Incidental Mutation 'R5729:Pcdh1'
ID 452687
Institutional Source Beutler Lab
Gene Symbol Pcdh1
Ensembl Gene ENSMUSG00000051375
Gene Name protocadherin 1
Synonyms 2010005A06Rik
MMRRC Submission 043346-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.365) question?
Stock # R5729 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 38318967-38345023 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 38335999 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 73 (V73D)
Ref Sequence ENSEMBL: ENSMUSP00000125576 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057185] [ENSMUST00000159405] [ENSMUST00000160721] [ENSMUST00000161701] [ENSMUST00000193828] [ENSMUST00000194312]
AlphaFold Q8CFX3
Predicted Effect probably damaging
Transcript: ENSMUST00000057185
AA Change: V212D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: V212D

DomainStartEndE-ValueType
signal peptide 1 33 N/A INTRINSIC
Pfam:Cadherin_2 36 120 2e-8 PFAM
CA 168 256 5.18e-18 SMART
CA 280 363 5.68e-24 SMART
CA 395 482 1.84e-23 SMART
CA 506 588 2.99e-32 SMART
CA 612 691 9.36e-25 SMART
CA 717 798 9.9e-15 SMART
transmembrane domain 830 852 N/A INTRINSIC
low complexity region 876 903 N/A INTRINSIC
low complexity region 951 964 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000159405
AA Change: V212D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: V212D

DomainStartEndE-ValueType
signal peptide 1 33 N/A INTRINSIC
Pfam:Cadherin_2 36 120 2e-8 PFAM
CA 168 256 5.18e-18 SMART
CA 280 363 5.68e-24 SMART
CA 395 482 1.84e-23 SMART
CA 506 588 2.99e-32 SMART
CA 612 691 9.36e-25 SMART
CA 717 798 9.9e-15 SMART
transmembrane domain 830 852 N/A INTRINSIC
low complexity region 876 903 N/A INTRINSIC
low complexity region 951 964 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000160721
AA Change: V212D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375
AA Change: V212D

DomainStartEndE-ValueType
signal peptide 1 33 N/A INTRINSIC
Pfam:Cadherin_2 36 120 9.9e-10 PFAM
CA 168 256 5.18e-18 SMART
low complexity region 310 321 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000161701
AA Change: V73D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: V73D

DomainStartEndE-ValueType
CA 29 117 5.18e-18 SMART
CA 141 224 5.68e-24 SMART
CA 256 343 1.84e-23 SMART
CA 367 449 2.99e-32 SMART
CA 473 552 9.36e-25 SMART
CA 578 659 9.9e-15 SMART
transmembrane domain 691 713 N/A INTRINSIC
low complexity region 737 764 N/A INTRINSIC
low complexity region 812 825 N/A INTRINSIC
low complexity region 903 914 N/A INTRINSIC
low complexity region 1029 1040 N/A INTRINSIC
low complexity region 1059 1071 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193828
SMART Domains Protein: ENSMUSP00000142328
Gene: ENSMUSG00000051375

DomainStartEndE-ValueType
low complexity region 18 48 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194312
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 95.2%
Validation Efficiency 97% (62/64)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adss2 A T 1: 177,623,824 (GRCm39) V46E possibly damaging Het
Aldoart2 T C 12: 55,612,690 (GRCm39) V205A probably benign Het
Atp1a2 A G 1: 172,120,938 (GRCm39) S45P probably damaging Het
Atp4a A G 7: 30,411,851 (GRCm39) K29E possibly damaging Het
AU040320 T A 4: 126,724,208 (GRCm39) D428E probably damaging Het
Bend7 T C 2: 4,768,085 (GRCm39) L347P probably damaging Het
Cacna2d1 T A 5: 16,140,037 (GRCm39) L9* probably null Het
Ccdc103 A T 11: 102,773,904 (GRCm39) I50F probably damaging Het
Cdc5l T C 17: 45,737,495 (GRCm39) I88V probably benign Het
Cracr2a T C 6: 127,584,199 (GRCm39) V86A possibly damaging Het
Cybb C G X: 9,316,989 (GRCm39) D246H probably benign Het
Dgkd C T 1: 87,864,054 (GRCm39) Q90* probably null Het
Dnajc21 A T 15: 10,449,682 (GRCm39) D446E probably benign Het
Fam13a T G 6: 58,916,292 (GRCm39) R648S probably damaging Het
Gabrg2 A G 11: 41,858,450 (GRCm39) V226A probably damaging Het
Gm5499 A T 17: 87,385,944 (GRCm39) noncoding transcript Het
Gprc5c G T 11: 114,755,093 (GRCm39) V257L possibly damaging Het
Irf2bp1 G T 7: 18,739,172 (GRCm39) E271* probably null Het
Krt86 T G 15: 101,374,429 (GRCm39) V274G probably benign Het
Lats2 A T 14: 57,960,192 (GRCm39) C151S probably benign Het
Mapk3 A T 7: 126,363,979 (GRCm39) T254S probably benign Het
Mat2b A T 11: 40,573,373 (GRCm39) M202K probably damaging Het
Mos A G 4: 3,870,971 (GRCm39) Y282H probably benign Het
Myo3b A G 2: 69,936,083 (GRCm39) K108R probably damaging Het
Naa16 A G 14: 79,593,220 (GRCm39) Y417H probably damaging Het
Oat A T 7: 132,159,984 (GRCm39) I412N probably damaging Het
Or4d11 A T 19: 12,013,272 (GRCm39) I278N probably damaging Het
Pigv A T 4: 133,392,134 (GRCm39) Y345* probably null Het
Pitpnc1 G T 11: 107,228,264 (GRCm39) F34L probably benign Het
Plxnd1 A G 6: 115,942,838 (GRCm39) L1282P probably damaging Het
Ppp1r3a T C 6: 14,719,762 (GRCm39) D384G probably benign Het
Ppp2ca G A 11: 52,008,856 (GRCm39) E119K probably damaging Het
Psg29 A T 7: 16,944,459 (GRCm39) N323I probably damaging Het
Rasa4 T C 5: 136,122,016 (GRCm39) V108A probably benign Het
Rbm14 A G 19: 4,852,577 (GRCm39) probably benign Het
Rfc1 A T 5: 65,434,795 (GRCm39) V657E probably damaging Het
Rhcg A T 7: 79,250,371 (GRCm39) N237K probably damaging Het
Rpgrip1 A G 14: 52,397,617 (GRCm39) Q1302R probably benign Het
Rragc A G 4: 123,818,645 (GRCm39) M287V possibly damaging Het
Scn7a A G 2: 66,572,301 (GRCm39) probably null Het
Sema6a C T 18: 47,414,410 (GRCm39) C506Y probably damaging Het
Senp1 G T 15: 97,964,412 (GRCm39) H267Q possibly damaging Het
Skor2 A G 18: 76,946,578 (GRCm39) E100G unknown Het
Slc38a11 A T 2: 65,147,365 (GRCm39) C371S probably benign Het
Snai3 G A 8: 123,181,629 (GRCm39) A276V probably benign Het
Sp110 C G 1: 85,516,839 (GRCm39) E219D probably damaging Het
Spag6 C T 2: 18,720,525 (GRCm39) T99I probably benign Het
Spop A G 11: 95,376,675 (GRCm39) I243V possibly damaging Het
Sra1 A T 18: 36,800,496 (GRCm39) probably benign Het
Stag3 T A 5: 138,288,485 (GRCm39) S140T possibly damaging Het
Stx16 G A 2: 173,935,292 (GRCm39) G156R probably damaging Het
Tbc1d2b G C 9: 90,089,925 (GRCm39) A868G probably benign Het
Tead2 A G 7: 44,870,166 (GRCm39) probably benign Het
Tmem53 C A 4: 117,125,669 (GRCm39) H261N probably damaging Het
Ube4a A T 9: 44,844,627 (GRCm39) S932T probably damaging Het
Usp9y A T Y: 1,381,339 (GRCm39) D827E probably damaging Het
Vmn2r53 T C 7: 12,334,733 (GRCm39) E309G probably damaging Het
Wrn T C 8: 33,758,806 (GRCm39) S1026G probably benign Het
Zfp646 G A 7: 127,484,626 (GRCm39) A1760T probably damaging Het
Other mutations in Pcdh1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00714:Pcdh1 APN 18 38,331,782 (GRCm39) missense possibly damaging 0.65
IGL00919:Pcdh1 APN 18 38,335,865 (GRCm39) nonsense probably null
IGL01744:Pcdh1 APN 18 38,336,302 (GRCm39) missense probably damaging 1.00
PIT4260001:Pcdh1 UTSW 18 38,336,419 (GRCm39) missense probably damaging 0.99
R0542:Pcdh1 UTSW 18 38,322,975 (GRCm39) missense probably damaging 0.99
R1449:Pcdh1 UTSW 18 38,322,929 (GRCm39) missense probably damaging 0.99
R1540:Pcdh1 UTSW 18 38,322,779 (GRCm39) missense probably benign 0.01
R1642:Pcdh1 UTSW 18 38,332,283 (GRCm39) missense possibly damaging 0.84
R1672:Pcdh1 UTSW 18 38,325,233 (GRCm39) missense probably damaging 1.00
R1695:Pcdh1 UTSW 18 38,335,921 (GRCm39) missense probably damaging 1.00
R1727:Pcdh1 UTSW 18 38,336,085 (GRCm39) nonsense probably null
R1781:Pcdh1 UTSW 18 38,322,977 (GRCm39) missense probably damaging 1.00
R1793:Pcdh1 UTSW 18 38,331,938 (GRCm39) missense probably damaging 0.99
R1839:Pcdh1 UTSW 18 38,332,538 (GRCm39) missense possibly damaging 0.82
R1843:Pcdh1 UTSW 18 38,325,278 (GRCm39) splice site probably null
R1882:Pcdh1 UTSW 18 38,335,895 (GRCm39) missense possibly damaging 0.49
R2261:Pcdh1 UTSW 18 38,331,710 (GRCm39) missense probably benign 0.01
R2262:Pcdh1 UTSW 18 38,331,710 (GRCm39) missense probably benign 0.01
R2263:Pcdh1 UTSW 18 38,331,710 (GRCm39) missense probably benign 0.01
R2511:Pcdh1 UTSW 18 38,332,532 (GRCm39) missense possibly damaging 0.95
R2937:Pcdh1 UTSW 18 38,322,815 (GRCm39) missense probably benign 0.40
R3941:Pcdh1 UTSW 18 38,332,511 (GRCm39) missense probably benign 0.02
R3942:Pcdh1 UTSW 18 38,332,511 (GRCm39) missense probably benign 0.02
R4057:Pcdh1 UTSW 18 38,331,950 (GRCm39) missense probably damaging 0.98
R4155:Pcdh1 UTSW 18 38,336,159 (GRCm39) missense probably damaging 0.99
R4169:Pcdh1 UTSW 18 38,331,358 (GRCm39) missense probably damaging 1.00
R4617:Pcdh1 UTSW 18 38,330,913 (GRCm39) missense probably benign 0.00
R4690:Pcdh1 UTSW 18 38,336,528 (GRCm39) missense probably benign 0.33
R4825:Pcdh1 UTSW 18 38,322,912 (GRCm39) missense possibly damaging 0.77
R5201:Pcdh1 UTSW 18 38,331,971 (GRCm39) missense probably damaging 0.98
R5266:Pcdh1 UTSW 18 38,325,252 (GRCm39) missense probably damaging 1.00
R5267:Pcdh1 UTSW 18 38,325,252 (GRCm39) missense probably damaging 1.00
R5351:Pcdh1 UTSW 18 38,330,819 (GRCm39) missense probably damaging 1.00
R5568:Pcdh1 UTSW 18 38,330,420 (GRCm39) missense probably damaging 1.00
R5731:Pcdh1 UTSW 18 38,331,651 (GRCm39) missense probably damaging 1.00
R6043:Pcdh1 UTSW 18 38,336,327 (GRCm39) missense probably damaging 0.97
R6278:Pcdh1 UTSW 18 38,332,263 (GRCm39) missense probably benign 0.29
R6333:Pcdh1 UTSW 18 38,331,860 (GRCm39) missense probably benign 0.25
R6498:Pcdh1 UTSW 18 38,330,490 (GRCm39) missense probably benign 0.18
R6937:Pcdh1 UTSW 18 38,336,528 (GRCm39) missense possibly damaging 0.86
R6994:Pcdh1 UTSW 18 38,331,553 (GRCm39) missense probably damaging 1.00
R7242:Pcdh1 UTSW 18 38,336,270 (GRCm39) missense probably benign 0.06
R7289:Pcdh1 UTSW 18 38,322,966 (GRCm39) missense probably damaging 0.99
R7391:Pcdh1 UTSW 18 38,335,838 (GRCm39) missense possibly damaging 0.95
R7702:Pcdh1 UTSW 18 38,336,569 (GRCm39) missense unknown
R7738:Pcdh1 UTSW 18 38,330,529 (GRCm39) missense probably benign 0.02
R7849:Pcdh1 UTSW 18 38,322,662 (GRCm39) missense probably benign 0.01
R7941:Pcdh1 UTSW 18 38,332,133 (GRCm39) missense probably damaging 1.00
R8109:Pcdh1 UTSW 18 38,332,049 (GRCm39) missense probably damaging 1.00
R8675:Pcdh1 UTSW 18 38,332,229 (GRCm39) missense probably damaging 1.00
R8851:Pcdh1 UTSW 18 38,325,155 (GRCm39) missense probably damaging 1.00
R8947:Pcdh1 UTSW 18 38,332,073 (GRCm39) missense possibly damaging 0.89
R9443:Pcdh1 UTSW 18 38,330,633 (GRCm39) missense probably damaging 1.00
R9448:Pcdh1 UTSW 18 38,330,492 (GRCm39) missense probably damaging 1.00
R9608:Pcdh1 UTSW 18 38,330,904 (GRCm39) missense possibly damaging 0.91
X0027:Pcdh1 UTSW 18 38,322,841 (GRCm39) nonsense probably null
Z1088:Pcdh1 UTSW 18 38,331,120 (GRCm39) missense probably damaging 1.00
Z1176:Pcdh1 UTSW 18 38,331,741 (GRCm39) missense possibly damaging 0.79
Predicted Primers PCR Primer
(F):5'- ATGGGACTGTTCTCAGACAGC -3'
(R):5'- AATGACAACACGCCGAACTTTG -3'

Sequencing Primer
(F):5'- ACAGCTCGGCTTCGTAGGTAG -3'
(R):5'- CGAACTTTGCCTCGCCAG -3'
Posted On 2017-01-03