Incidental Mutation 'R6435:Pcdh9'
ID 518758
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 044573-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.166) question?
Stock # R6435 (G1)
Quality Score 225.009
Status Validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 94125280 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Serine at position 297 (P297S)
Ref Sequence ENSEMBL: ENSMUSP00000141602 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000194056] [ENSMUST00000195376] [ENSMUST00000195826]
AlphaFold F8VPK8
Predicted Effect probably benign
Transcript: ENSMUST00000068992
AA Change: P297S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: P297S

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
AA Change: P174S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: P174S

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 noncoding transcript
Transcript: ENSMUST00000192817
Predicted Effect probably benign
Transcript: ENSMUST00000193901
AA Change: P297S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: P297S

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: ENSMUST00000194056
AA Change: P297S

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: P297S

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 860 873 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194129
Predicted Effect probably benign
Transcript: ENSMUST00000195376
AA Change: P297S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: P297S

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: P297S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: P297S

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.2%
Validation Efficiency 100% (32/32)
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: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abl1 A T 2: 31,691,561 (GRCm39) T1027S possibly damaging Het
Ablim1 T C 19: 57,049,787 (GRCm39) I159V possibly damaging Het
Adcy1 A G 11: 7,111,367 (GRCm39) N886S possibly damaging Het
Baz1b G A 5: 135,266,799 (GRCm39) D1203N probably damaging Het
Chmp2a A T 7: 12,766,701 (GRCm39) Y72* probably null Het
Col6a1 A T 10: 76,546,957 (GRCm39) I755N unknown Het
Defa24 T A 8: 22,224,690 (GRCm39) F46L possibly damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Gcn1 A T 5: 115,749,081 (GRCm39) probably null Het
Gfpt2 A G 11: 49,726,478 (GRCm39) S628G probably benign Het
Hsdl2 C A 4: 59,610,668 (GRCm39) Q222K unknown Het
Ighv1-9 T A 12: 114,547,206 (GRCm39) I111F probably benign Het
Itch G A 2: 155,051,049 (GRCm39) D579N probably benign Het
Jdp2 A T 12: 85,655,132 (GRCm39) K65M probably damaging Het
Kif15 A T 9: 122,815,556 (GRCm39) E222V probably damaging Het
Map1b A G 13: 99,652,871 (GRCm39) V42A probably damaging Het
Mecom T A 3: 30,034,398 (GRCm39) E426V probably damaging Het
Meiosin T C 7: 18,834,844 (GRCm39) probably benign Het
Mfsd6 G T 1: 52,748,603 (GRCm39) Y87* probably null Het
Mybpc2 A G 7: 44,155,481 (GRCm39) V924A possibly damaging Het
Naip6 A T 13: 100,431,249 (GRCm39) M1196K probably benign Het
Nscme3l T C 19: 5,553,446 (GRCm39) I112V probably benign Het
Or52n5 A G 7: 104,588,041 (GRCm39) M103V probably damaging Het
Pold1 G A 7: 44,188,202 (GRCm39) R559C probably damaging Het
Rgs21 A G 1: 144,395,565 (GRCm39) F108L probably damaging Het
Runx1 A T 16: 92,441,183 (GRCm39) S209T possibly damaging Het
Sdccag8 G T 1: 176,642,428 (GRCm39) probably benign Het
Smc1b C T 15: 84,976,232 (GRCm39) R825Q probably benign Het
Srgap1 T C 10: 121,636,732 (GRCm39) D741G possibly damaging Het
Srsf11 C T 3: 157,728,981 (GRCm39) probably benign Homo
Tsc1 G A 2: 28,566,464 (GRCm39) V627M probably benign Het
Vmn2r106 C T 17: 20,488,725 (GRCm39) C558Y probably damaging Het
Zfp612 A G 8: 110,815,952 (GRCm39) I347M 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
R5034:Pcdh9 UTSW 14 93,564,285 (GRCm39) missense probably benign 0.13
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
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'- TGGGACTTATAATGTACCTGAGGTC -3'
(R):5'- AGCACAGCTATTCTCCAGGTC -3'

Sequencing Primer
(F):5'- AATGTACCTGAGGTCTATGTTTGGAG -3'
(R):5'- GCTATTCTCCAGGTCACAGTAAG -3'
Posted On 2018-05-24