Incidental Mutation 'R0542:Pcdh1'
ID 50015
Institutional Source Beutler Lab
Gene Symbol Pcdh1
Ensembl Gene ENSMUSG00000051375
Gene Name protocadherin 1
Synonyms 2010005A06Rik
MMRRC Submission 038734-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.365) question?
Stock # R0542 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 38318967-38345023 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 38322975 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Isoleucine at position 953 (V953I)
Ref Sequence ENSEMBL: ENSMUSP00000125576 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000160721] [ENSMUST00000161701]
AlphaFold Q8CFX3
Predicted Effect probably benign
Transcript: ENSMUST00000160721
SMART Domains Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375

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: V953I

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: V953I

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
Meta Mutation Damage Score 0.1472 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 95.0%
Validation Efficiency 99% (70/71)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd12b C A 12: 70,210,269 (GRCm39) N71K possibly damaging Het
Adgrl2 A G 3: 148,564,854 (GRCm39) I242T probably damaging Het
Adgrv1 A G 13: 81,721,437 (GRCm39) S714P probably damaging Het
Agap3 G A 5: 24,705,184 (GRCm39) R704Q possibly damaging Het
Ankrd11 T C 8: 123,622,509 (GRCm39) R448G probably damaging Het
Anks1b T C 10: 89,909,829 (GRCm39) probably benign Het
Caml A T 13: 55,770,974 (GRCm39) Q24L possibly damaging Het
Cdc14b G A 13: 64,391,497 (GRCm39) T124I probably benign Het
Clca3a2 A G 3: 144,781,571 (GRCm39) probably benign Het
Col12a1 A G 9: 79,512,610 (GRCm39) probably null Het
Crispld1 T C 1: 17,816,992 (GRCm39) V183A possibly damaging Het
Cstdc1 A G 2: 148,624,092 (GRCm39) N22S probably benign Het
Dhx40 C T 11: 86,695,082 (GRCm39) probably null Het
Dmxl1 T A 18: 50,026,761 (GRCm39) D1956E probably benign Het
Dsc2 A G 18: 20,184,283 (GRCm39) V35A probably damaging Het
Dync2i2 A G 2: 29,921,837 (GRCm39) V508A probably damaging Het
Elovl2 A G 13: 41,345,452 (GRCm39) probably benign Het
Gapvd1 T C 2: 34,615,048 (GRCm39) probably benign Het
Gnaq T A 19: 16,196,982 (GRCm39) I56N probably damaging Het
Gpr139 T C 7: 118,744,306 (GRCm39) D93G probably benign Het
Hars1 C T 18: 36,904,234 (GRCm39) R215H probably benign Het
Helz2 C A 2: 180,873,882 (GRCm39) W2204L probably damaging Het
Ift70b A G 2: 75,767,055 (GRCm39) V566A probably damaging Het
Itgb6 A T 2: 60,435,480 (GRCm39) C757S possibly damaging Het
Kpnb1 G A 11: 97,078,398 (GRCm39) T5I probably benign Het
Krt82 T C 15: 101,454,035 (GRCm39) probably benign Het
Lgals9 T A 11: 78,860,546 (GRCm39) K175N possibly damaging Het
Lrp2 A G 2: 69,258,998 (GRCm39) I4564T probably benign Het
Mblac1 A G 5: 138,192,798 (GRCm39) T47A possibly damaging Het
Med12l G A 3: 58,949,822 (GRCm39) D182N probably damaging Het
Megf9 A G 4: 70,353,585 (GRCm39) I407T probably benign Het
Mtmr6 A T 14: 60,529,578 (GRCm39) probably null Het
Mtor A G 4: 148,624,907 (GRCm39) T2173A probably benign Het
Mzt1 A T 14: 99,277,938 (GRCm39) probably benign Het
Narf T C 11: 121,143,690 (GRCm39) L444P probably damaging Het
Nsd1 A T 13: 55,408,271 (GRCm39) Q1305L possibly damaging Het
Ntsr1 A G 2: 180,184,374 (GRCm39) Y359C probably damaging Het
Olfm1 A G 2: 28,104,640 (GRCm39) D159G possibly damaging Het
Or2l13b A T 16: 19,348,732 (GRCm39) *313R probably null Het
Pcdhb11 A T 18: 37,556,887 (GRCm39) D739V probably damaging Het
Pdgfd A G 9: 6,359,769 (GRCm39) N280S probably damaging Het
Per2 A T 1: 91,366,054 (GRCm39) probably null Het
Pfkp G T 13: 6,672,028 (GRCm39) C122* probably null Het
Plxna4 G A 6: 32,169,232 (GRCm39) R1322W probably damaging Het
Ppox A G 1: 171,106,818 (GRCm39) L202P probably damaging Het
Ppp1r3e G A 14: 55,114,588 (GRCm39) P58L probably benign Het
Prr23a2 A C 9: 98,739,086 (GRCm39) N148T probably benign Het
Psd T C 19: 46,302,649 (GRCm39) T842A probably damaging Het
Ranbp2 C T 10: 58,314,236 (GRCm39) A1652V probably benign Het
Rragd G A 4: 33,007,103 (GRCm39) V144M probably damaging Het
Sema6a T G 18: 47,381,643 (GRCm39) D968A probably damaging Het
Slc30a5 A T 13: 100,945,793 (GRCm39) probably null Het
Snx17 G T 5: 31,353,895 (GRCm39) probably null Het
Styxl2 A T 1: 165,928,853 (GRCm39) M253K possibly damaging Het
Syt14 G T 1: 192,613,111 (GRCm39) T563K probably damaging Het
Tada3 T C 6: 113,352,175 (GRCm39) K85E probably damaging Het
Tspear T C 10: 77,716,921 (GRCm39) V532A probably benign Het
Ttn A T 2: 76,723,453 (GRCm39) C6426S possibly damaging Het
Unc79 T C 12: 103,060,437 (GRCm39) probably benign Het
Usp19 A G 9: 108,371,584 (GRCm39) probably null Het
Vav3 G A 3: 109,434,746 (GRCm39) D426N probably damaging Het
Vezt T C 10: 93,842,958 (GRCm39) probably null Het
Vldlr G T 19: 27,213,655 (GRCm39) R114L probably benign Het
Wwc2 C T 8: 48,321,414 (GRCm39) V567I unknown Het
Zfp423 T C 8: 88,507,237 (GRCm39) T911A probably damaging Het
Zfp719 A G 7: 43,238,677 (GRCm39) probably null Het
Zkscan16 A T 4: 58,956,597 (GRCm39) H293L possibly damaging Het
Zkscan6 A C 11: 65,719,525 (GRCm39) N515T possibly damaging Het
Znfx1 A G 2: 166,897,575 (GRCm39) S450P 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
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
R5729:Pcdh1 UTSW 18 38,335,999 (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'- TCACAGGTAGATCTCACGCTTGGC -3'
(R):5'- TCCTAGAGGGCAGCAGAATAGTGAC -3'

Sequencing Primer
(F):5'- CTACTGTGGGAGAAGGCACTG -3'
(R):5'- ATAGTGACAGCGGGCCAC -3'
Posted On 2013-06-12