Incidental Mutation 'R9486:Pcdh9'
ID 716616
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission
Accession Numbers
Essential gene? Probably non essential (E-score: 0.194) question?
Stock # R9486 (G1)
Quality Score 225.009
Status Not validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 93797956 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 1032 (S1032P)
Ref Sequence ENSEMBL: ENSMUSP00000070935 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000195376] [ENSMUST00000195826]
AlphaFold F8VPK8
Predicted Effect possibly damaging
Transcript: ENSMUST00000068992
AA Change: S1032P

PolyPhen 2 Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: S1032P

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
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421

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
Predicted Effect probably damaging
Transcript: ENSMUST00000195376
AA Change: S1032P

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: S1032P

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 possibly damaging
Transcript: ENSMUST00000195826
AA Change: S1032P

PolyPhen 2 Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: S1032P

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
Validation Efficiency
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2ml1 A G 6: 128,546,942 (GRCm39) F396L probably damaging Het
Abca13 T C 11: 9,240,621 (GRCm39) I828T possibly damaging Het
Ace3 A T 11: 105,896,219 (GRCm39) T722S probably benign Het
Acot2 A G 12: 84,039,426 (GRCm39) T312A probably benign Het
Adra2a A G 19: 54,035,963 (GRCm39) I440V probably damaging Het
Arhgap22 T A 14: 33,073,303 (GRCm39) M4K probably benign Het
Atp8b3 C T 10: 80,366,821 (GRCm39) C259Y probably damaging Het
Bcl2 T A 1: 106,471,109 (GRCm39) Y199F probably benign Het
Brca1 A T 11: 101,414,520 (GRCm39) C1205S probably benign Het
Col7a1 T C 9: 108,811,396 (GRCm39) V2743A unknown Het
Crybg1 A G 10: 43,880,145 (GRCm39) probably benign Het
Cyp2c40 T A 19: 39,755,808 (GRCm39) H502L probably benign Het
Cyp2c40 A T 19: 39,796,050 (GRCm39) Y109* probably null Het
Cyp4a29 T C 4: 115,106,916 (GRCm39) M191T probably damaging Het
Dcaf1 A G 9: 106,735,916 (GRCm39) R955G possibly damaging Het
Dcaf4 G T 12: 83,582,726 (GRCm39) A274S probably damaging Het
Dlx1 A G 2: 71,362,828 (GRCm39) H245R probably damaging Het
Dnah14 A G 1: 181,508,494 (GRCm39) N1891D possibly damaging Het
Dock10 A T 1: 80,479,452 (GRCm39) V2167D unknown Het
Epyc A G 10: 97,511,697 (GRCm39) Q230R probably benign Het
Etnk1 G A 6: 143,130,310 (GRCm39) R143H probably damaging Het
Fhip2b T C 14: 70,826,479 (GRCm39) D203G probably benign Het
Fmo2 T C 1: 162,708,292 (GRCm39) E281G probably damaging Het
Gm2042 T A 12: 87,925,963 (GRCm39) Y304N possibly damaging Het
Hecw2 T C 1: 53,852,466 (GRCm39) D1551G probably damaging Het
Hgd A T 16: 37,413,811 (GRCm39) D91V probably benign Het
Hspa12a A G 19: 58,797,891 (GRCm39) F276L probably benign Het
Ifitm10 C T 7: 141,909,812 (GRCm39) V95M probably damaging Het
Ints3 G A 3: 90,313,579 (GRCm39) R350* probably null Het
Kdm4c T A 4: 74,252,966 (GRCm39) I511K probably benign Het
Kif27 A G 13: 58,492,348 (GRCm39) S264P probably damaging Het
L1td1 A G 4: 98,624,899 (GRCm39) T365A probably benign Het
Ltbp2 T A 12: 84,878,648 (GRCm39) T304S possibly damaging Het
Mamdc4 T A 2: 25,455,164 (GRCm39) Y962F probably benign Het
Map3k4 C T 17: 12,489,860 (GRCm39) A524T probably damaging Het
Mfsd8 C T 3: 40,789,627 (GRCm39) R140H probably damaging Het
Mmp3 A G 9: 7,451,256 (GRCm39) I331V possibly damaging Het
Mpdz T A 4: 81,254,043 (GRCm39) I1030F probably damaging Het
Mtx1 A T 3: 89,120,163 (GRCm39) C62S Het
Muc20 A T 16: 32,615,248 (GRCm39) V43E possibly damaging Het
Naa25 A G 5: 121,577,958 (GRCm39) E955G probably damaging Het
Nelfcd A G 2: 174,268,635 (GRCm39) Y562C probably damaging Het
Nsd2 T A 5: 34,018,493 (GRCm39) M509K probably benign Het
Obscn T C 11: 58,918,272 (GRCm39) T207A Het
Or1ad1 T A 11: 50,875,691 (GRCm39) H54Q possibly damaging Het
Or4a39 C T 2: 89,236,959 (GRCm39) V155M possibly damaging Het
Or4k5 T A 14: 50,385,672 (GRCm39) I220L probably benign Het
Osbpl11 A T 16: 33,006,283 (GRCm39) N37I possibly damaging Het
Pde6b T A 5: 108,551,241 (GRCm39) I175N probably damaging Het
Pfkl T A 10: 77,824,184 (GRCm39) M735L probably benign Het
Pkp4 T C 2: 59,138,722 (GRCm39) V324A probably benign Het
Ptprb T A 10: 116,155,494 (GRCm39) C462* probably null Het
Rasal3 T C 17: 32,617,910 (GRCm39) N221S probably benign Het
Reep1 A T 6: 71,684,969 (GRCm39) I6F probably benign Het
Rhobtb1 T A 10: 69,106,621 (GRCm39) F457L probably damaging Het
Ryr1 T C 7: 28,777,965 (GRCm39) N2184S probably benign Het
Scn11a T G 9: 119,624,774 (GRCm39) H516P possibly damaging Het
Sipa1l1 T C 12: 82,404,139 (GRCm39) probably null Het
Slc17a7 A G 7: 44,821,606 (GRCm39) N381S possibly damaging Het
Slc38a3 C T 9: 107,536,322 (GRCm39) V25M probably benign Het
Spag1 T G 15: 36,181,954 (GRCm39) D37E probably damaging Het
Spib G T 7: 44,178,815 (GRCm39) D114E possibly damaging Het
Tpx2 A T 2: 152,726,933 (GRCm39) Y400F probably damaging Het
Trhde A G 10: 114,532,014 (GRCm39) I362T possibly damaging Het
Usp17ld C T 7: 102,899,381 (GRCm39) G517E probably benign Het
Vmn1r22 A T 6: 57,877,404 (GRCm39) M191K probably damaging Het
Wdr6 G A 9: 108,453,182 (GRCm39) R234C probably damaging Het
Zdhhc22 C T 12: 87,030,398 (GRCm39) M183I probably benign Het
Zfp1007 C A 5: 109,824,062 (GRCm39) G463* probably null Het
Zfp949 C A 9: 88,452,182 (GRCm39) T584N probably benign 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
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
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'- AGAAGCGTGGTAAATTCAGAGTTATAC -3'
(R):5'- TGGAGCCTGCTTAGTTGAAAG -3'

Sequencing Primer
(F):5'- TACTATTTGAAATGGGGGATAGGATC -3'
(R):5'- GCCTGCTTAGTTGAAAGTACATTCC -3'
Posted On 2022-07-18