Incidental Mutation 'R7944:Pcdha6'
ID 649259
Institutional Source Beutler Lab
Gene Symbol Pcdha6
Ensembl Gene ENSMUSG00000103707
Gene Name protocadherin alpha 6
Synonyms Cnr2, Crnr2
MMRRC Submission 045990-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.172) question?
Stock # R7944 (G1)
Quality Score 225.009
Status Not validated
Chromosome 18
Chromosomal Location 37100684-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 37101965 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Asparagine at position 386 (T386N)
Ref Sequence ENSEMBL: ENSMUSP00000141587 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000193777] [ENSMUST00000192631] [ENSMUST00000193389] [ENSMUST00000193839] [ENSMUST00000194544] [ENSMUST00000194751] [ENSMUST00000195590]
AlphaFold Q91Y14
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: 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: 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 possibly damaging
Transcript: ENSMUST00000193777
AA Change: T386N

PolyPhen 2 Score 0.551 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: T386N

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: 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
AA Change: T386N

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: T386N

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: 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: 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: 99.4%
  • 20x: 98.0%
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]
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adprhl1 T A 8: 13,271,929 (GRCm39) R1610W probably damaging Het
Aig1 A T 10: 13,744,417 (GRCm39) M29K probably damaging Het
Alms1 A T 6: 85,618,362 (GRCm39) I2334F probably benign Het
Ano6 A G 15: 95,839,190 (GRCm39) Y423C probably damaging Het
Arap3 T C 18: 38,122,232 (GRCm39) M619V probably benign Het
Armh4 T A 14: 50,010,670 (GRCm39) T346S probably benign Het
Asb13 T A 13: 3,699,413 (GRCm39) F204L probably damaging Het
Btaf1 T C 19: 36,926,565 (GRCm39) V79A probably benign Het
Casp8ap2 A G 4: 32,645,909 (GRCm39) T1661A probably benign Het
Ccna1 G T 3: 54,958,010 (GRCm39) T165K possibly damaging Het
Cdc42ep1 T A 15: 78,731,973 (GRCm39) S139R possibly damaging Het
Chil3 A C 3: 106,057,464 (GRCm39) Y233* probably null Het
Clec1a T C 6: 129,409,150 (GRCm39) S159G probably benign Het
Cltc A T 11: 86,627,967 (GRCm39) N60K probably benign Het
Dlgap4 T A 2: 156,591,054 (GRCm39) Y747N probably damaging Het
Dnah7b A G 1: 46,266,163 (GRCm39) N2244S probably benign Het
Ephb3 A G 16: 21,040,434 (GRCm39) T811A probably damaging Het
Fbxo21 T C 5: 118,146,212 (GRCm39) Y612H possibly damaging Het
Gale T C 4: 135,692,982 (GRCm39) L75P probably damaging Het
Golgb1 T C 16: 36,734,466 (GRCm39) S1279P probably benign Het
Hdgfl3 T C 7: 81,583,706 (GRCm39) Y22C possibly damaging Het
Hmx3 T G 7: 131,146,111 (GRCm39) I273S probably damaging Het
Hpse2 T C 19: 43,373,248 (GRCm39) N127S probably benign Het
Hsf2bp C T 17: 32,226,743 (GRCm39) R204H probably damaging Het
Ifit1bl1 T A 19: 34,571,224 (GRCm39) H411L probably benign Het
Krtap27-1 T C 16: 88,468,340 (GRCm39) N68S probably benign Het
Ltbp1 T G 17: 75,697,546 (GRCm39) *1713G probably null Het
Lypd6b A G 2: 49,833,612 (GRCm39) E84G probably damaging Het
Meiosin T A 7: 18,834,011 (GRCm39) K508N unknown Het
Mrgprx2 T C 7: 48,132,753 (GRCm39) T22A probably benign Het
Mrto4 T C 4: 139,077,000 (GRCm39) Y39C probably benign Het
Mtmr4 T C 11: 87,495,254 (GRCm39) V437A probably damaging Het
Mylk4 T C 13: 32,911,096 (GRCm39) T221A probably benign Het
Neb T C 2: 52,161,360 (GRCm39) D2144G probably damaging Het
Nup210 T G 6: 91,050,179 (GRCm39) D430A probably damaging Het
Obscn T A 11: 58,984,235 (GRCm39) E1740V probably damaging Het
Or8i2 A G 2: 86,852,657 (GRCm39) V77A probably benign Het
Panx1 A G 9: 14,919,125 (GRCm39) C245R probably damaging Het
Pcsk1 G A 13: 75,280,211 (GRCm39) A679T probably benign Het
Pdzph1 T C 17: 59,239,455 (GRCm39) T958A probably damaging Het
Pkd2l2 T A 18: 34,560,481 (GRCm39) Y363N possibly damaging Het
Plekha5 T A 6: 140,526,201 (GRCm39) H946Q possibly damaging Het
Rhbg A G 3: 88,155,007 (GRCm39) L168P probably benign Het
Rictor C T 15: 6,801,635 (GRCm39) S441L probably benign Het
Rtn2 T A 7: 19,020,987 (GRCm39) S153R probably benign Het
Serpinb1a C A 13: 33,034,239 (GRCm39) A51S probably benign Het
Serpinb6e T A 13: 34,016,588 (GRCm39) T382S probably damaging Het
Sgip1 T G 4: 102,772,298 (GRCm39) M229R probably benign Het
Slc1a5 C A 7: 16,523,807 (GRCm39) R271S possibly damaging Het
Slc23a3 A G 1: 75,106,040 (GRCm39) probably null Het
Slc7a6 C T 8: 106,906,239 (GRCm39) P157L possibly damaging Het
Spsb1 T C 4: 149,990,903 (GRCm39) I222V probably benign Het
Syne2 A T 12: 75,951,079 (GRCm39) E410V probably damaging Het
Trappc3 T C 4: 126,168,999 (GRCm39) I163T probably damaging Het
Treh T C 9: 44,592,584 (GRCm39) V63A probably damaging Het
Ttc6 T G 12: 57,707,229 (GRCm39) L712R possibly damaging Het
Ttn G T 2: 76,715,309 (GRCm39) Q7928K unknown Het
Tuft1 G A 3: 94,539,909 (GRCm39) P159S probably benign Het
Vmn2r108 T C 17: 20,691,890 (GRCm39) H211R probably damaging Het
Wapl T C 14: 34,399,105 (GRCm39) I58T probably benign Het
Zfp78 C T 7: 6,381,589 (GRCm39) T213I possibly damaging Het
Zmat4 T A 8: 24,238,436 (GRCm39) I6N possibly damaging Het
Zp3r G T 1: 130,524,560 (GRCm39) P226Q probably damaging Het
Other mutations in Pcdha6
AlleleSourceChrCoordTypePredicted EffectPPH Score
R3734:Pcdha6 UTSW 18 37,102,454 (GRCm39) missense probably damaging 1.00
R3859:Pcdha6 UTSW 18 37,102,984 (GRCm39) missense possibly damaging 0.89
R3875:Pcdha6 UTSW 18 37,101,119 (GRCm39) missense probably damaging 1.00
R4446:Pcdha6 UTSW 18 37,100,813 (GRCm39) missense probably benign 0.28
R4647:Pcdha6 UTSW 18 37,102,189 (GRCm39) missense probably damaging 0.98
R4659:Pcdha6 UTSW 18 37,102,292 (GRCm39) missense probably damaging 1.00
R4780:Pcdha6 UTSW 18 37,102,906 (GRCm39) missense probably damaging 1.00
R4839:Pcdha6 UTSW 18 37,101,485 (GRCm39) missense possibly damaging 0.73
R4915:Pcdha6 UTSW 18 37,101,510 (GRCm39) missense probably damaging 1.00
R5011:Pcdha6 UTSW 18 37,100,960 (GRCm39) missense probably damaging 1.00
R5084:Pcdha6 UTSW 18 37,102,016 (GRCm39) missense probably damaging 1.00
R5090:Pcdha6 UTSW 18 37,101,770 (GRCm39) missense probably benign 0.15
R5189:Pcdha6 UTSW 18 37,101,844 (GRCm39) missense probably damaging 1.00
R5652:Pcdha6 UTSW 18 37,101,889 (GRCm39) splice site probably null
R5773:Pcdha6 UTSW 18 37,102,643 (GRCm39) missense probably benign 0.00
R5890:Pcdha6 UTSW 18 37,102,121 (GRCm39) missense possibly damaging 0.94
R6135:Pcdha6 UTSW 18 37,102,269 (GRCm39) missense probably damaging 1.00
R6276:Pcdha6 UTSW 18 37,102,820 (GRCm39) splice site probably null
R6346:Pcdha6 UTSW 18 37,101,113 (GRCm39) missense probably damaging 1.00
R6889:Pcdha6 UTSW 18 37,101,396 (GRCm39) missense probably damaging 1.00
R7295:Pcdha6 UTSW 18 37,101,189 (GRCm39) missense probably damaging 1.00
R7776:Pcdha6 UTSW 18 37,103,034 (GRCm39) missense probably benign 0.27
R7950:Pcdha6 UTSW 18 37,102,479 (GRCm39) missense probably damaging 1.00
R8371:Pcdha6 UTSW 18 37,102,920 (GRCm39) nonsense probably null
R8513:Pcdha6 UTSW 18 37,102,229 (GRCm39) missense probably damaging 1.00
R8549:Pcdha6 UTSW 18 37,101,594 (GRCm39) missense possibly damaging 0.83
R8735:Pcdha6 UTSW 18 37,101,203 (GRCm39) missense possibly damaging 0.55
R8827:Pcdha6 UTSW 18 37,102,802 (GRCm39) missense probably damaging 1.00
R8881:Pcdha6 UTSW 18 37,101,484 (GRCm39) missense probably damaging 1.00
R9094:Pcdha6 UTSW 18 37,101,593 (GRCm39) missense probably damaging 0.98
R9357:Pcdha6 UTSW 18 37,102,226 (GRCm39) missense probably benign 0.16
Z1088:Pcdha6 UTSW 18 37,102,270 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CGTTGATGCGACGGACAAAG -3'
(R):5'- AGGCGCATTGTCGTTCACATC -3'

Sequencing Primer
(F):5'- AAGGACACCCTCCGATGG -3'
(R):5'- GTCGTTCACATCGGCCAC -3'
Posted On 2020-09-15