Incidental Mutation 'R5034:Pcdh9'
ID 389465
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 042625-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.194) question?
Stock # R5034 (G1)
Quality Score 225
Status Validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 93564285 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 1023 (D1023V)
Ref Sequence ENSEMBL: ENSMUSP00000141759 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000195376] [ENSMUST00000195826]
AlphaFold F8VPK8
Predicted Effect probably benign
Transcript: ENSMUST00000068992
AA Change: D1057V

PolyPhen 2 Score 0.069 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: D1057V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192221
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421

DomainStartEndE-ValueType
CA 41 127 1.01e-20 SMART
CA 151 233 2.34e-25 SMART
CA 263 344 2.14e-19 SMART
CA 368 447 4.27e-28 SMART
CA 471 550 2.45e-28 SMART
CA 577 659 1.01e-6 SMART
transmembrane domain 691 713 N/A INTRINSIC
low complexity region 735 760 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193901
AA Change: D1023V

PolyPhen 2 Score 0.134 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: D1023V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194129
Predicted Effect probably benign
Transcript: ENSMUST00000195376
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 4.1e-5 SMART
CA 164 250 4.8e-23 SMART
CA 274 356 1.2e-27 SMART
CA 386 467 1.1e-21 SMART
CA 491 570 2e-30 SMART
CA 594 673 1.2e-30 SMART
CA 700 782 4.9e-9 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000195826
AA Change: D1057V

PolyPhen 2 Score 0.069 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: D1057V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Meta Mutation Damage Score 0.1973 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.6%
Validation Efficiency 97% (67/69)
MGI Phenotype FUNCTION: This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca T A 11: 84,136,090 (GRCm39) S482T probably benign Het
Adam6b G T 12: 113,454,547 (GRCm39) G455C probably damaging Het
Ahsg C A 16: 22,717,650 (GRCm39) P237Q probably damaging Het
Asxl2 A G 12: 3,552,193 (GRCm39) S1312G probably damaging Het
Brinp3 C T 1: 146,603,458 (GRCm39) probably benign Het
Col12a1 T C 9: 79,564,649 (GRCm39) H1677R probably damaging Het
Cops7a A G 6: 124,939,583 (GRCm39) probably null Het
Csmd2 G A 4: 127,952,901 (GRCm39) A117T probably damaging Het
Csmd3 T C 15: 47,492,683 (GRCm39) R3153G possibly damaging Het
Dctn4 A G 18: 60,685,956 (GRCm39) N342D probably benign Het
Dennd5a A T 7: 109,499,004 (GRCm39) I953N probably damaging Het
Dmwd T C 7: 18,814,219 (GRCm39) S290P probably damaging Het
Dsc1 T A 18: 20,228,084 (GRCm39) Y424F possibly damaging Het
Far2 C A 6: 148,074,939 (GRCm39) L391M probably benign Het
Foxd3 G A 4: 99,545,327 (GRCm39) G156S probably damaging Het
Galk2 A T 2: 125,771,495 (GRCm39) E173D probably benign Het
Hcar1 T C 5: 124,017,732 (GRCm39) probably benign Het
Hsd17b11 C T 5: 104,166,087 (GRCm39) V91M possibly damaging Het
Ighv1-77 C T 12: 115,825,494 (GRCm39) C115Y probably damaging Het
Ighv9-2 A G 12: 114,073,025 (GRCm39) F9S probably damaging Het
Kdm6b A G 11: 69,292,736 (GRCm39) probably benign Het
Kif21a T A 15: 90,852,561 (GRCm39) R890W probably null Het
Lin9 T A 1: 180,496,763 (GRCm39) L351I probably benign Het
Magel2 A T 7: 62,029,616 (GRCm39) H840L unknown Het
Mrgpra4 A G 7: 47,631,317 (GRCm39) F95L probably benign Het
Myo7b A G 18: 32,104,440 (GRCm39) L1436P probably damaging Het
Nf1 C T 11: 79,334,976 (GRCm39) P943S probably damaging Het
Obscn T A 11: 58,952,502 (GRCm39) R4153* probably null Het
Oosp2 T C 19: 11,628,899 (GRCm39) I67M probably damaging Het
Or5m13b C A 2: 85,753,891 (GRCm39) S93Y probably damaging Het
Pcdhb14 T C 18: 37,581,859 (GRCm39) S322P probably damaging Het
Pde2a A G 7: 101,151,231 (GRCm39) D285G probably benign Het
Pde5a G C 3: 122,646,235 (GRCm39) G809R probably damaging Het
Pde5a G T 3: 122,646,236 (GRCm39) G809V probably damaging Het
Pphln1 T C 15: 93,350,010 (GRCm39) V120A probably benign Het
Rictor T C 15: 6,797,576 (GRCm39) S311P probably damaging Het
Rilpl1 T C 5: 124,631,887 (GRCm39) D153G probably damaging Het
Rmdn3 G T 2: 118,978,058 (GRCm39) A181E probably damaging Het
Rnf213 G A 11: 119,301,633 (GRCm39) V369M probably damaging Het
Scyl1 T A 19: 5,810,022 (GRCm39) R601S probably benign Het
Sdcbp G A 4: 6,393,118 (GRCm39) probably null Het
Septin8 A G 11: 53,425,265 (GRCm39) T53A probably damaging Het
Sfpq A G 4: 126,917,462 (GRCm39) probably benign Het
Slc35b3 A G 13: 39,127,134 (GRCm39) Y163H probably damaging Het
Sra1 A G 18: 36,812,048 (GRCm39) probably null Het
Sspo A T 6: 48,457,757 (GRCm39) N3231Y possibly damaging Het
Tcf3 A G 10: 80,253,377 (GRCm39) V218A possibly damaging Het
Tgm3 T C 2: 129,879,404 (GRCm39) V332A possibly damaging Het
Tmprss11f C T 5: 86,739,243 (GRCm39) probably benign Het
Trbv4 A G 6: 41,036,624 (GRCm39) T50A probably benign Het
Trdv2-2 C A 14: 54,198,882 (GRCm39) Y57* probably null Het
Trim50 T C 5: 135,396,147 (GRCm39) V365A possibly damaging Het
Ubash3b T C 9: 40,941,036 (GRCm39) Q245R probably benign Het
Ulk3 T A 9: 57,501,047 (GRCm39) V338E possibly damaging Het
Usf3 A C 16: 44,036,762 (GRCm39) K414T probably damaging Het
Usp48 C T 4: 137,334,068 (GRCm39) R161* probably null Het
Vps18 A T 2: 119,123,787 (GRCm39) D238V probably benign Het
Vps35l T C 7: 118,390,611 (GRCm39) V368A probably damaging Het
Zfp354c T C 11: 50,705,866 (GRCm39) E403G probably benign Het
Zscan18 A G 7: 12,508,072 (GRCm39) V476A probably damaging Het
Other mutations in Pcdh9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00482:Pcdh9 APN 14 93,564,130 (GRCm39) missense probably damaging 1.00
IGL02183:Pcdh9 APN 14 94,123,720 (GRCm39) missense probably benign 0.01
IGL02244:Pcdh9 APN 14 93,564,204 (GRCm39) missense probably damaging 1.00
IGL02571:Pcdh9 APN 14 93,798,023 (GRCm39) splice site probably benign
IGL03018:Pcdh9 APN 14 93,253,012 (GRCm39) missense probably null
I1329:Pcdh9 UTSW 14 94,123,645 (GRCm39) missense probably benign 0.00
R0027:Pcdh9 UTSW 14 94,126,081 (GRCm39) missense probably null 0.99
R0027:Pcdh9 UTSW 14 94,126,081 (GRCm39) missense probably null 0.99
R0477:Pcdh9 UTSW 14 94,125,114 (GRCm39) missense probably damaging 0.99
R0499:Pcdh9 UTSW 14 94,123,671 (GRCm39) missense probably damaging 1.00
R0787:Pcdh9 UTSW 14 94,124,193 (GRCm39) missense possibly damaging 0.88
R1205:Pcdh9 UTSW 14 94,123,501 (GRCm39) missense probably benign 0.01
R1616:Pcdh9 UTSW 14 94,124,405 (GRCm39) nonsense probably null
R1620:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1622:Pcdh9 UTSW 14 94,123,311 (GRCm39) missense probably benign 0.03
R1708:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1721:Pcdh9 UTSW 14 94,125,471 (GRCm39) missense probably damaging 1.00
R1753:Pcdh9 UTSW 14 94,124,661 (GRCm39) missense probably benign 0.33
R1799:Pcdh9 UTSW 14 94,126,107 (GRCm39) missense probably benign 0.36
R1867:Pcdh9 UTSW 14 94,125,471 (GRCm39) missense probably damaging 1.00
R1987:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1988:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R2444:Pcdh9 UTSW 14 94,124,227 (GRCm39) missense probably benign 0.10
R3895:Pcdh9 UTSW 14 94,124,974 (GRCm39) missense probably damaging 1.00
R3926:Pcdh9 UTSW 14 94,124,246 (GRCm39) nonsense probably null
R4166:Pcdh9 UTSW 14 94,124,956 (GRCm39) nonsense probably null
R4429:Pcdh9 UTSW 14 94,124,820 (GRCm39) missense probably damaging 0.96
R4589:Pcdh9 UTSW 14 94,125,628 (GRCm39) missense probably damaging 1.00
R4604:Pcdh9 UTSW 14 94,124,616 (GRCm39) missense probably damaging 1.00
R4607:Pcdh9 UTSW 14 93,253,009 (GRCm39) missense probably benign 0.08
R4621:Pcdh9 UTSW 14 94,125,079 (GRCm39) missense probably benign 0.12
R4624:Pcdh9 UTSW 14 94,123,845 (GRCm39) missense probably damaging 1.00
R4712:Pcdh9 UTSW 14 94,126,067 (GRCm39) missense probably damaging 1.00
R4788:Pcdh9 UTSW 14 94,124,851 (GRCm39) missense probably damaging 1.00
R4831:Pcdh9 UTSW 14 94,125,377 (GRCm39) missense probably damaging 1.00
R4883:Pcdh9 UTSW 14 94,126,164 (GRCm39) missense possibly damaging 0.83
R5175:Pcdh9 UTSW 14 94,125,879 (GRCm39) missense probably damaging 1.00
R5637:Pcdh9 UTSW 14 94,123,198 (GRCm39) missense possibly damaging 0.91
R5743:Pcdh9 UTSW 14 94,124,160 (GRCm39) missense probably damaging 1.00
R5753:Pcdh9 UTSW 14 94,125,597 (GRCm39) missense probably damaging 1.00
R5770:Pcdh9 UTSW 14 94,124,379 (GRCm39) missense probably damaging 1.00
R5900:Pcdh9 UTSW 14 93,564,156 (GRCm39) missense probably damaging 0.98
R5986:Pcdh9 UTSW 14 94,124,484 (GRCm39) missense probably damaging 1.00
R6052:Pcdh9 UTSW 14 94,123,282 (GRCm39) missense probably benign 0.40
R6113:Pcdh9 UTSW 14 94,124,544 (GRCm39) missense probably damaging 1.00
R6223:Pcdh9 UTSW 14 93,253,169 (GRCm39) missense probably benign 0.18
R6415:Pcdh9 UTSW 14 93,253,278 (GRCm39) missense possibly damaging 0.83
R6435:Pcdh9 UTSW 14 94,125,280 (GRCm39) missense probably benign 0.01
R7064:Pcdh9 UTSW 14 94,123,585 (GRCm39) missense probably damaging 1.00
R7143:Pcdh9 UTSW 14 94,125,708 (GRCm39) missense probably damaging 0.99
R7219:Pcdh9 UTSW 14 93,253,216 (GRCm39) missense possibly damaging 0.87
R7262:Pcdh9 UTSW 14 93,253,141 (GRCm39) missense probably benign 0.01
R7354:Pcdh9 UTSW 14 94,125,706 (GRCm39) missense probably benign 0.28
R7369:Pcdh9 UTSW 14 94,123,803 (GRCm39) missense possibly damaging 0.67
R7427:Pcdh9 UTSW 14 94,124,547 (GRCm39) missense probably damaging 1.00
R7428:Pcdh9 UTSW 14 94,124,547 (GRCm39) missense probably damaging 1.00
R7780:Pcdh9 UTSW 14 94,123,987 (GRCm39) missense possibly damaging 0.91
R7870:Pcdh9 UTSW 14 94,124,693 (GRCm39) missense probably damaging 0.97
R7921:Pcdh9 UTSW 14 93,253,001 (GRCm39) missense probably benign
R8052:Pcdh9 UTSW 14 94,123,222 (GRCm39) missense probably benign 0.00
R8252:Pcdh9 UTSW 14 94,126,086 (GRCm39) missense probably damaging 1.00
R8671:Pcdh9 UTSW 14 94,126,086 (GRCm39) missense probably damaging 1.00
R8672:Pcdh9 UTSW 14 94,124,529 (GRCm39) missense probably benign 0.08
R8724:Pcdh9 UTSW 14 94,124,583 (GRCm39) missense probably benign 0.19
R8974:Pcdh9 UTSW 14 94,125,113 (GRCm39) missense probably benign 0.20
R9044:Pcdh9 UTSW 14 94,124,247 (GRCm39) missense probably damaging 1.00
R9486:Pcdh9 UTSW 14 93,797,956 (GRCm39) missense possibly damaging 0.73
R9534:Pcdh9 UTSW 14 94,123,656 (GRCm39) missense probably damaging 0.99
X0012:Pcdh9 UTSW 14 94,124,080 (GRCm39) missense possibly damaging 0.71
X0067:Pcdh9 UTSW 14 93,564,285 (GRCm39) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- TACAGCCCATTGTCCGTCAC -3'
(R):5'- AAAATGCTGGCTCTTTGTTCC -3'

Sequencing Primer
(F):5'- ATTGTCCGTCACTGGCACAAC -3'
(R):5'- AAAATGCTGGCTCTTTGTTCCTAGAC -3'
Posted On 2016-06-06