Incidental Mutation 'R9349:Pcdhac1'
ID 707984
Institutional Source Beutler Lab
Gene Symbol Pcdhac1
Ensembl Gene ENSMUSG00000103255
Gene Name protocadherin alpha subfamily C, 1
Synonyms CNRc1
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9349 (G1)
Quality Score 225.009
Status Not validated
Chromosome 18
Chromosomal Location 37223189-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 37224021 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Valine at position 278 (A278V)
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: A278V

PolyPhen 2 Score 0.496 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000007584
Gene: ENSMUSG00000103255
AA Change: A278V

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
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]
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: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A230072I06Rik A G 8: 12,329,665 (GRCm39) Q40R unknown Het
A730015C16Rik C T 4: 108,705,053 (GRCm39) V89I unknown Het
Adam19 G T 11: 46,022,570 (GRCm39) E508* probably null Het
Arhgef33 C T 17: 80,644,736 (GRCm39) Q22* probably null Het
Arih2 C G 9: 108,488,938 (GRCm39) R260P probably damaging Het
Astn2 T A 4: 66,184,492 (GRCm39) T202S unknown Het
Bpifb5 T A 2: 154,067,005 (GRCm39) L86Q possibly damaging Het
Brpf3 G A 17: 29,040,276 (GRCm39) S899N probably benign Het
Ccl20 T C 1: 83,095,586 (GRCm39) F49S Het
Ctse A G 1: 131,592,111 (GRCm39) T146A probably benign Het
Dhx35 T C 2: 158,671,444 (GRCm39) S292P possibly damaging Het
Fut7 C T 2: 25,314,993 (GRCm39) P84S possibly damaging Het
Gm9736 A C 10: 77,586,393 (GRCm39) S266A unknown Het
Gsdma T A 11: 98,566,771 (GRCm39) L366Q probably benign Het
Ifna15 T A 4: 88,476,283 (GRCm39) D67V probably benign Het
Igkv2-112 G A 6: 68,197,678 (GRCm39) V117I probably benign Het
Kcnh2 C T 5: 24,538,003 (GRCm39) G120E probably damaging Het
Kcnip1 T G 11: 33,601,548 (GRCm39) Y29S probably benign Het
Lrrc37a T G 11: 103,388,454 (GRCm39) M2324L unknown Het
Mettl5 T A 2: 69,702,113 (GRCm39) D185V possibly damaging Het
Mmp1b T A 9: 7,369,271 (GRCm39) M359L probably benign Het
Ndufa5 G A 6: 24,522,749 (GRCm39) T31I probably benign Het
Ngly1 T A 14: 16,281,801 (GRCm38) C352* probably null Het
Or14c45 A G 7: 86,176,373 (GRCm39) H136R probably benign Het
Or51a39 A T 7: 102,362,875 (GRCm39) C248* probably null Het
Ppp2r3c T A 12: 55,345,268 (GRCm39) K73N probably benign Het
Rasgrf1 T C 9: 89,884,460 (GRCm39) V975A probably damaging Het
Rps27rt C T 9: 114,811,673 (GRCm39) V35M probably benign Het
Slc22a8 A G 19: 8,571,469 (GRCm39) N67D probably benign Het
Slc39a6 C A 18: 24,718,493 (GRCm39) M521I probably benign Het
Snx31 C T 15: 36,555,430 (GRCm39) S39N probably damaging Het
Speer1b C T 5: 11,823,221 (GRCm39) T130I possibly damaging Het
Sv2a T C 3: 96,096,795 (GRCm39) probably null Het
Thg1l G A 11: 45,846,273 (GRCm39) A7V probably benign Het
Ttc39c C T 18: 12,822,932 (GRCm39) Q147* probably null Het
Ube2u A G 4: 100,407,194 (GRCm39) N352D unknown Het
Uhrf1 T C 17: 56,617,737 (GRCm39) V153A possibly damaging Het
Wdfy4 A G 14: 32,875,996 (GRCm39) S143P 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
R8088:Pcdhac1 UTSW 18 37,224,807 (GRCm39) missense possibly damaging 0.74
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
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'- GTCACTATCACTGTGGTGGAC -3'
(R):5'- TCCTCGAGTATTGAGCTGGAG -3'

Sequencing Primer
(F):5'- GTGGACACCAACGACAATGC -3'
(R):5'- AGGTCATGAAGTCCATCTGGG -3'
Posted On 2022-04-18