign Het
Sprr2k C T 3: 92,340,796 (GRCm39) R49W unknown Het
Sspo G A 6: 48,434,547 (GRCm39) C1013Y probably damaging Het
Ssr2 A G 3: 88,487,190 (GRCm39) R2G possibly damaging Het
St18 C A 1: 6,898,229 (GRCm39) T677K probably benign Het
Thap11 A T 8: 106,582,527 (GRCm39) I179F probably damaging Het
Trf C A 9: 103,089,130 (GRCm39) G586C probably damaging Het
Umodl1 A G 17: 31,192,770 (GRCm39) N299S probably benign Het
Xrcc5 C A 1: 72,351,595 (GRCm39) A55E probably damaging Het
Other mutations in Pcdhac1
AlleleSourceChrCoordTypePredicted EffectPPH Score
G1patch:Pcdhac1 UTSW 18 37,223,381 (GRCm39) missense probably damaging 1.00
R2418:Pcdhac1 UTSW 18 37,224,381 (GRCm39) missense probably benign 0.12
R2419:Pcdhac1 UTSW 18 37,224,381 (GRCm39) missense probably benign 0.12
R3876:Pcdhac1 UTSW 18 37,224,945 (GRCm39) missense probably damaging 1.00
R4234:Pcdhac1 UTSW 18 37,224,011 (GRCm39) missense probably damaging 1.00
R4515:Pcdhac1 UTSW 18 37,224,432 (GRCm39) missense probably damaging 1.00
R4722:Pcdhac1 UTSW 18 37,224,933 (GRCm39) missense probably damaging 1.00
R4804:Pcdhac1 UTSW 18 37,224,231 (GRCm39) missense possibly damaging 0.67
R4996:Pcdhac1 UTSW 18 37,225,580 (GRCm39) nonsense probably null
R5093:Pcdhac1 UTSW 18 37,223,595 (GRCm39) missense probably damaging 1.00
R5111:Pcdhac1 UTSW 18 37,224,558 (GRCm39) missense probably damaging 1.00
R5116:Pcdhac1 UTSW 18 37,224,500 (GRCm39) missense probably damaging 1.00
R5203:Pcdhac1 UTSW 18 37,224,243 (GRCm39) missense probably damaging 1.00
R5659:Pcdhac1 UTSW 18 37,225,470 (GRCm39) missense probably damaging 1.00
R5679:Pcdhac1 UTSW 18 37,225,530 (GRCm39) missense probably damaging 1.00
R5765:Pcdhac1 UTSW 18 37,223,372 (GRCm39) nonsense probably null
R6536:Pcdhac1 UTSW 18 37,223,367 (GRCm39) missense probably benign 0.00
R6725:Pcdhac1 UTSW 18 37,223,381 (GRCm39) missense probably damaging 1.00
R6764:Pcdhac1 UTSW 18 37,223,732 (GRCm39) missense probably damaging 1.00
R6772:Pcdhac1 UTSW 18 37,223,289 (GRCm39) missense probably benign 0.05
R6870:Pcdhac1 UTSW 18 37,225,140 (GRCm39) missense probably damaging 1.00
R7426:Pcdhac1 UTSW 18 37,225,550 (GRCm39) missense probably benign
R7809:Pcdhac1 UTSW 18 37,224,009 (GRCm39) missense possibly damaging 0.55
R8201:Pcdhac1 UTSW 18 37,223,892 (GRCm39) missense probably benign 0.16
R8400:Pcdhac1 UTSW 18 37,225,453 (GRCm39) nonsense probably null
R8787:Pcdhac1 UTSW 18 37,224,942 (GRCm39) missense probably damaging 1.00
R9349:Pcdhac1 UTSW 18 37,224,021 (GRCm39) missense possibly damaging 0.50
R9733:Pcdhac1 UTSW 18 37,225,506 (GRCm39) missense probably benign
Z1088:Pcdhac1 UTSW 18 37,225,619 (GRCm39) missense probably damaging 0.97
Z1088:Pcdhac1 UTSW 18 37,225,243 (GRCm39) missense probably damaging 1.00
Z1177:Pcdhac1 UTSW 18 37,225,476 (GRCm39) missense possibly damaging 0.90
Predicted Primers PCR Primer
(F):5'- AGCCCTGGAGTTTCCTTAGG -3'
(R):5'- AGGCATTGGAACCACTGTCTG -3'

Sequencing Primer
(F):5'- GTTTGCTCAGGACCCAGATCTG -3'
(R):5'- GGAACCACTGTCTGCATCC -3'
Posted On 2020-06-30